diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc.jsonld b/examples/from_parsers/afni/afni_alt_onesided_proc.jsonld index d2258842..db99f7d5 100644 --- a/examples/from_parsers/afni/afni_alt_onesided_proc.jsonld +++ b/examples/from_parsers/afni/afni_alt_onesided_proc.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:makedire-SqYwHN3W", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "mkdir $output_dir", "Parameters": {}, "Used": [] @@ -23,7 +23,7 @@ { "@id": "urn:makedire-QxnJipKo", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "mkdir $output_dir/stimuli", "Parameters": {}, "Used": [] @@ -31,7 +31,7 @@ { "@id": "urn:cp-HUFM8Z9b", "Label": "cp", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "cp ./afni_one_sided_t_test/tone_counting_onset_times.txt ./afni_one_sided_t_test/tone_counting_probe_duration.txt $output_dir/stimuli", "Parameters": {}, "Used": [ @@ -42,7 +42,7 @@ { "@id": "urn:3dcopy-l2qGknLF", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w", "Parameters": {}, "Used": [ @@ -52,7 +52,7 @@ { "@id": "urn:3dtcat-2fMcNxfG", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'", "Parameters": {}, "Used": [ @@ -62,7 +62,7 @@ { "@id": "urn:3dtoutco-yFRBtHgF", "Label": "3dToutcount", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D", "Parameters": {}, "Used": [ @@ -72,7 +72,7 @@ { "@id": "urn:cat-dqhcebkF", "Label": "cat", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "cat outcount.r*.1D > outcount_rall.1D", "Parameters": {}, "Used": [ @@ -82,7 +82,7 @@ { "@id": "urn:3dtshift-dO16EIrj", "Label": "3dTshift", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig", "Parameters": {}, "Used": [ @@ -92,7 +92,7 @@ { "@id": "urn:alignepi-Br6aVj6Q", "Label": "align_epi_anat.py", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off", "Parameters": {}, "Used": [ @@ -103,7 +103,7 @@ { "@id": "urn:autotlrc-SLmdPYCT", "Label": "@auto_tlrc", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss", "Parameters": {}, "Used": [ @@ -114,7 +114,7 @@ { "@id": "urn:catmatve-8kR6WPCJ", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D", "Parameters": {}, "Used": [ @@ -124,7 +124,7 @@ { "@id": "urn:3dvolreg-MO2QPl4S", "Label": "3dvolreg", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig", "Parameters": {}, "Used": [ @@ -134,7 +134,7 @@ { "@id": "urn:3dcalc-vWik6uf0", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1", "Parameters": {}, "Used": [ @@ -144,7 +144,7 @@ { "@id": "urn:catmatve-WX7hvT4l", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D", "Parameters": {}, "Used": [ @@ -154,7 +154,7 @@ { "@id": "urn:3dalline-P5dVQGMq", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run", "Parameters": {}, "Used": [ @@ -166,7 +166,7 @@ { "@id": "urn:3dalline-IQbhXwPW", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run", "Parameters": {}, "Used": [ @@ -178,7 +178,7 @@ { "@id": "urn:3dtstat-aHNJsJpN", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc", "Parameters": {}, "Used": [ @@ -188,7 +188,7 @@ { "@id": "urn:cat-ooV5oiCZ", "Label": "cat", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "cat dfile.r*.1D > dfile_rall.1D", "Parameters": {}, "Used": [ @@ -198,7 +198,7 @@ { "@id": "urn:3dcopy-Qd51Dq5h", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents", "Parameters": {}, "Used": [ @@ -208,7 +208,7 @@ { "@id": "urn:3dcalc-F1a82z5E", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg", "Parameters": {}, "Used": [ @@ -219,7 +219,7 @@ { "@id": "urn:3dcopy-xSIXkAbw", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj", "Parameters": {}, "Used": [ @@ -229,7 +229,7 @@ { "@id": "urn:3dalline-egS8PqoA", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped", "Parameters": {}, "Used": [ @@ -240,7 +240,7 @@ { "@id": "urn:3dmerge-9O9531Yb", "Label": "3dmerge", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc", "Parameters": {}, "Used": [ @@ -251,7 +251,7 @@ { "@id": "urn:3dautoma-V6BI7yr8", "Label": "3dAutomask", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -261,7 +261,7 @@ { "@id": "urn:3dmaskto-gzb3Ebjx", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj", "Parameters": {}, "Used": [] @@ -269,7 +269,7 @@ { "@id": "urn:3dresamp-aq8ZMB1d", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat", "Parameters": {}, "Used": [ @@ -280,7 +280,7 @@ { "@id": "urn:3dmaskto-YgHNOP1P", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj", "Parameters": {}, "Used": [ @@ -290,7 +290,7 @@ { "@id": "urn:3dabover-F1iBpqow", "Label": "3dABoverlap", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt", "Parameters": {}, "Used": [ @@ -301,7 +301,7 @@ { "@id": "urn:3ddot-aNumrLXq", "Label": "3ddot", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt", "Parameters": {}, "Used": [ @@ -312,7 +312,7 @@ { "@id": "urn:3dresamp-XlduVezT", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc", "Parameters": {}, "Used": [ @@ -323,7 +323,7 @@ { "@id": "urn:3dmaskto-KnI1R4hJ", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group", "Parameters": {}, "Used": [ @@ -333,7 +333,7 @@ { "@id": "urn:3dtstat-gqenW7Kx", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -343,7 +343,7 @@ { "@id": "urn:3dcalc-BfEIk4TY", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale", "Parameters": {}, "Used": [ @@ -355,7 +355,7 @@ { "@id": "urn:1dtoolpy-dlVV0iVy", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D", "Parameters": {}, "Used": [ @@ -365,7 +365,7 @@ { "@id": "urn:1dtoolpy-9aAS3KMx", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D", "Parameters": {}, "Used": [ @@ -375,7 +375,7 @@ { "@id": "urn:1dtoolpy-H0OYkGwb", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}", "Parameters": {}, "Used": [ @@ -385,7 +385,7 @@ { "@id": "urn:3ddeconv-vvEyyOkM", "Label": "3dDeconvolve", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj", "Parameters": {}, "Used": [ @@ -395,7 +395,7 @@ { "@id": "urn:1dtoolpy-huXhI1mz", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt", "Parameters": {}, "Used": [ @@ -405,7 +405,7 @@ { "@id": "urn:3dtcat-FuFiO3Gd", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD", "Parameters": {}, "Used": [ @@ -415,7 +415,7 @@ { "@id": "urn:3dtstat-dXEp8W3V", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -425,7 +425,7 @@ { "@id": "urn:3dtstat-Qc8wnCbA", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -435,7 +435,7 @@ { "@id": "urn:3dcalc-DXPGfw54", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj", "Parameters": {}, "Used": [ @@ -447,7 +447,7 @@ { "@id": "urn:3dtnorm-aL7aVzi7", "Label": "3dTnorm", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc", "Parameters": {}, "Used": [ @@ -457,7 +457,7 @@ { "@id": "urn:3dmaskav-r6J6hrSP", "Label": "3dmaskave", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D", "Parameters": {}, "Used": [ @@ -467,7 +467,7 @@ { "@id": "urn:3dtstat-SK7HPnMN", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D", "Parameters": {}, "Used": [ @@ -477,7 +477,7 @@ { "@id": "urn:3dcalc-AtoT3iN7", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP", "Parameters": {}, "Used": [ @@ -488,7 +488,7 @@ { "@id": "urn:3dtstat-OyyA0af6", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc", "Parameters": {}, "Used": [ @@ -498,7 +498,7 @@ { "@id": "urn:1dcat-cOD2csn8", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D", "Parameters": {}, "Used": [ @@ -508,7 +508,7 @@ { "@id": "urn:1dcat-66f4THnB", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D", "Parameters": {}, "Used": [ @@ -518,7 +518,7 @@ { "@id": "urn:3dtstat-8UaSUhxA", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"", "Parameters": {}, "Used": [ @@ -528,7 +528,7 @@ { "@id": "urn:1dcat-VP7bb6XX", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D", "Parameters": {}, "Used": [ @@ -538,7 +538,7 @@ { "@id": "urn:3dfwhmx-YOrRfjvt", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D", "Parameters": {}, "Used": [ @@ -548,7 +548,7 @@ { "@id": "urn:3dfwhmx-d666scW1", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D", "Parameters": {}, "Used": [ @@ -558,7 +558,7 @@ { "@id": "urn:3dclusts-duYWBtRe", "Label": "3dClustSim", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim", "Parameters": {}, "Used": [ @@ -568,7 +568,7 @@ { "@id": "urn:genepire-sz6pO5DZ", "Label": "gen_epi_review.py", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD", "Parameters": {}, "Used": [ @@ -578,7 +578,7 @@ { "@id": "urn:genssrev-50k1KCS5", "Label": "gen_ss_review_scripts.py", - "AssociatedWith": "urn:urn:afni-Gro6QPto", + "AssociatedWith": "urn:afni-Gro6QPto", "Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0", "Parameters": { "-mot_limit": "0.3", diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc.png b/examples/from_parsers/afni/afni_alt_onesided_proc.png index 9d85c0cc..25de549a 100644 Binary files a/examples/from_parsers/afni/afni_alt_onesided_proc.png and b/examples/from_parsers/afni/afni_alt_onesided_proc.png differ diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc_block.jsonld b/examples/from_parsers/afni/afni_alt_onesided_proc_block.jsonld index 748825a0..90d10c5e 100644 --- a/examples/from_parsers/afni/afni_alt_onesided_proc_block.jsonld +++ b/examples/from_parsers/afni/afni_alt_onesided_proc_block.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:autobloc-v8H5Ogxq", "Label": "auto block: setup", - "AssociatedWith": "urn:urn:afni-CUfM2GF9", + "AssociatedWith": "urn:afni-CUfM2GF9", "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_one_sided_t_test/tone_counting_onset_times.txt ./afni_one_sided_t_test/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ", "Used": [ "bids::afni_one_sided_t_test/tone_counting_onset_times.txt", @@ -26,7 +26,7 @@ { "@id": "urn:autobloc-X3Kz90HY", "Label": "auto block: tcat", - "AssociatedWith": "urn:urn:afni-CUfM2GF9", + "AssociatedWith": "urn:afni-CUfM2GF9", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ", "Used": [ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'" @@ -35,7 +35,7 @@ { "@id": "urn:autobloc-GVYJczpS", "Label": "auto block: outcount", - "AssociatedWith": "urn:urn:afni-CUfM2GF9", + "AssociatedWith": "urn:afni-CUfM2GF9", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig", @@ -45,7 +45,7 @@ { "@id": "urn:tshift-HGyQiLrF", "Label": "tshift", - "AssociatedWith": "urn:urn:afni-CUfM2GF9", + "AssociatedWith": "urn:afni-CUfM2GF9", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig" @@ -54,7 +54,7 @@ { "@id": "urn:align-dbfMq7NE", "Label": "align", - "AssociatedWith": "urn:urn:afni-CUfM2GF9", + "AssociatedWith": "urn:afni-CUfM2GF9", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ", "Used": [ "bids::pb01.$subj.r01.tshift+orig", @@ -64,7 +64,7 @@ { "@id": "urn:tlrc-RV1CChcN", "Label": "tlrc", - "AssociatedWith": "urn:urn:afni-CUfM2GF9", + "AssociatedWith": "urn:afni-CUfM2GF9", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ", "Used": [ "bids::TT_N27+tlrc", @@ -75,7 +75,7 @@ { "@id": "urn:volreg-qY8NgHG7", "Label": "volreg", - "AssociatedWith": "urn:urn:afni-CUfM2GF9", + "AssociatedWith": "urn:afni-CUfM2GF9", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ", "Used": [ "bids::pb01.$subj.r$run.tshift+orig", @@ -98,7 +98,7 @@ { "@id": "urn:blur-2ufpOLNQ", "Label": "blur", - "AssociatedWith": "urn:urn:afni-CUfM2GF9", + "AssociatedWith": "urn:afni-CUfM2GF9", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ", "Used": [ "bids::pb02.$subj.r$run.volreg+tlrc", @@ -108,7 +108,7 @@ { "@id": "urn:mask-YfQVxxPi", "Label": "mask", - "AssociatedWith": "urn:urn:afni-CUfM2GF9", + "AssociatedWith": "urn:afni-CUfM2GF9", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -127,7 +127,7 @@ { "@id": "urn:scale-GmmL0l7Q", "Label": "scale", - "AssociatedWith": "urn:urn:afni-CUfM2GF9", + "AssociatedWith": "urn:afni-CUfM2GF9", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -139,7 +139,7 @@ { "@id": "urn:regress-JwuObKc8", "Label": "regress", - "AssociatedWith": "urn:urn:afni-CUfM2GF9", + "AssociatedWith": "urn:afni-CUfM2GF9", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ", "Used": [ "bids::dfile_rall.1D", @@ -166,7 +166,7 @@ { "@id": "urn:bluresti-QW19fifr", "Label": "blur estimation", - "AssociatedWith": "urn:urn:afni-CUfM2GF9", + "AssociatedWith": "urn:afni-CUfM2GF9", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ", "Used": [ "bids::full_mask.$subj+tlrc", @@ -177,7 +177,7 @@ { "@id": "urn:autobloc-44jc0p9G", "Label": "auto block: generate review scripts", - "AssociatedWith": "urn:urn:afni-CUfM2GF9", + "AssociatedWith": "urn:afni-CUfM2GF9", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ", "Used": [ "bids::pb00.$subj.r*.tcat+orig.HEAD" diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc_block.png b/examples/from_parsers/afni/afni_alt_onesided_proc_block.png index 5c53d453..f7742fd7 100644 Binary files a/examples/from_parsers/afni/afni_alt_onesided_proc_block.png and b/examples/from_parsers/afni/afni_alt_onesided_proc_block.png differ diff --git a/examples/from_parsers/afni/afni_bi_sided_t_test_proc.jsonld b/examples/from_parsers/afni/afni_bi_sided_t_test_proc.jsonld index 7d2e5faf..cc5b7809 100644 --- a/examples/from_parsers/afni/afni_bi_sided_t_test_proc.jsonld +++ b/examples/from_parsers/afni/afni_bi_sided_t_test_proc.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:makedire-0Fti9SVV", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "mkdir $output_dir", "Parameters": {}, "Used": [] @@ -23,7 +23,7 @@ { "@id": "urn:makedire-bcLbDmzU", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "mkdir $output_dir/stimuli", "Parameters": {}, "Used": [] @@ -31,7 +31,7 @@ { "@id": "urn:cp-b7zqj7dm", "Label": "cp", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "cp ./afni_bi_sided_t_test/tone_counting_onset_times.txt ./afni_bi_sided_t_test/tone_counting_probe_duration.txt $output_dir/stimuli", "Parameters": {}, "Used": [ @@ -42,7 +42,7 @@ { "@id": "urn:3dcopy-2WaosrZR", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w", "Parameters": {}, "Used": [ @@ -52,7 +52,7 @@ { "@id": "urn:3dtcat-vsgPEg41", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'", "Parameters": {}, "Used": [ @@ -62,7 +62,7 @@ { "@id": "urn:3dtoutco-ua12ThWL", "Label": "3dToutcount", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D", "Parameters": {}, "Used": [ @@ -72,7 +72,7 @@ { "@id": "urn:cat-eN68PKM4", "Label": "cat", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "cat outcount.r*.1D > outcount_rall.1D", "Parameters": {}, "Used": [ @@ -82,7 +82,7 @@ { "@id": "urn:3dtshift-Uz9V0GCp", "Label": "3dTshift", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig", "Parameters": {}, "Used": [ @@ -92,7 +92,7 @@ { "@id": "urn:alignepi-TOfxbivF", "Label": "align_epi_anat.py", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off", "Parameters": {}, "Used": [ @@ -103,7 +103,7 @@ { "@id": "urn:autotlrc-fCMHL5Be", "Label": "@auto_tlrc", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss", "Parameters": {}, "Used": [ @@ -114,7 +114,7 @@ { "@id": "urn:catmatve-EA5f1njv", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D", "Parameters": {}, "Used": [ @@ -124,7 +124,7 @@ { "@id": "urn:3dvolreg-AMq9LYqj", "Label": "3dvolreg", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig", "Parameters": {}, "Used": [ @@ -134,7 +134,7 @@ { "@id": "urn:3dcalc-tCPpupxx", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1", "Parameters": {}, "Used": [ @@ -144,7 +144,7 @@ { "@id": "urn:catmatve-ASEHsX2B", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D", "Parameters": {}, "Used": [ @@ -154,7 +154,7 @@ { "@id": "urn:3dalline-c8Wq1xUb", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run", "Parameters": {}, "Used": [ @@ -166,7 +166,7 @@ { "@id": "urn:3dalline-vga6PrVm", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run", "Parameters": {}, "Used": [ @@ -178,7 +178,7 @@ { "@id": "urn:3dtstat-u3xfjqu5", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc", "Parameters": {}, "Used": [ @@ -188,7 +188,7 @@ { "@id": "urn:cat-BB7nFSIT", "Label": "cat", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "cat dfile.r*.1D > dfile_rall.1D", "Parameters": {}, "Used": [ @@ -198,7 +198,7 @@ { "@id": "urn:3dcopy-ItJcDYQh", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents", "Parameters": {}, "Used": [ @@ -208,7 +208,7 @@ { "@id": "urn:3dcalc-QNV69JtD", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg", "Parameters": {}, "Used": [ @@ -219,7 +219,7 @@ { "@id": "urn:3dcopy-TwtrebDo", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj", "Parameters": {}, "Used": [ @@ -229,7 +229,7 @@ { "@id": "urn:3dalline-nXJQxFlv", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped", "Parameters": {}, "Used": [ @@ -240,7 +240,7 @@ { "@id": "urn:3dmerge-uXqNQnGf", "Label": "3dmerge", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc", "Parameters": {}, "Used": [ @@ -251,7 +251,7 @@ { "@id": "urn:3dautoma-qCCyx8G0", "Label": "3dAutomask", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -261,7 +261,7 @@ { "@id": "urn:3dmaskto-jiLWLBrG", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj", "Parameters": {}, "Used": [] @@ -269,7 +269,7 @@ { "@id": "urn:3dresamp-FwzGbJVc", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat", "Parameters": {}, "Used": [ @@ -280,7 +280,7 @@ { "@id": "urn:3dmaskto-RVcsMKcS", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj", "Parameters": {}, "Used": [ @@ -290,7 +290,7 @@ { "@id": "urn:3dabover-OJyxHobE", "Label": "3dABoverlap", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt", "Parameters": {}, "Used": [ @@ -301,7 +301,7 @@ { "@id": "urn:3ddot-E9GgrurE", "Label": "3ddot", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt", "Parameters": {}, "Used": [ @@ -312,7 +312,7 @@ { "@id": "urn:3dresamp-XGsxOkPW", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc", "Parameters": {}, "Used": [ @@ -323,7 +323,7 @@ { "@id": "urn:3dmaskto-LUJAYzmp", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group", "Parameters": {}, "Used": [ @@ -333,7 +333,7 @@ { "@id": "urn:3dtstat-cKPGlKpB", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -343,7 +343,7 @@ { "@id": "urn:3dcalc-tPKcNwoc", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale", "Parameters": {}, "Used": [ @@ -355,7 +355,7 @@ { "@id": "urn:1dtoolpy-hvoaibny", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D", "Parameters": {}, "Used": [ @@ -365,7 +365,7 @@ { "@id": "urn:1dtoolpy-v7BEH6Xe", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D", "Parameters": {}, "Used": [ @@ -375,7 +375,7 @@ { "@id": "urn:1dtoolpy-bcpmMe0c", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}", "Parameters": {}, "Used": [ @@ -385,7 +385,7 @@ { "@id": "urn:3ddeconv-cRZYLlEP", "Label": "3dDeconvolve", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj", "Parameters": {}, "Used": [ @@ -395,7 +395,7 @@ { "@id": "urn:1dtoolpy-AyaX1uPn", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt", "Parameters": {}, "Used": [ @@ -405,7 +405,7 @@ { "@id": "urn:3dtcat-RWGfnPWP", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD", "Parameters": {}, "Used": [ @@ -415,7 +415,7 @@ { "@id": "urn:3dtstat-q51vxYT3", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -425,7 +425,7 @@ { "@id": "urn:3dtstat-8sPDnE0L", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -435,7 +435,7 @@ { "@id": "urn:3dcalc-RGwLKWHE", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj", "Parameters": {}, "Used": [ @@ -447,7 +447,7 @@ { "@id": "urn:3dtnorm-4ZPKtBfb", "Label": "3dTnorm", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc", "Parameters": {}, "Used": [ @@ -457,7 +457,7 @@ { "@id": "urn:3dmaskav-hV4DuJDG", "Label": "3dmaskave", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D", "Parameters": {}, "Used": [ @@ -467,7 +467,7 @@ { "@id": "urn:3dtstat-QdOKIy3R", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D", "Parameters": {}, "Used": [ @@ -477,7 +477,7 @@ { "@id": "urn:3dcalc-04jOYgES", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP", "Parameters": {}, "Used": [ @@ -488,7 +488,7 @@ { "@id": "urn:3dtstat-GsOJRmrW", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc", "Parameters": {}, "Used": [ @@ -498,7 +498,7 @@ { "@id": "urn:1dcat-XCdniniz", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D", "Parameters": {}, "Used": [ @@ -508,7 +508,7 @@ { "@id": "urn:1dcat-1e0KL3UX", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D", "Parameters": {}, "Used": [ @@ -518,7 +518,7 @@ { "@id": "urn:3dtstat-HjsESDaO", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"", "Parameters": {}, "Used": [ @@ -528,7 +528,7 @@ { "@id": "urn:1dcat-kqae8pGw", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D", "Parameters": {}, "Used": [ @@ -538,7 +538,7 @@ { "@id": "urn:3dfwhmx-c2Id8xz4", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D", "Parameters": {}, "Used": [ @@ -548,7 +548,7 @@ { "@id": "urn:3dfwhmx-1pDteEI5", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D", "Parameters": {}, "Used": [ @@ -558,7 +558,7 @@ { "@id": "urn:3dclusts-ANy7O8lb", "Label": "3dClustSim", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim", "Parameters": {}, "Used": [ @@ -568,7 +568,7 @@ { "@id": "urn:genepire-eciHyYWL", "Label": "gen_epi_review.py", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD", "Parameters": {}, "Used": [ @@ -578,7 +578,7 @@ { "@id": "urn:genssrev-Mk4Ku1i2", "Label": "gen_ss_review_scripts.py", - "AssociatedWith": "urn:urn:afni-txVAU8vU", + "AssociatedWith": "urn:afni-txVAU8vU", "Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0", "Parameters": { "-mot_limit": "0.3", diff --git a/examples/from_parsers/afni/afni_bi_sided_t_test_proc.png b/examples/from_parsers/afni/afni_bi_sided_t_test_proc.png index ab473b70..7c0c124e 100644 Binary files a/examples/from_parsers/afni/afni_bi_sided_t_test_proc.png and b/examples/from_parsers/afni/afni_bi_sided_t_test_proc.png differ diff --git a/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.jsonld b/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.jsonld index 14136127..ea593d94 100644 --- a/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.jsonld +++ b/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:autobloc-tFuAHJrf", "Label": "auto block: setup", - "AssociatedWith": "urn:urn:afni-3nwbHacO", + "AssociatedWith": "urn:afni-3nwbHacO", "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_bi_sided_t_test/tone_counting_onset_times.txt ./afni_bi_sided_t_test/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ", "Used": [ "bids::afni_bi_sided_t_test/tone_counting_onset_times.txt", @@ -26,7 +26,7 @@ { "@id": "urn:autobloc-MwLVnXkn", "Label": "auto block: tcat", - "AssociatedWith": "urn:urn:afni-3nwbHacO", + "AssociatedWith": "urn:afni-3nwbHacO", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ", "Used": [ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'" @@ -35,7 +35,7 @@ { "@id": "urn:autobloc-2Iba5XAL", "Label": "auto block: outcount", - "AssociatedWith": "urn:urn:afni-3nwbHacO", + "AssociatedWith": "urn:afni-3nwbHacO", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig", @@ -45,7 +45,7 @@ { "@id": "urn:tshift-J20yUWRy", "Label": "tshift", - "AssociatedWith": "urn:urn:afni-3nwbHacO", + "AssociatedWith": "urn:afni-3nwbHacO", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig" @@ -54,7 +54,7 @@ { "@id": "urn:align-Y6FaxgZA", "Label": "align", - "AssociatedWith": "urn:urn:afni-3nwbHacO", + "AssociatedWith": "urn:afni-3nwbHacO", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ", "Used": [ "bids::pb01.$subj.r01.tshift+orig", @@ -64,7 +64,7 @@ { "@id": "urn:tlrc-grbWf7H9", "Label": "tlrc", - "AssociatedWith": "urn:urn:afni-3nwbHacO", + "AssociatedWith": "urn:afni-3nwbHacO", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ", "Used": [ "bids::TT_N27+tlrc", @@ -75,7 +75,7 @@ { "@id": "urn:volreg-M7Va6mGv", "Label": "volreg", - "AssociatedWith": "urn:urn:afni-3nwbHacO", + "AssociatedWith": "urn:afni-3nwbHacO", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ", "Used": [ "bids::pb01.$subj.r$run.tshift+orig", @@ -98,7 +98,7 @@ { "@id": "urn:blur-KDTQ0s9b", "Label": "blur", - "AssociatedWith": "urn:urn:afni-3nwbHacO", + "AssociatedWith": "urn:afni-3nwbHacO", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ", "Used": [ "bids::pb02.$subj.r$run.volreg+tlrc", @@ -108,7 +108,7 @@ { "@id": "urn:mask-5kCG03AG", "Label": "mask", - "AssociatedWith": "urn:urn:afni-3nwbHacO", + "AssociatedWith": "urn:afni-3nwbHacO", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -127,7 +127,7 @@ { "@id": "urn:scale-wdQCkfkN", "Label": "scale", - "AssociatedWith": "urn:urn:afni-3nwbHacO", + "AssociatedWith": "urn:afni-3nwbHacO", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -139,7 +139,7 @@ { "@id": "urn:regress-8sCPNBhu", "Label": "regress", - "AssociatedWith": "urn:urn:afni-3nwbHacO", + "AssociatedWith": "urn:afni-3nwbHacO", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ", "Used": [ "bids::dfile_rall.1D", @@ -166,7 +166,7 @@ { "@id": "urn:bluresti-ZYY6Uhpa", "Label": "blur estimation", - "AssociatedWith": "urn:urn:afni-3nwbHacO", + "AssociatedWith": "urn:afni-3nwbHacO", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ", "Used": [ "bids::full_mask.$subj+tlrc", @@ -177,7 +177,7 @@ { "@id": "urn:autobloc-2YsKSu6y", "Label": "auto block: generate review scripts", - "AssociatedWith": "urn:urn:afni-3nwbHacO", + "AssociatedWith": "urn:afni-3nwbHacO", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ", "Used": [ "bids::pb00.$subj.r*.tcat+orig.HEAD" diff --git a/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.png b/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.png index 396d5c29..688dbf4e 100644 Binary files a/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.png and b/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.png differ diff --git a/examples/from_parsers/afni/afni_clustconn_18_proc.jsonld b/examples/from_parsers/afni/afni_clustconn_18_proc.jsonld index 2f95ca88..07238e1d 100644 --- a/examples/from_parsers/afni/afni_clustconn_18_proc.jsonld +++ b/examples/from_parsers/afni/afni_clustconn_18_proc.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:makedire-kNRtyUuW", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "mkdir $output_dir", "Parameters": {}, "Used": [] @@ -23,7 +23,7 @@ { "@id": "urn:makedire-PUa4faAM", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "mkdir $output_dir/stimuli", "Parameters": {}, "Used": [] @@ -31,7 +31,7 @@ { "@id": "urn:cp-Dp5byids", "Label": "cp", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "cp ./afni_cluster_nn2/tone_counting_onset_times.txt ./afni_cluster_nn2/tone_counting_probe_duration.txt $output_dir/stimuli", "Parameters": {}, "Used": [ @@ -42,7 +42,7 @@ { "@id": "urn:3dcopy-ZOmCezCl", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w", "Parameters": {}, "Used": [ @@ -52,7 +52,7 @@ { "@id": "urn:3dtcat-SM2Sndnh", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'", "Parameters": {}, "Used": [ @@ -62,7 +62,7 @@ { "@id": "urn:3dtoutco-JB2Lmf2M", "Label": "3dToutcount", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D", "Parameters": {}, "Used": [ @@ -72,7 +72,7 @@ { "@id": "urn:cat-w53akqHB", "Label": "cat", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "cat outcount.r*.1D > outcount_rall.1D", "Parameters": {}, "Used": [ @@ -82,7 +82,7 @@ { "@id": "urn:3dtshift-F2nPSes4", "Label": "3dTshift", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig", "Parameters": {}, "Used": [ @@ -92,7 +92,7 @@ { "@id": "urn:alignepi-JN8RFfYg", "Label": "align_epi_anat.py", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off", "Parameters": {}, "Used": [ @@ -103,7 +103,7 @@ { "@id": "urn:autotlrc-TOu6eKo1", "Label": "@auto_tlrc", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss", "Parameters": {}, "Used": [ @@ -114,7 +114,7 @@ { "@id": "urn:catmatve-7fuoAhEa", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D", "Parameters": {}, "Used": [ @@ -124,7 +124,7 @@ { "@id": "urn:3dvolreg-aQqyS7dV", "Label": "3dvolreg", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig", "Parameters": {}, "Used": [ @@ -134,7 +134,7 @@ { "@id": "urn:3dcalc-qreOQ2px", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1", "Parameters": {}, "Used": [ @@ -144,7 +144,7 @@ { "@id": "urn:catmatve-wpNIh7gg", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D", "Parameters": {}, "Used": [ @@ -154,7 +154,7 @@ { "@id": "urn:3dalline-vUSZLTiK", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run", "Parameters": {}, "Used": [ @@ -166,7 +166,7 @@ { "@id": "urn:3dalline-VXjfo3UX", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run", "Parameters": {}, "Used": [ @@ -178,7 +178,7 @@ { "@id": "urn:3dtstat-6bAohDhA", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc", "Parameters": {}, "Used": [ @@ -188,7 +188,7 @@ { "@id": "urn:cat-1rmVDUgs", "Label": "cat", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "cat dfile.r*.1D > dfile_rall.1D", "Parameters": {}, "Used": [ @@ -198,7 +198,7 @@ { "@id": "urn:3dcopy-npAyTgUe", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents", "Parameters": {}, "Used": [ @@ -208,7 +208,7 @@ { "@id": "urn:3dcalc-WXiyZGcZ", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg", "Parameters": {}, "Used": [ @@ -219,7 +219,7 @@ { "@id": "urn:3dcopy-DESJSJWt", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj", "Parameters": {}, "Used": [ @@ -229,7 +229,7 @@ { "@id": "urn:3dalline-ukfO7Wly", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped", "Parameters": {}, "Used": [ @@ -240,7 +240,7 @@ { "@id": "urn:3dmerge-sMOoqBuW", "Label": "3dmerge", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc", "Parameters": {}, "Used": [ @@ -251,7 +251,7 @@ { "@id": "urn:3dautoma-EBQGL8Bo", "Label": "3dAutomask", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -261,7 +261,7 @@ { "@id": "urn:3dmaskto-j2ye3Qb7", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj", "Parameters": {}, "Used": [] @@ -269,7 +269,7 @@ { "@id": "urn:3dresamp-iOYl3J2l", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat", "Parameters": {}, "Used": [ @@ -280,7 +280,7 @@ { "@id": "urn:3dmaskto-BJdYm5m3", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj", "Parameters": {}, "Used": [ @@ -290,7 +290,7 @@ { "@id": "urn:3dabover-xm30TwwO", "Label": "3dABoverlap", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt", "Parameters": {}, "Used": [ @@ -301,7 +301,7 @@ { "@id": "urn:3ddot-hr8gK19k", "Label": "3ddot", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt", "Parameters": {}, "Used": [ @@ -312,7 +312,7 @@ { "@id": "urn:3dresamp-9i4ByXB3", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc", "Parameters": {}, "Used": [ @@ -323,7 +323,7 @@ { "@id": "urn:3dmaskto-eWyRvmXR", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group", "Parameters": {}, "Used": [ @@ -333,7 +333,7 @@ { "@id": "urn:3dtstat-uIZaJ3D4", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -343,7 +343,7 @@ { "@id": "urn:3dcalc-NqtKgN7L", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale", "Parameters": {}, "Used": [ @@ -355,7 +355,7 @@ { "@id": "urn:1dtoolpy-TH6fQ5VG", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D", "Parameters": {}, "Used": [ @@ -365,7 +365,7 @@ { "@id": "urn:1dtoolpy-ymzHf0Gt", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D", "Parameters": {}, "Used": [ @@ -375,7 +375,7 @@ { "@id": "urn:1dtoolpy-JHoBwjXn", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}", "Parameters": {}, "Used": [ @@ -385,7 +385,7 @@ { "@id": "urn:3ddeconv-XxUCoLoi", "Label": "3dDeconvolve", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj", "Parameters": {}, "Used": [ @@ -395,7 +395,7 @@ { "@id": "urn:1dtoolpy-RC3RWfGm", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt", "Parameters": {}, "Used": [ @@ -405,7 +405,7 @@ { "@id": "urn:3dtcat-RC7eDphV", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD", "Parameters": {}, "Used": [ @@ -415,7 +415,7 @@ { "@id": "urn:3dtstat-pa05OoSF", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -425,7 +425,7 @@ { "@id": "urn:3dtstat-mwrkqknK", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -435,7 +435,7 @@ { "@id": "urn:3dcalc-rtR4c6Y4", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj", "Parameters": {}, "Used": [ @@ -447,7 +447,7 @@ { "@id": "urn:3dtnorm-eRPmyiHR", "Label": "3dTnorm", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc", "Parameters": {}, "Used": [ @@ -457,7 +457,7 @@ { "@id": "urn:3dmaskav-3wIxLLzt", "Label": "3dmaskave", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D", "Parameters": {}, "Used": [ @@ -467,7 +467,7 @@ { "@id": "urn:3dtstat-PJSc92bW", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D", "Parameters": {}, "Used": [ @@ -477,7 +477,7 @@ { "@id": "urn:3dcalc-55Y24Rhd", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP", "Parameters": {}, "Used": [ @@ -488,7 +488,7 @@ { "@id": "urn:3dtstat-NRg8dT0t", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc", "Parameters": {}, "Used": [ @@ -498,7 +498,7 @@ { "@id": "urn:1dcat-qhgW9VR8", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D", "Parameters": {}, "Used": [ @@ -508,7 +508,7 @@ { "@id": "urn:1dcat-11fOLdjb", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D", "Parameters": {}, "Used": [ @@ -518,7 +518,7 @@ { "@id": "urn:3dtstat-S8EVxl05", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"", "Parameters": {}, "Used": [ @@ -528,7 +528,7 @@ { "@id": "urn:1dcat-oVquvz2m", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D", "Parameters": {}, "Used": [ @@ -538,7 +538,7 @@ { "@id": "urn:3dfwhmx-mYW0j1Yc", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D", "Parameters": {}, "Used": [ @@ -548,7 +548,7 @@ { "@id": "urn:3dfwhmx-Nasmfxwc", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D", "Parameters": {}, "Used": [ @@ -558,7 +558,7 @@ { "@id": "urn:3dclusts-TCHGcw3f", "Label": "3dClustSim", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim", "Parameters": {}, "Used": [ @@ -568,7 +568,7 @@ { "@id": "urn:genepire-Q3xYfLZ1", "Label": "gen_epi_review.py", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD", "Parameters": {}, "Used": [ @@ -578,7 +578,7 @@ { "@id": "urn:genssrev-6S179is9", "Label": "gen_ss_review_scripts.py", - "AssociatedWith": "urn:urn:afni-CmWIlveU", + "AssociatedWith": "urn:afni-CmWIlveU", "Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0", "Parameters": { "-mot_limit": "0.3", diff --git a/examples/from_parsers/afni/afni_clustconn_18_proc.png b/examples/from_parsers/afni/afni_clustconn_18_proc.png index 559606fa..e41fdd48 100644 Binary files a/examples/from_parsers/afni/afni_clustconn_18_proc.png and b/examples/from_parsers/afni/afni_clustconn_18_proc.png differ diff --git a/examples/from_parsers/afni/afni_clustconn_18_proc_block.jsonld b/examples/from_parsers/afni/afni_clustconn_18_proc_block.jsonld index 67abffe4..de82cb46 100644 --- a/examples/from_parsers/afni/afni_clustconn_18_proc_block.jsonld +++ b/examples/from_parsers/afni/afni_clustconn_18_proc_block.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:autobloc-lncqLtf4", "Label": "auto block: setup", - "AssociatedWith": "urn:urn:afni-z9kTdI7Z", + "AssociatedWith": "urn:afni-z9kTdI7Z", "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_cluster_nn2/tone_counting_onset_times.txt ./afni_cluster_nn2/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ", "Used": [ "bids::afni_cluster_nn2/tone_counting_onset_times.txt", @@ -26,7 +26,7 @@ { "@id": "urn:autobloc-Zf7w9JEy", "Label": "auto block: tcat", - "AssociatedWith": "urn:urn:afni-z9kTdI7Z", + "AssociatedWith": "urn:afni-z9kTdI7Z", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ", "Used": [ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'" @@ -35,7 +35,7 @@ { "@id": "urn:autobloc-j56ceVlC", "Label": "auto block: outcount", - "AssociatedWith": "urn:urn:afni-z9kTdI7Z", + "AssociatedWith": "urn:afni-z9kTdI7Z", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig", @@ -45,7 +45,7 @@ { "@id": "urn:tshift-5OatDA2b", "Label": "tshift", - "AssociatedWith": "urn:urn:afni-z9kTdI7Z", + "AssociatedWith": "urn:afni-z9kTdI7Z", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig" @@ -54,7 +54,7 @@ { "@id": "urn:align-BGiZ7wtY", "Label": "align", - "AssociatedWith": "urn:urn:afni-z9kTdI7Z", + "AssociatedWith": "urn:afni-z9kTdI7Z", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ", "Used": [ "bids::pb01.$subj.r01.tshift+orig", @@ -64,7 +64,7 @@ { "@id": "urn:tlrc-1wOwYQxO", "Label": "tlrc", - "AssociatedWith": "urn:urn:afni-z9kTdI7Z", + "AssociatedWith": "urn:afni-z9kTdI7Z", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ", "Used": [ "bids::TT_N27+tlrc", @@ -75,7 +75,7 @@ { "@id": "urn:volreg-i4b2s3ls", "Label": "volreg", - "AssociatedWith": "urn:urn:afni-z9kTdI7Z", + "AssociatedWith": "urn:afni-z9kTdI7Z", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ", "Used": [ "bids::pb01.$subj.r$run.tshift+orig", @@ -98,7 +98,7 @@ { "@id": "urn:blur-4wgzuIvB", "Label": "blur", - "AssociatedWith": "urn:urn:afni-z9kTdI7Z", + "AssociatedWith": "urn:afni-z9kTdI7Z", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ", "Used": [ "bids::pb02.$subj.r$run.volreg+tlrc", @@ -108,7 +108,7 @@ { "@id": "urn:mask-0nTKbiWT", "Label": "mask", - "AssociatedWith": "urn:urn:afni-z9kTdI7Z", + "AssociatedWith": "urn:afni-z9kTdI7Z", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -127,7 +127,7 @@ { "@id": "urn:scale-ZalM8U1e", "Label": "scale", - "AssociatedWith": "urn:urn:afni-z9kTdI7Z", + "AssociatedWith": "urn:afni-z9kTdI7Z", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -139,7 +139,7 @@ { "@id": "urn:regress-I0fV2FI8", "Label": "regress", - "AssociatedWith": "urn:urn:afni-z9kTdI7Z", + "AssociatedWith": "urn:afni-z9kTdI7Z", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ", "Used": [ "bids::dfile_rall.1D", @@ -166,7 +166,7 @@ { "@id": "urn:bluresti-9I25pzvg", "Label": "blur estimation", - "AssociatedWith": "urn:urn:afni-z9kTdI7Z", + "AssociatedWith": "urn:afni-z9kTdI7Z", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ", "Used": [ "bids::full_mask.$subj+tlrc", @@ -177,7 +177,7 @@ { "@id": "urn:autobloc-oFzbi7jF", "Label": "auto block: generate review scripts", - "AssociatedWith": "urn:urn:afni-z9kTdI7Z", + "AssociatedWith": "urn:afni-z9kTdI7Z", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ", "Used": [ "bids::pb00.$subj.r*.tcat+orig.HEAD" diff --git a/examples/from_parsers/afni/afni_clustconn_18_proc_block.png b/examples/from_parsers/afni/afni_clustconn_18_proc_block.png index b1ee2cbe..e5c60a25 100644 Binary files a/examples/from_parsers/afni/afni_clustconn_18_proc_block.png and b/examples/from_parsers/afni/afni_clustconn_18_proc_block.png differ diff --git a/examples/from_parsers/afni/afni_clustconn_26_proc.jsonld b/examples/from_parsers/afni/afni_clustconn_26_proc.jsonld index 613bfa8e..32d6783a 100644 --- a/examples/from_parsers/afni/afni_clustconn_26_proc.jsonld +++ b/examples/from_parsers/afni/afni_clustconn_26_proc.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:makedire-kHWIFSta", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "mkdir $output_dir", "Parameters": {}, "Used": [] @@ -23,7 +23,7 @@ { "@id": "urn:makedire-zchaN5s7", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "mkdir $output_dir/stimuli", "Parameters": {}, "Used": [] @@ -31,7 +31,7 @@ { "@id": "urn:cp-pJJ01Duo", "Label": "cp", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "cp ./afni_cluster_nn3/tone_counting_onset_times.txt ./afni_cluster_nn3/tone_counting_probe_duration.txt $output_dir/stimuli", "Parameters": {}, "Used": [ @@ -42,7 +42,7 @@ { "@id": "urn:3dcopy-CFq8ivQe", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w", "Parameters": {}, "Used": [ @@ -52,7 +52,7 @@ { "@id": "urn:3dtcat-o4ryHUvB", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'", "Parameters": {}, "Used": [ @@ -62,7 +62,7 @@ { "@id": "urn:3dtoutco-V195mr84", "Label": "3dToutcount", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D", "Parameters": {}, "Used": [ @@ -72,7 +72,7 @@ { "@id": "urn:cat-oplZknOp", "Label": "cat", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "cat outcount.r*.1D > outcount_rall.1D", "Parameters": {}, "Used": [ @@ -82,7 +82,7 @@ { "@id": "urn:3dtshift-A8ONAV4i", "Label": "3dTshift", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig", "Parameters": {}, "Used": [ @@ -92,7 +92,7 @@ { "@id": "urn:alignepi-FPNGWQ3q", "Label": "align_epi_anat.py", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off", "Parameters": {}, "Used": [ @@ -103,7 +103,7 @@ { "@id": "urn:autotlrc-tzW1b3Mo", "Label": "@auto_tlrc", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss", "Parameters": {}, "Used": [ @@ -114,7 +114,7 @@ { "@id": "urn:catmatve-uVdPf8fA", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D", "Parameters": {}, "Used": [ @@ -124,7 +124,7 @@ { "@id": "urn:3dvolreg-zM9H4lk7", "Label": "3dvolreg", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig", "Parameters": {}, "Used": [ @@ -134,7 +134,7 @@ { "@id": "urn:3dcalc-l0e6HDgL", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1", "Parameters": {}, "Used": [ @@ -144,7 +144,7 @@ { "@id": "urn:catmatve-cz4w4ciN", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D", "Parameters": {}, "Used": [ @@ -154,7 +154,7 @@ { "@id": "urn:3dalline-fX5euqYh", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run", "Parameters": {}, "Used": [ @@ -166,7 +166,7 @@ { "@id": "urn:3dalline-TPR4Lm3D", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run", "Parameters": {}, "Used": [ @@ -178,7 +178,7 @@ { "@id": "urn:3dtstat-aCZ46C6B", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc", "Parameters": {}, "Used": [ @@ -188,7 +188,7 @@ { "@id": "urn:cat-Euapflnv", "Label": "cat", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "cat dfile.r*.1D > dfile_rall.1D", "Parameters": {}, "Used": [ @@ -198,7 +198,7 @@ { "@id": "urn:3dcopy-PJwYcYCL", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents", "Parameters": {}, "Used": [ @@ -208,7 +208,7 @@ { "@id": "urn:3dcalc-vQmwqsuZ", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg", "Parameters": {}, "Used": [ @@ -219,7 +219,7 @@ { "@id": "urn:3dcopy-F8z4WYm7", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj", "Parameters": {}, "Used": [ @@ -229,7 +229,7 @@ { "@id": "urn:3dalline-CKdjxtz1", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped", "Parameters": {}, "Used": [ @@ -240,7 +240,7 @@ { "@id": "urn:3dmerge-5sbgCFxR", "Label": "3dmerge", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc", "Parameters": {}, "Used": [ @@ -251,7 +251,7 @@ { "@id": "urn:3dautoma-D1LJF0af", "Label": "3dAutomask", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -261,7 +261,7 @@ { "@id": "urn:3dmaskto-hJsNwKG6", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj", "Parameters": {}, "Used": [] @@ -269,7 +269,7 @@ { "@id": "urn:3dresamp-pmoCtLWS", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat", "Parameters": {}, "Used": [ @@ -280,7 +280,7 @@ { "@id": "urn:3dmaskto-3KxzVryU", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj", "Parameters": {}, "Used": [ @@ -290,7 +290,7 @@ { "@id": "urn:3dabover-nW4bIw9t", "Label": "3dABoverlap", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt", "Parameters": {}, "Used": [ @@ -301,7 +301,7 @@ { "@id": "urn:3ddot-z0QzuRgL", "Label": "3ddot", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt", "Parameters": {}, "Used": [ @@ -312,7 +312,7 @@ { "@id": "urn:3dresamp-rKiLK5l3", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc", "Parameters": {}, "Used": [ @@ -323,7 +323,7 @@ { "@id": "urn:3dmaskto-AtbA6aKd", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group", "Parameters": {}, "Used": [ @@ -333,7 +333,7 @@ { "@id": "urn:3dtstat-tRADjMrz", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -343,7 +343,7 @@ { "@id": "urn:3dcalc-XM5Og8FN", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale", "Parameters": {}, "Used": [ @@ -355,7 +355,7 @@ { "@id": "urn:1dtoolpy-YhGXZbB6", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D", "Parameters": {}, "Used": [ @@ -365,7 +365,7 @@ { "@id": "urn:1dtoolpy-Som6XeES", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D", "Parameters": {}, "Used": [ @@ -375,7 +375,7 @@ { "@id": "urn:1dtoolpy-3HdHPQUT", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}", "Parameters": {}, "Used": [ @@ -385,7 +385,7 @@ { "@id": "urn:3ddeconv-BMg9ILIN", "Label": "3dDeconvolve", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj", "Parameters": {}, "Used": [ @@ -395,7 +395,7 @@ { "@id": "urn:1dtoolpy-7vFHTBen", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt", "Parameters": {}, "Used": [ @@ -405,7 +405,7 @@ { "@id": "urn:3dtcat-hZaDOJov", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD", "Parameters": {}, "Used": [ @@ -415,7 +415,7 @@ { "@id": "urn:3dtstat-gMVMVnnv", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -425,7 +425,7 @@ { "@id": "urn:3dtstat-Zngd2T3h", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -435,7 +435,7 @@ { "@id": "urn:3dcalc-c55gFJ4p", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj", "Parameters": {}, "Used": [ @@ -447,7 +447,7 @@ { "@id": "urn:3dtnorm-CGD6UuHs", "Label": "3dTnorm", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc", "Parameters": {}, "Used": [ @@ -457,7 +457,7 @@ { "@id": "urn:3dmaskav-qgH8zcGm", "Label": "3dmaskave", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D", "Parameters": {}, "Used": [ @@ -467,7 +467,7 @@ { "@id": "urn:3dtstat-1aRdzV5C", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D", "Parameters": {}, "Used": [ @@ -477,7 +477,7 @@ { "@id": "urn:3dcalc-VorpNvMG", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP", "Parameters": {}, "Used": [ @@ -488,7 +488,7 @@ { "@id": "urn:3dtstat-FkNkpleh", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc", "Parameters": {}, "Used": [ @@ -498,7 +498,7 @@ { "@id": "urn:1dcat-VxIRgqMS", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D", "Parameters": {}, "Used": [ @@ -508,7 +508,7 @@ { "@id": "urn:1dcat-QBu2vYst", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D", "Parameters": {}, "Used": [ @@ -518,7 +518,7 @@ { "@id": "urn:3dtstat-lCq7pBIS", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"", "Parameters": {}, "Used": [ @@ -528,7 +528,7 @@ { "@id": "urn:1dcat-ZX8bODEi", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D", "Parameters": {}, "Used": [ @@ -538,7 +538,7 @@ { "@id": "urn:3dfwhmx-Cyw8XHhT", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D", "Parameters": {}, "Used": [ @@ -548,7 +548,7 @@ { "@id": "urn:3dfwhmx-gvqns3P7", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D", "Parameters": {}, "Used": [ @@ -558,7 +558,7 @@ { "@id": "urn:3dclusts-tJOYZHF3", "Label": "3dClustSim", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim", "Parameters": {}, "Used": [ @@ -568,7 +568,7 @@ { "@id": "urn:genepire-TKiF0wxd", "Label": "gen_epi_review.py", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD", "Parameters": {}, "Used": [ @@ -578,7 +578,7 @@ { "@id": "urn:genssrev-nmpXt1CC", "Label": "gen_ss_review_scripts.py", - "AssociatedWith": "urn:urn:afni-vU2XdaEn", + "AssociatedWith": "urn:afni-vU2XdaEn", "Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0", "Parameters": { "-mot_limit": "0.3", diff --git a/examples/from_parsers/afni/afni_clustconn_26_proc.png b/examples/from_parsers/afni/afni_clustconn_26_proc.png index fe70ac4c..7531d359 100644 Binary files a/examples/from_parsers/afni/afni_clustconn_26_proc.png and b/examples/from_parsers/afni/afni_clustconn_26_proc.png differ diff --git a/examples/from_parsers/afni/afni_clustconn_26_proc_block.jsonld b/examples/from_parsers/afni/afni_clustconn_26_proc_block.jsonld index 86090bd6..d1a0e427 100644 --- a/examples/from_parsers/afni/afni_clustconn_26_proc_block.jsonld +++ b/examples/from_parsers/afni/afni_clustconn_26_proc_block.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:autobloc-aS8nTmCG", "Label": "auto block: setup", - "AssociatedWith": "urn:urn:afni-reNtbBWO", + "AssociatedWith": "urn:afni-reNtbBWO", "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_cluster_nn3/tone_counting_onset_times.txt ./afni_cluster_nn3/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ", "Used": [ "bids::afni_cluster_nn3/tone_counting_onset_times.txt", @@ -26,7 +26,7 @@ { "@id": "urn:autobloc-ia4ddT4y", "Label": "auto block: tcat", - "AssociatedWith": "urn:urn:afni-reNtbBWO", + "AssociatedWith": "urn:afni-reNtbBWO", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ", "Used": [ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'" @@ -35,7 +35,7 @@ { "@id": "urn:autobloc-VVyUPAJF", "Label": "auto block: outcount", - "AssociatedWith": "urn:urn:afni-reNtbBWO", + "AssociatedWith": "urn:afni-reNtbBWO", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig", @@ -45,7 +45,7 @@ { "@id": "urn:tshift-nWUsm1PO", "Label": "tshift", - "AssociatedWith": "urn:urn:afni-reNtbBWO", + "AssociatedWith": "urn:afni-reNtbBWO", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig" @@ -54,7 +54,7 @@ { "@id": "urn:align-Ir8eJ48B", "Label": "align", - "AssociatedWith": "urn:urn:afni-reNtbBWO", + "AssociatedWith": "urn:afni-reNtbBWO", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ", "Used": [ "bids::pb01.$subj.r01.tshift+orig", @@ -64,7 +64,7 @@ { "@id": "urn:tlrc-3vkBmAg4", "Label": "tlrc", - "AssociatedWith": "urn:urn:afni-reNtbBWO", + "AssociatedWith": "urn:afni-reNtbBWO", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ", "Used": [ "bids::TT_N27+tlrc", @@ -75,7 +75,7 @@ { "@id": "urn:volreg-6cRFx5Uu", "Label": "volreg", - "AssociatedWith": "urn:urn:afni-reNtbBWO", + "AssociatedWith": "urn:afni-reNtbBWO", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ", "Used": [ "bids::pb01.$subj.r$run.tshift+orig", @@ -98,7 +98,7 @@ { "@id": "urn:blur-6u7MxnsO", "Label": "blur", - "AssociatedWith": "urn:urn:afni-reNtbBWO", + "AssociatedWith": "urn:afni-reNtbBWO", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ", "Used": [ "bids::pb02.$subj.r$run.volreg+tlrc", @@ -108,7 +108,7 @@ { "@id": "urn:mask-SiQp3rcH", "Label": "mask", - "AssociatedWith": "urn:urn:afni-reNtbBWO", + "AssociatedWith": "urn:afni-reNtbBWO", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -127,7 +127,7 @@ { "@id": "urn:scale-VpuXgWB1", "Label": "scale", - "AssociatedWith": "urn:urn:afni-reNtbBWO", + "AssociatedWith": "urn:afni-reNtbBWO", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -139,7 +139,7 @@ { "@id": "urn:regress-c23cHR6X", "Label": "regress", - "AssociatedWith": "urn:urn:afni-reNtbBWO", + "AssociatedWith": "urn:afni-reNtbBWO", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ", "Used": [ "bids::dfile_rall.1D", @@ -166,7 +166,7 @@ { "@id": "urn:bluresti-qlH4zhL5", "Label": "blur estimation", - "AssociatedWith": "urn:urn:afni-reNtbBWO", + "AssociatedWith": "urn:afni-reNtbBWO", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ", "Used": [ "bids::full_mask.$subj+tlrc", @@ -177,7 +177,7 @@ { "@id": "urn:autobloc-RIT2DdIu", "Label": "auto block: generate review scripts", - "AssociatedWith": "urn:urn:afni-reNtbBWO", + "AssociatedWith": "urn:afni-reNtbBWO", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ", "Used": [ "bids::pb00.$subj.r*.tcat+orig.HEAD" diff --git a/examples/from_parsers/afni/afni_clustconn_26_proc_block.png b/examples/from_parsers/afni/afni_clustconn_26_proc_block.png index 76085a55..b4aec9b1 100644 Binary files a/examples/from_parsers/afni/afni_clustconn_26_proc_block.png and b/examples/from_parsers/afni/afni_clustconn_26_proc_block.png differ diff --git a/examples/from_parsers/afni/afni_con_f_proc.jsonld b/examples/from_parsers/afni/afni_con_f_proc.jsonld index 93b09aa3..851dd457 100644 --- a/examples/from_parsers/afni/afni_con_f_proc.jsonld +++ b/examples/from_parsers/afni/afni_con_f_proc.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:makedire-EjFu5Gzs", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "mkdir $output_dir", "Parameters": {}, "Used": [] @@ -23,7 +23,7 @@ { "@id": "urn:makedire-YONHeB75", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "mkdir $output_dir/stimuli", "Parameters": {}, "Used": [] @@ -31,7 +31,7 @@ { "@id": "urn:cp-S3UpI0F6", "Label": "cp", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "cp ./afni_f_test/tone_counting_onset_times.txt ./afni_f_test/tone_counting_probe_duration.txt $output_dir/stimuli", "Parameters": {}, "Used": [ @@ -42,7 +42,7 @@ { "@id": "urn:3dcopy-wnZoB6GV", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w", "Parameters": {}, "Used": [ @@ -52,7 +52,7 @@ { "@id": "urn:3dtcat-p93OvsNc", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'", "Parameters": {}, "Used": [ @@ -62,7 +62,7 @@ { "@id": "urn:3dtoutco-MaaJHpvs", "Label": "3dToutcount", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D", "Parameters": {}, "Used": [ @@ -72,7 +72,7 @@ { "@id": "urn:cat-g7cf5SRg", "Label": "cat", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "cat outcount.r*.1D > outcount_rall.1D", "Parameters": {}, "Used": [ @@ -82,7 +82,7 @@ { "@id": "urn:3dtshift-7SbFVAaD", "Label": "3dTshift", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig", "Parameters": {}, "Used": [ @@ -92,7 +92,7 @@ { "@id": "urn:alignepi-enozA4y8", "Label": "align_epi_anat.py", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off", "Parameters": {}, "Used": [ @@ -103,7 +103,7 @@ { "@id": "urn:autotlrc-oduZ40ZK", "Label": "@auto_tlrc", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss", "Parameters": {}, "Used": [ @@ -114,7 +114,7 @@ { "@id": "urn:catmatve-D7J6hS1Y", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D", "Parameters": {}, "Used": [ @@ -124,7 +124,7 @@ { "@id": "urn:3dvolreg-iMulinnK", "Label": "3dvolreg", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig", "Parameters": {}, "Used": [ @@ -134,7 +134,7 @@ { "@id": "urn:3dcalc-snZ2MgYQ", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1", "Parameters": {}, "Used": [ @@ -144,7 +144,7 @@ { "@id": "urn:catmatve-Kk6oC6ZE", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D", "Parameters": {}, "Used": [ @@ -154,7 +154,7 @@ { "@id": "urn:3dalline-EJAmmrdL", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run", "Parameters": {}, "Used": [ @@ -166,7 +166,7 @@ { "@id": "urn:3dalline-LXY21VdU", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run", "Parameters": {}, "Used": [ @@ -178,7 +178,7 @@ { "@id": "urn:3dtstat-HGyCHkmT", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc", "Parameters": {}, "Used": [ @@ -188,7 +188,7 @@ { "@id": "urn:cat-iFjDMi8K", "Label": "cat", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "cat dfile.r*.1D > dfile_rall.1D", "Parameters": {}, "Used": [ @@ -198,7 +198,7 @@ { "@id": "urn:3dcopy-7zdBDXoH", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents", "Parameters": {}, "Used": [ @@ -208,7 +208,7 @@ { "@id": "urn:3dcalc-I4FH3Fdh", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg", "Parameters": {}, "Used": [ @@ -219,7 +219,7 @@ { "@id": "urn:3dcopy-UjphDPUg", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj", "Parameters": {}, "Used": [ @@ -229,7 +229,7 @@ { "@id": "urn:3dalline-99Vqvx8a", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped", "Parameters": {}, "Used": [ @@ -240,7 +240,7 @@ { "@id": "urn:3dmerge-1NLLMplG", "Label": "3dmerge", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc", "Parameters": {}, "Used": [ @@ -251,7 +251,7 @@ { "@id": "urn:3dautoma-ypPBwJMM", "Label": "3dAutomask", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -261,7 +261,7 @@ { "@id": "urn:3dmaskto-I5XcPV9z", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj", "Parameters": {}, "Used": [] @@ -269,7 +269,7 @@ { "@id": "urn:3dresamp-5CCglnUH", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat", "Parameters": {}, "Used": [ @@ -280,7 +280,7 @@ { "@id": "urn:3dmaskto-oB4HfACz", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj", "Parameters": {}, "Used": [ @@ -290,7 +290,7 @@ { "@id": "urn:3dabover-BuBtQnVp", "Label": "3dABoverlap", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt", "Parameters": {}, "Used": [ @@ -301,7 +301,7 @@ { "@id": "urn:3ddot-UX3KoLiE", "Label": "3ddot", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt", "Parameters": {}, "Used": [ @@ -312,7 +312,7 @@ { "@id": "urn:3dresamp-00IhFrmJ", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc", "Parameters": {}, "Used": [ @@ -323,7 +323,7 @@ { "@id": "urn:3dmaskto-YhUONgz0", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group", "Parameters": {}, "Used": [ @@ -333,7 +333,7 @@ { "@id": "urn:3dtstat-2NVb1sut", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -343,7 +343,7 @@ { "@id": "urn:3dcalc-zgipgUrz", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale", "Parameters": {}, "Used": [ @@ -355,7 +355,7 @@ { "@id": "urn:1dtoolpy-5WTFf33A", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D", "Parameters": {}, "Used": [ @@ -365,7 +365,7 @@ { "@id": "urn:1dtoolpy-jER2iZP1", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D", "Parameters": {}, "Used": [ @@ -375,7 +375,7 @@ { "@id": "urn:1dtoolpy-75HvwUVU", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}", "Parameters": {}, "Used": [ @@ -385,7 +385,7 @@ { "@id": "urn:3ddeconv-X5zHlyKF", "Label": "3dDeconvolve", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj", "Parameters": {}, "Used": [ @@ -395,7 +395,7 @@ { "@id": "urn:1dtoolpy-cWNMH41s", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt", "Parameters": {}, "Used": [ @@ -405,7 +405,7 @@ { "@id": "urn:3dtcat-yAzPOFHP", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD", "Parameters": {}, "Used": [ @@ -415,7 +415,7 @@ { "@id": "urn:3dtstat-F1ly8H7E", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -425,7 +425,7 @@ { "@id": "urn:3dtstat-6yntd6Sh", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -435,7 +435,7 @@ { "@id": "urn:3dcalc-2Y6jSVAp", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj", "Parameters": {}, "Used": [ @@ -447,7 +447,7 @@ { "@id": "urn:3dtnorm-ousknqOT", "Label": "3dTnorm", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc", "Parameters": {}, "Used": [ @@ -457,7 +457,7 @@ { "@id": "urn:3dmaskav-Sruq3WoS", "Label": "3dmaskave", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D", "Parameters": {}, "Used": [ @@ -467,7 +467,7 @@ { "@id": "urn:3dtstat-pms0xbvC", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D", "Parameters": {}, "Used": [ @@ -477,7 +477,7 @@ { "@id": "urn:3dcalc-56JypSy4", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP", "Parameters": {}, "Used": [ @@ -488,7 +488,7 @@ { "@id": "urn:3dtstat-QXdZP1fq", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc", "Parameters": {}, "Used": [ @@ -498,7 +498,7 @@ { "@id": "urn:1dcat-ad96m6UQ", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D", "Parameters": {}, "Used": [ @@ -508,7 +508,7 @@ { "@id": "urn:1dcat-2K9ekGxY", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D", "Parameters": {}, "Used": [ @@ -518,7 +518,7 @@ { "@id": "urn:3dtstat-eAA6J8hu", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"", "Parameters": {}, "Used": [ @@ -528,7 +528,7 @@ { "@id": "urn:1dcat-GlOIdXgH", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D", "Parameters": {}, "Used": [ @@ -538,7 +538,7 @@ { "@id": "urn:3dfwhmx-DtOKeO5X", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D", "Parameters": {}, "Used": [ @@ -548,7 +548,7 @@ { "@id": "urn:3dfwhmx-sWc6Z41Y", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D", "Parameters": {}, "Used": [ @@ -558,7 +558,7 @@ { "@id": "urn:3dclusts-1uLxHtpf", "Label": "3dClustSim", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim", "Parameters": {}, "Used": [ @@ -568,7 +568,7 @@ { "@id": "urn:genepire-dgvg4PFX", "Label": "gen_epi_review.py", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD", "Parameters": {}, "Used": [ @@ -578,7 +578,7 @@ { "@id": "urn:genssrev-Ap2cZwro", "Label": "gen_ss_review_scripts.py", - "AssociatedWith": "urn:urn:afni-fUbLl1Ef", + "AssociatedWith": "urn:afni-fUbLl1Ef", "Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0", "Parameters": { "-mot_limit": "0.3", diff --git a/examples/from_parsers/afni/afni_con_f_proc.png b/examples/from_parsers/afni/afni_con_f_proc.png index 22133beb..584e3d9a 100644 Binary files a/examples/from_parsers/afni/afni_con_f_proc.png and b/examples/from_parsers/afni/afni_con_f_proc.png differ diff --git a/examples/from_parsers/afni/afni_con_f_proc_block.jsonld b/examples/from_parsers/afni/afni_con_f_proc_block.jsonld index f80cb3e4..378989d5 100644 --- a/examples/from_parsers/afni/afni_con_f_proc_block.jsonld +++ b/examples/from_parsers/afni/afni_con_f_proc_block.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:autobloc-gx5Gs1iF", "Label": "auto block: setup", - "AssociatedWith": "urn:urn:afni-JCuJkKkJ", + "AssociatedWith": "urn:afni-JCuJkKkJ", "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_f_test/tone_counting_onset_times.txt ./afni_f_test/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ", "Used": [ "bids::afni_f_test/tone_counting_onset_times.txt", @@ -26,7 +26,7 @@ { "@id": "urn:autobloc-aWD77U1W", "Label": "auto block: tcat", - "AssociatedWith": "urn:urn:afni-JCuJkKkJ", + "AssociatedWith": "urn:afni-JCuJkKkJ", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ", "Used": [ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'" @@ -35,7 +35,7 @@ { "@id": "urn:autobloc-ItX0hSbT", "Label": "auto block: outcount", - "AssociatedWith": "urn:urn:afni-JCuJkKkJ", + "AssociatedWith": "urn:afni-JCuJkKkJ", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig", @@ -45,7 +45,7 @@ { "@id": "urn:tshift-qJQPUAmK", "Label": "tshift", - "AssociatedWith": "urn:urn:afni-JCuJkKkJ", + "AssociatedWith": "urn:afni-JCuJkKkJ", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig" @@ -54,7 +54,7 @@ { "@id": "urn:align-2yy5MCs2", "Label": "align", - "AssociatedWith": "urn:urn:afni-JCuJkKkJ", + "AssociatedWith": "urn:afni-JCuJkKkJ", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ", "Used": [ "bids::pb01.$subj.r01.tshift+orig", @@ -64,7 +64,7 @@ { "@id": "urn:tlrc-LkdaOXQO", "Label": "tlrc", - "AssociatedWith": "urn:urn:afni-JCuJkKkJ", + "AssociatedWith": "urn:afni-JCuJkKkJ", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ", "Used": [ "bids::TT_N27+tlrc", @@ -75,7 +75,7 @@ { "@id": "urn:volreg-QjASoC7j", "Label": "volreg", - "AssociatedWith": "urn:urn:afni-JCuJkKkJ", + "AssociatedWith": "urn:afni-JCuJkKkJ", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ", "Used": [ "bids::pb01.$subj.r$run.tshift+orig", @@ -98,7 +98,7 @@ { "@id": "urn:blur-RHUHuJ7U", "Label": "blur", - "AssociatedWith": "urn:urn:afni-JCuJkKkJ", + "AssociatedWith": "urn:afni-JCuJkKkJ", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ", "Used": [ "bids::pb02.$subj.r$run.volreg+tlrc", @@ -108,7 +108,7 @@ { "@id": "urn:mask-veDX9g76", "Label": "mask", - "AssociatedWith": "urn:urn:afni-JCuJkKkJ", + "AssociatedWith": "urn:afni-JCuJkKkJ", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -127,7 +127,7 @@ { "@id": "urn:scale-TZk2BHod", "Label": "scale", - "AssociatedWith": "urn:urn:afni-JCuJkKkJ", + "AssociatedWith": "urn:afni-JCuJkKkJ", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -139,7 +139,7 @@ { "@id": "urn:regress-VfuA197y", "Label": "regress", - "AssociatedWith": "urn:urn:afni-JCuJkKkJ", + "AssociatedWith": "urn:afni-JCuJkKkJ", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ", "Used": [ "bids::dfile_rall.1D", @@ -166,7 +166,7 @@ { "@id": "urn:bluresti-Qz0unv2Z", "Label": "blur estimation", - "AssociatedWith": "urn:urn:afni-JCuJkKkJ", + "AssociatedWith": "urn:afni-JCuJkKkJ", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ", "Used": [ "bids::full_mask.$subj+tlrc", @@ -177,7 +177,7 @@ { "@id": "urn:autobloc-2RxNDsvi", "Label": "auto block: generate review scripts", - "AssociatedWith": "urn:urn:afni-JCuJkKkJ", + "AssociatedWith": "urn:afni-JCuJkKkJ", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ", "Used": [ "bids::pb00.$subj.r*.tcat+orig.HEAD" diff --git a/examples/from_parsers/afni/afni_con_f_proc_block.png b/examples/from_parsers/afni/afni_con_f_proc_block.png index 4cecc857..66e528a3 100644 Binary files a/examples/from_parsers/afni/afni_con_f_proc_block.png and b/examples/from_parsers/afni/afni_con_f_proc_block.png differ diff --git a/examples/from_parsers/afni/afni_default_proc.jsonld b/examples/from_parsers/afni/afni_default_proc.jsonld index 19c67555..78eca316 100644 --- a/examples/from_parsers/afni/afni_default_proc.jsonld +++ b/examples/from_parsers/afni/afni_default_proc.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:makedire-GKieyNlP", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "mkdir $output_dir", "Parameters": {}, "Used": [] @@ -23,7 +23,7 @@ { "@id": "urn:makedire-UVm2hYna", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "mkdir $output_dir/stimuli", "Parameters": {}, "Used": [] @@ -31,7 +31,7 @@ { "@id": "urn:cp-fMIzX1pE", "Label": "cp", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "cp ./afni_voxelwise_p0001/tone_counting_onset_times.txt ./afni_voxelwise_p0001/tone_counting_probe_duration.txt $output_dir/stimuli", "Parameters": {}, "Used": [ @@ -42,7 +42,7 @@ { "@id": "urn:3dcopy-TNNinI1i", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dcopy ./afni_voxelwise_p0001/sub-01_T1w.nii.gz $output_dir/sub-01_T1w", "Parameters": {}, "Used": [ @@ -52,7 +52,7 @@ { "@id": "urn:3dtcat-dwXz4e0G", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_voxelwise_p0001/sub-01_task-tonecounting_bold.nii.gz'[0..$]'", "Parameters": {}, "Used": [ @@ -62,7 +62,7 @@ { "@id": "urn:3dtoutco-Bm38cl8G", "Label": "3dToutcount", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D", "Parameters": {}, "Used": [ @@ -72,7 +72,7 @@ { "@id": "urn:cat-DjwBZT3w", "Label": "cat", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "cat outcount.r*.1D > outcount_rall.1D", "Parameters": {}, "Used": [ @@ -82,7 +82,7 @@ { "@id": "urn:3dtshift-TjxbHsNe", "Label": "3dTshift", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig", "Parameters": {}, "Used": [ @@ -92,7 +92,7 @@ { "@id": "urn:alignepi-qzMviOnv", "Label": "align_epi_anat.py", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off", "Parameters": {}, "Used": [ @@ -103,7 +103,7 @@ { "@id": "urn:autotlrc-Ye1q2rYP", "Label": "@auto_tlrc", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss", "Parameters": {}, "Used": [ @@ -114,7 +114,7 @@ { "@id": "urn:catmatve-terER4Y4", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D", "Parameters": {}, "Used": [ @@ -124,7 +124,7 @@ { "@id": "urn:3dvolreg-tS8mWkCy", "Label": "3dvolreg", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig", "Parameters": {}, "Used": [ @@ -134,7 +134,7 @@ { "@id": "urn:3dcalc-lVv6vmhn", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1", "Parameters": {}, "Used": [ @@ -144,7 +144,7 @@ { "@id": "urn:catmatve-YaBZGpgm", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D", "Parameters": {}, "Used": [ @@ -154,7 +154,7 @@ { "@id": "urn:3dalline-mAEHSFbA", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run", "Parameters": {}, "Used": [ @@ -166,7 +166,7 @@ { "@id": "urn:3dalline-oSNVZLhS", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run", "Parameters": {}, "Used": [ @@ -178,7 +178,7 @@ { "@id": "urn:3dtstat-sybsb09m", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc", "Parameters": {}, "Used": [ @@ -188,7 +188,7 @@ { "@id": "urn:cat-2fz5ttpF", "Label": "cat", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "cat dfile.r*.1D > dfile_rall.1D", "Parameters": {}, "Used": [ @@ -198,7 +198,7 @@ { "@id": "urn:3dcopy-6anXD3J3", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents", "Parameters": {}, "Used": [ @@ -208,7 +208,7 @@ { "@id": "urn:3dcalc-aAV2PGan", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg", "Parameters": {}, "Used": [ @@ -219,7 +219,7 @@ { "@id": "urn:3dcopy-4bzRrv4x", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj", "Parameters": {}, "Used": [ @@ -229,7 +229,7 @@ { "@id": "urn:3dalline-14yOSmwP", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped", "Parameters": {}, "Used": [ @@ -240,7 +240,7 @@ { "@id": "urn:3dmerge-dro1prKM", "Label": "3dmerge", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc", "Parameters": {}, "Used": [ @@ -251,7 +251,7 @@ { "@id": "urn:3dautoma-bcOPYTPN", "Label": "3dAutomask", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -261,7 +261,7 @@ { "@id": "urn:3dmaskto-mSRxvjzr", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj", "Parameters": {}, "Used": [] @@ -269,7 +269,7 @@ { "@id": "urn:3dresamp-ZosW2ivc", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat", "Parameters": {}, "Used": [ @@ -280,7 +280,7 @@ { "@id": "urn:3dmaskto-XYoCnOGa", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj", "Parameters": {}, "Used": [ @@ -290,7 +290,7 @@ { "@id": "urn:3dabover-1842EkJd", "Label": "3dABoverlap", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt", "Parameters": {}, "Used": [ @@ -301,7 +301,7 @@ { "@id": "urn:3ddot-mS7k1Zi6", "Label": "3ddot", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt", "Parameters": {}, "Used": [ @@ -312,7 +312,7 @@ { "@id": "urn:3dresamp-jEcqiAZS", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc", "Parameters": {}, "Used": [ @@ -323,7 +323,7 @@ { "@id": "urn:3dmaskto-Fp5LFGAY", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group", "Parameters": {}, "Used": [ @@ -333,7 +333,7 @@ { "@id": "urn:3dtstat-1LKfPoWn", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -343,7 +343,7 @@ { "@id": "urn:3dcalc-Gkx96YT7", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale", "Parameters": {}, "Used": [ @@ -355,7 +355,7 @@ { "@id": "urn:1dtoolpy-nkvl2lAw", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D", "Parameters": {}, "Used": [ @@ -365,7 +365,7 @@ { "@id": "urn:1dtoolpy-XEzwoJee", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D", "Parameters": {}, "Used": [ @@ -375,7 +375,7 @@ { "@id": "urn:1dtoolpy-s3Oil2R1", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}", "Parameters": {}, "Used": [ @@ -385,7 +385,7 @@ { "@id": "urn:3ddeconv-7obQPDKT", "Label": "3dDeconvolve", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj", "Parameters": {}, "Used": [ @@ -395,7 +395,7 @@ { "@id": "urn:1dtoolpy-UGmO4TdG", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt", "Parameters": {}, "Used": [ @@ -405,7 +405,7 @@ { "@id": "urn:3dtcat-KMmrJrK3", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD", "Parameters": {}, "Used": [ @@ -415,7 +415,7 @@ { "@id": "urn:3dtstat-byrkkVkB", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -425,7 +425,7 @@ { "@id": "urn:3dtstat-VI3XkDVU", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -435,7 +435,7 @@ { "@id": "urn:3dcalc-roPISxqF", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj", "Parameters": {}, "Used": [ @@ -447,7 +447,7 @@ { "@id": "urn:3dtnorm-nfo0JwJ6", "Label": "3dTnorm", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc", "Parameters": {}, "Used": [ @@ -457,7 +457,7 @@ { "@id": "urn:3dmaskav-nm5FLxqI", "Label": "3dmaskave", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D", "Parameters": {}, "Used": [ @@ -467,7 +467,7 @@ { "@id": "urn:3dtstat-UQVvH69i", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D", "Parameters": {}, "Used": [ @@ -477,7 +477,7 @@ { "@id": "urn:3dcalc-dd4aneC8", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP", "Parameters": {}, "Used": [ @@ -488,7 +488,7 @@ { "@id": "urn:3dtstat-Un5JiITd", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc", "Parameters": {}, "Used": [ @@ -498,7 +498,7 @@ { "@id": "urn:1dcat-eyAicARn", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D", "Parameters": {}, "Used": [ @@ -508,7 +508,7 @@ { "@id": "urn:1dcat-6OiK19Zo", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D", "Parameters": {}, "Used": [ @@ -518,7 +518,7 @@ { "@id": "urn:3dtstat-m1M13vmy", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"", "Parameters": {}, "Used": [ @@ -528,7 +528,7 @@ { "@id": "urn:1dcat-A6WOvFVZ", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D", "Parameters": {}, "Used": [ @@ -538,7 +538,7 @@ { "@id": "urn:3dfwhmx-Eild0vbL", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D", "Parameters": {}, "Used": [ @@ -548,7 +548,7 @@ { "@id": "urn:3dfwhmx-6itTOS0r", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D", "Parameters": {}, "Used": [ @@ -558,7 +558,7 @@ { "@id": "urn:3dclusts-owXwdfFv", "Label": "3dClustSim", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim", "Parameters": {}, "Used": [ @@ -568,7 +568,7 @@ { "@id": "urn:genepire-NvZnjQj9", "Label": "gen_epi_review.py", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD", "Parameters": {}, "Used": [ @@ -578,7 +578,7 @@ { "@id": "urn:genssrev-XsBgNJCx", "Label": "gen_ss_review_scripts.py", - "AssociatedWith": "urn:urn:afni-J4qIgUS6", + "AssociatedWith": "urn:afni-J4qIgUS6", "Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0", "Parameters": { "-mot_limit": "0.3", diff --git a/examples/from_parsers/afni/afni_default_proc.png b/examples/from_parsers/afni/afni_default_proc.png index b9d5aa75..560357f4 100644 Binary files a/examples/from_parsers/afni/afni_default_proc.png and b/examples/from_parsers/afni/afni_default_proc.png differ diff --git a/examples/from_parsers/afni/afni_default_proc_block.jsonld b/examples/from_parsers/afni/afni_default_proc_block.jsonld index c81de183..e7c08c80 100644 --- a/examples/from_parsers/afni/afni_default_proc_block.jsonld +++ b/examples/from_parsers/afni/afni_default_proc_block.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:autobloc-YPIV47Dx", "Label": "auto block: setup", - "AssociatedWith": "urn:urn:afni-kOck4tYs", + "AssociatedWith": "urn:afni-kOck4tYs", "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_voxelwise_p0001/tone_counting_onset_times.txt ./afni_voxelwise_p0001/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy ./afni_voxelwise_p0001/sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ", "Used": [ "bids::afni_voxelwise_p0001/tone_counting_onset_times.txt", @@ -26,7 +26,7 @@ { "@id": "urn:autobloc-jOINcnrz", "Label": "auto block: tcat", - "AssociatedWith": "urn:urn:afni-kOck4tYs", + "AssociatedWith": "urn:afni-kOck4tYs", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_voxelwise_p0001/sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ", "Used": [ "bids::afni_voxelwise_p0001/sub-01_task-tonecounting_bold.nii.gz'[0..$]'" @@ -35,7 +35,7 @@ { "@id": "urn:autobloc-oMmfgA8Z", "Label": "auto block: outcount", - "AssociatedWith": "urn:urn:afni-kOck4tYs", + "AssociatedWith": "urn:afni-kOck4tYs", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig", @@ -45,7 +45,7 @@ { "@id": "urn:tshift-1y89hpW4", "Label": "tshift", - "AssociatedWith": "urn:urn:afni-kOck4tYs", + "AssociatedWith": "urn:afni-kOck4tYs", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig" @@ -54,7 +54,7 @@ { "@id": "urn:align-59hUVXxz", "Label": "align", - "AssociatedWith": "urn:urn:afni-kOck4tYs", + "AssociatedWith": "urn:afni-kOck4tYs", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ", "Used": [ "bids::pb01.$subj.r01.tshift+orig", @@ -64,7 +64,7 @@ { "@id": "urn:tlrc-Djxy7vcJ", "Label": "tlrc", - "AssociatedWith": "urn:urn:afni-kOck4tYs", + "AssociatedWith": "urn:afni-kOck4tYs", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ", "Used": [ "bids::TT_N27+tlrc", @@ -75,7 +75,7 @@ { "@id": "urn:volreg-l63WyLnA", "Label": "volreg", - "AssociatedWith": "urn:urn:afni-kOck4tYs", + "AssociatedWith": "urn:afni-kOck4tYs", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ", "Used": [ "bids::pb01.$subj.r$run.tshift+orig", @@ -98,7 +98,7 @@ { "@id": "urn:blur-aro2m421", "Label": "blur", - "AssociatedWith": "urn:urn:afni-kOck4tYs", + "AssociatedWith": "urn:afni-kOck4tYs", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ", "Used": [ "bids::pb02.$subj.r$run.volreg+tlrc", @@ -108,7 +108,7 @@ { "@id": "urn:mask-ljR4ulK8", "Label": "mask", - "AssociatedWith": "urn:urn:afni-kOck4tYs", + "AssociatedWith": "urn:afni-kOck4tYs", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -127,7 +127,7 @@ { "@id": "urn:scale-ruEsLOtV", "Label": "scale", - "AssociatedWith": "urn:urn:afni-kOck4tYs", + "AssociatedWith": "urn:afni-kOck4tYs", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -139,7 +139,7 @@ { "@id": "urn:regress-uKPvbnOr", "Label": "regress", - "AssociatedWith": "urn:urn:afni-kOck4tYs", + "AssociatedWith": "urn:afni-kOck4tYs", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ", "Used": [ "bids::dfile_rall.1D", @@ -166,7 +166,7 @@ { "@id": "urn:bluresti-UQl2sHWq", "Label": "blur estimation", - "AssociatedWith": "urn:urn:afni-kOck4tYs", + "AssociatedWith": "urn:afni-kOck4tYs", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ", "Used": [ "bids::full_mask.$subj+tlrc", @@ -177,7 +177,7 @@ { "@id": "urn:autobloc-52StQ3NA", "Label": "auto block: generate review scripts", - "AssociatedWith": "urn:urn:afni-kOck4tYs", + "AssociatedWith": "urn:afni-kOck4tYs", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ", "Used": [ "bids::pb00.$subj.r*.tcat+orig.HEAD" diff --git a/examples/from_parsers/afni/afni_default_proc_block.png b/examples/from_parsers/afni/afni_default_proc_block.png index 4f14e5d3..0cb5b7d6 100644 Binary files a/examples/from_parsers/afni/afni_default_proc_block.png and b/examples/from_parsers/afni/afni_default_proc_block.png differ diff --git a/examples/from_parsers/afni/afni_gam_proc.jsonld b/examples/from_parsers/afni/afni_gam_proc.jsonld index d4989b6b..ee176b6f 100644 --- a/examples/from_parsers/afni/afni_gam_proc.jsonld +++ b/examples/from_parsers/afni/afni_gam_proc.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:makedire-zf7V0epM", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "mkdir $output_dir", "Parameters": {}, "Used": [] @@ -23,7 +23,7 @@ { "@id": "urn:makedire-UiQEc72f", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "mkdir $output_dir/stimuli", "Parameters": {}, "Used": [] @@ -31,7 +31,7 @@ { "@id": "urn:cp-n0wB3JC9", "Label": "cp", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "cp ./afni_gam/tone_counting_onset_times.txt $output_dir/stimuli", "Parameters": {}, "Used": [ @@ -41,7 +41,7 @@ { "@id": "urn:3dcopy-kRqgajxm", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dcopy ./afni_gam/sub-01_T1w.nii.gz $output_dir/sub-01_T1w", "Parameters": {}, "Used": [ @@ -51,7 +51,7 @@ { "@id": "urn:3dtcat-9hBx7Xb5", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_gam/sub-01_task-tonecounting_bold.nii.gz'[0..$]'", "Parameters": {}, "Used": [ @@ -61,7 +61,7 @@ { "@id": "urn:3dtoutco-6h2RpeoD", "Label": "3dToutcount", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D", "Parameters": {}, "Used": [ @@ -71,7 +71,7 @@ { "@id": "urn:cat-ec1ecOF8", "Label": "cat", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "cat outcount.r*.1D > outcount_rall.1D", "Parameters": {}, "Used": [ @@ -81,7 +81,7 @@ { "@id": "urn:3dtshift-IbSPdLhN", "Label": "3dTshift", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig", "Parameters": {}, "Used": [ @@ -91,7 +91,7 @@ { "@id": "urn:alignepi-7BZjwJ25", "Label": "align_epi_anat.py", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off", "Parameters": {}, "Used": [ @@ -102,7 +102,7 @@ { "@id": "urn:autotlrc-Y70c9vNS", "Label": "@auto_tlrc", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss", "Parameters": {}, "Used": [ @@ -113,7 +113,7 @@ { "@id": "urn:catmatve-gKDe15pu", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D", "Parameters": {}, "Used": [ @@ -123,7 +123,7 @@ { "@id": "urn:3dvolreg-7EILeENF", "Label": "3dvolreg", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig", "Parameters": {}, "Used": [ @@ -133,7 +133,7 @@ { "@id": "urn:3dcalc-2zrP85y3", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1", "Parameters": {}, "Used": [ @@ -143,7 +143,7 @@ { "@id": "urn:catmatve-RDcYdGjZ", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D", "Parameters": {}, "Used": [ @@ -153,7 +153,7 @@ { "@id": "urn:3dalline-DsMduKfA", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run", "Parameters": {}, "Used": [ @@ -165,7 +165,7 @@ { "@id": "urn:3dalline-kcJ790Fq", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run", "Parameters": {}, "Used": [ @@ -177,7 +177,7 @@ { "@id": "urn:3dtstat-GD8XVCMR", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc", "Parameters": {}, "Used": [ @@ -187,7 +187,7 @@ { "@id": "urn:cat-mQD6kcqM", "Label": "cat", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "cat dfile.r*.1D > dfile_rall.1D", "Parameters": {}, "Used": [ @@ -197,7 +197,7 @@ { "@id": "urn:3dcopy-kCVFiKEn", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents", "Parameters": {}, "Used": [ @@ -207,7 +207,7 @@ { "@id": "urn:3dcalc-nV98IIGh", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg", "Parameters": {}, "Used": [ @@ -218,7 +218,7 @@ { "@id": "urn:3dcopy-7imt6vzx", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj", "Parameters": {}, "Used": [ @@ -228,7 +228,7 @@ { "@id": "urn:3dalline-TzJZcFHG", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped", "Parameters": {}, "Used": [ @@ -239,7 +239,7 @@ { "@id": "urn:3dmerge-31GahazW", "Label": "3dmerge", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc", "Parameters": {}, "Used": [ @@ -250,7 +250,7 @@ { "@id": "urn:3dautoma-RiQw0F5h", "Label": "3dAutomask", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -260,7 +260,7 @@ { "@id": "urn:3dmaskto-zDFuqYZj", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj", "Parameters": {}, "Used": [] @@ -268,7 +268,7 @@ { "@id": "urn:3dresamp-VLobe46F", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat", "Parameters": {}, "Used": [ @@ -279,7 +279,7 @@ { "@id": "urn:3dmaskto-xRqeKVKk", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj", "Parameters": {}, "Used": [ @@ -289,7 +289,7 @@ { "@id": "urn:3dabover-TKBoabul", "Label": "3dABoverlap", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt", "Parameters": {}, "Used": [ @@ -300,7 +300,7 @@ { "@id": "urn:3ddot-Hus14uyn", "Label": "3ddot", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt", "Parameters": {}, "Used": [ @@ -311,7 +311,7 @@ { "@id": "urn:3dresamp-R1fiidPv", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc", "Parameters": {}, "Used": [ @@ -322,7 +322,7 @@ { "@id": "urn:3dmaskto-hTtHnRLQ", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group", "Parameters": {}, "Used": [ @@ -332,7 +332,7 @@ { "@id": "urn:3dtstat-OetYnP1M", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -342,7 +342,7 @@ { "@id": "urn:3dcalc-iKl15WK0", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale", "Parameters": {}, "Used": [ @@ -354,7 +354,7 @@ { "@id": "urn:1dtoolpy-UU0BxZHZ", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D", "Parameters": {}, "Used": [ @@ -364,7 +364,7 @@ { "@id": "urn:1dtoolpy-TyRwruqu", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D", "Parameters": {}, "Used": [ @@ -374,7 +374,7 @@ { "@id": "urn:1dtoolpy-HCa0bU14", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}", "Parameters": {}, "Used": [ @@ -384,7 +384,7 @@ { "@id": "urn:3ddeconv-5AwXZgCN", "Label": "3dDeconvolve", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 7 -stim_times 1 stimuli/tone_counting_onset_times.txt 'GAM' -stim_label 1 tone_counting_onset_times.txt -stim_file 2 motion_demean.1D'[0]' -stim_base 2 -stim_label 2 roll -stim_file 3 motion_demean.1D'[1]' -stim_base 3 -stim_label 3 pitch -stim_file 4 motion_demean.1D'[2]' -stim_base 4 -stim_label 4 yaw -stim_file 5 motion_demean.1D'[3]' -stim_base 5 -stim_label 5 dS -stim_file 6 motion_demean.1D'[4]' -stim_base 6 -stim_label 6 dL -stim_file 7 motion_demean.1D'[5]' -stim_base 7 -stim_label 7 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj", "Parameters": {}, "Used": [ @@ -394,7 +394,7 @@ { "@id": "urn:1dtoolpy-nbOjPaaJ", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt", "Parameters": {}, "Used": [ @@ -404,7 +404,7 @@ { "@id": "urn:3dtcat-oM0YiFdz", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD", "Parameters": {}, "Used": [ @@ -414,7 +414,7 @@ { "@id": "urn:3dtstat-1QgQV99M", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -424,7 +424,7 @@ { "@id": "urn:3dtstat-zOhAVK8U", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -434,7 +434,7 @@ { "@id": "urn:3dcalc-tnX6Xq31", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj", "Parameters": {}, "Used": [ @@ -446,7 +446,7 @@ { "@id": "urn:3dtnorm-oxtrR3Pw", "Label": "3dTnorm", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc", "Parameters": {}, "Used": [ @@ -456,7 +456,7 @@ { "@id": "urn:3dmaskav-26CemRJA", "Label": "3dmaskave", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D", "Parameters": {}, "Used": [ @@ -466,7 +466,7 @@ { "@id": "urn:3dtstat-2DL2zRPf", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D", "Parameters": {}, "Used": [ @@ -476,7 +476,7 @@ { "@id": "urn:3dcalc-LxtFiCX3", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP", "Parameters": {}, "Used": [ @@ -487,7 +487,7 @@ { "@id": "urn:3dtstat-lgLdbXSA", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc", "Parameters": {}, "Used": [ @@ -497,7 +497,7 @@ { "@id": "urn:1dcat-VkGX450W", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting_onset_times.txt.1D", "Parameters": {}, "Used": [ @@ -507,7 +507,7 @@ { "@id": "urn:3dtstat-cbVn67pE", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"", "Parameters": {}, "Used": [ @@ -517,7 +517,7 @@ { "@id": "urn:1dcat-awTQMceY", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D", "Parameters": {}, "Used": [ @@ -527,7 +527,7 @@ { "@id": "urn:3dfwhmx-Z8naRoVj", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D", "Parameters": {}, "Used": [ @@ -537,7 +537,7 @@ { "@id": "urn:3dfwhmx-0fRbM5UT", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D", "Parameters": {}, "Used": [ @@ -547,7 +547,7 @@ { "@id": "urn:3dclusts-II6Bi7Zl", "Label": "3dClustSim", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim", "Parameters": {}, "Used": [ @@ -557,7 +557,7 @@ { "@id": "urn:genepire-3ZC3FA44", "Label": "gen_epi_review.py", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD", "Parameters": {}, "Used": [ @@ -567,7 +567,7 @@ { "@id": "urn:genssrev-EODYaufK", "Label": "gen_ss_review_scripts.py", - "AssociatedWith": "urn:urn:afni-f7u9iy8U", + "AssociatedWith": "urn:afni-f7u9iy8U", "Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0", "Parameters": { "-mot_limit": "0.3", diff --git a/examples/from_parsers/afni/afni_gam_proc.png b/examples/from_parsers/afni/afni_gam_proc.png index cee1e309..e277d5e7 100644 Binary files a/examples/from_parsers/afni/afni_gam_proc.png and b/examples/from_parsers/afni/afni_gam_proc.png differ diff --git a/examples/from_parsers/afni/afni_gam_proc_block.jsonld b/examples/from_parsers/afni/afni_gam_proc_block.jsonld index d2051616..e30c9cb2 100644 --- a/examples/from_parsers/afni/afni_gam_proc_block.jsonld +++ b/examples/from_parsers/afni/afni_gam_proc_block.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:autobloc-yawH2nHi", "Label": "auto block: setup", - "AssociatedWith": "urn:urn:afni-WGdKEOYU", + "AssociatedWith": "urn:afni-WGdKEOYU", "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_gam/tone_counting_onset_times.txt $output_dir/stimuli; 3dcopy ./afni_gam/sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ", "Used": [ "bids::afni_gam/tone_counting_onset_times.txt", @@ -25,7 +25,7 @@ { "@id": "urn:autobloc-3S8o18SD", "Label": "auto block: tcat", - "AssociatedWith": "urn:urn:afni-WGdKEOYU", + "AssociatedWith": "urn:afni-WGdKEOYU", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_gam/sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ", "Used": [ "bids::afni_gam/sub-01_task-tonecounting_bold.nii.gz'[0..$]'" @@ -34,7 +34,7 @@ { "@id": "urn:autobloc-nSqVpUzm", "Label": "auto block: outcount", - "AssociatedWith": "urn:urn:afni-WGdKEOYU", + "AssociatedWith": "urn:afni-WGdKEOYU", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig", @@ -44,7 +44,7 @@ { "@id": "urn:tshift-kA1RR45z", "Label": "tshift", - "AssociatedWith": "urn:urn:afni-WGdKEOYU", + "AssociatedWith": "urn:afni-WGdKEOYU", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig" @@ -53,7 +53,7 @@ { "@id": "urn:align-aiaahkOe", "Label": "align", - "AssociatedWith": "urn:urn:afni-WGdKEOYU", + "AssociatedWith": "urn:afni-WGdKEOYU", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ", "Used": [ "bids::pb01.$subj.r01.tshift+orig", @@ -63,7 +63,7 @@ { "@id": "urn:tlrc-PPEYvXwo", "Label": "tlrc", - "AssociatedWith": "urn:urn:afni-WGdKEOYU", + "AssociatedWith": "urn:afni-WGdKEOYU", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ", "Used": [ "bids::TT_N27+tlrc", @@ -74,7 +74,7 @@ { "@id": "urn:volreg-INMo0BDF", "Label": "volreg", - "AssociatedWith": "urn:urn:afni-WGdKEOYU", + "AssociatedWith": "urn:afni-WGdKEOYU", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ", "Used": [ "bids::pb01.$subj.r$run.tshift+orig", @@ -97,7 +97,7 @@ { "@id": "urn:blur-XtAAvg9l", "Label": "blur", - "AssociatedWith": "urn:urn:afni-WGdKEOYU", + "AssociatedWith": "urn:afni-WGdKEOYU", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ", "Used": [ "bids::pb02.$subj.r$run.volreg+tlrc", @@ -107,7 +107,7 @@ { "@id": "urn:mask-ZYjLayXi", "Label": "mask", - "AssociatedWith": "urn:urn:afni-WGdKEOYU", + "AssociatedWith": "urn:afni-WGdKEOYU", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -126,7 +126,7 @@ { "@id": "urn:scale-nNPoyA13", "Label": "scale", - "AssociatedWith": "urn:urn:afni-WGdKEOYU", + "AssociatedWith": "urn:afni-WGdKEOYU", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -138,7 +138,7 @@ { "@id": "urn:regress-g4vzalJ0", "Label": "regress", - "AssociatedWith": "urn:urn:afni-WGdKEOYU", + "AssociatedWith": "urn:afni-WGdKEOYU", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 7 -stim_times 1 stimuli/tone_counting_onset_times.txt 'GAM' -stim_label 1 tone_counting_onset_times.txt -stim_file 2 motion_demean.1D'[0]' -stim_base 2 -stim_label 2 roll -stim_file 3 motion_demean.1D'[1]' -stim_base 3 -stim_label 3 pitch -stim_file 4 motion_demean.1D'[2]' -stim_base 4 -stim_label 4 yaw -stim_file 5 motion_demean.1D'[3]' -stim_base 5 -stim_label 5 dS -stim_file 6 motion_demean.1D'[4]' -stim_base 6 -stim_label 6 dL -stim_file 7 motion_demean.1D'[5]' -stim_base 7 -stim_label 7 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting_onset_times.txt.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ", "Used": [ "bids::dfile_rall.1D", @@ -164,7 +164,7 @@ { "@id": "urn:bluresti-C7yt9SsZ", "Label": "blur estimation", - "AssociatedWith": "urn:urn:afni-WGdKEOYU", + "AssociatedWith": "urn:afni-WGdKEOYU", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ", "Used": [ "bids::full_mask.$subj+tlrc", @@ -175,7 +175,7 @@ { "@id": "urn:autobloc-dj10kUao", "Label": "auto block: generate review scripts", - "AssociatedWith": "urn:urn:afni-WGdKEOYU", + "AssociatedWith": "urn:afni-WGdKEOYU", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ", "Used": [ "bids::pb00.$subj.r*.tcat+orig.HEAD" diff --git a/examples/from_parsers/afni/afni_gam_proc_block.png b/examples/from_parsers/afni/afni_gam_proc_block.png index 2f55f84e..5ad3c3e7 100644 Binary files a/examples/from_parsers/afni/afni_gam_proc_block.png and b/examples/from_parsers/afni/afni_gam_proc_block.png differ diff --git a/examples/from_parsers/afni/afni_hrf_gammadiff_proc.jsonld b/examples/from_parsers/afni/afni_hrf_gammadiff_proc.jsonld index 051ef3d5..fc8b76e1 100644 --- a/examples/from_parsers/afni/afni_hrf_gammadiff_proc.jsonld +++ b/examples/from_parsers/afni/afni_hrf_gammadiff_proc.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:makedire-cRfuDYOz", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "mkdir $output_dir", "Parameters": {}, "Used": [] @@ -23,7 +23,7 @@ { "@id": "urn:makedire-EJ8DYuNJ", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "mkdir $output_dir/stimuli", "Parameters": {}, "Used": [] @@ -31,7 +31,7 @@ { "@id": "urn:cp-z68XKlh0", "Label": "cp", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "cp /Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_onset_times.txt /Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_probe_duration.txt $output_dir/stimuli", "Parameters": {}, "Used": [ @@ -42,7 +42,7 @@ { "@id": "urn:3dcopy-j7QzAy9Y", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dcopy /Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/anat/sub-01_T1w.nii.gz $output_dir/sub-01_T1w", "Parameters": {}, "Used": [ @@ -52,7 +52,7 @@ { "@id": "urn:3dtcat-dI1c6m9j", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat /Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'[0..$]'", "Parameters": {}, "Used": [ @@ -62,7 +62,7 @@ { "@id": "urn:3dtoutco-wsZI1sDP", "Label": "3dToutcount", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D", "Parameters": {}, "Used": [ @@ -72,7 +72,7 @@ { "@id": "urn:cat-u7xX4giX", "Label": "cat", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "cat outcount.r*.1D > outcount_rall.1D", "Parameters": {}, "Used": [ @@ -82,7 +82,7 @@ { "@id": "urn:3dtshift-sItZf4Nw", "Label": "3dTshift", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig", "Parameters": {}, "Used": [ @@ -92,7 +92,7 @@ { "@id": "urn:alignepi-oXmvtYx9", "Label": "align_epi_anat.py", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off", "Parameters": {}, "Used": [ @@ -103,7 +103,7 @@ { "@id": "urn:autotlrc-Aq2WvqW4", "Label": "@auto_tlrc", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss", "Parameters": {}, "Used": [ @@ -114,7 +114,7 @@ { "@id": "urn:catmatve-J2zFwWGS", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D", "Parameters": {}, "Used": [ @@ -124,7 +124,7 @@ { "@id": "urn:3dvolreg-Cq6T5XNy", "Label": "3dvolreg", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig", "Parameters": {}, "Used": [ @@ -134,7 +134,7 @@ { "@id": "urn:3dcalc-0Ja1pte4", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1", "Parameters": {}, "Used": [ @@ -144,7 +144,7 @@ { "@id": "urn:catmatve-SKhupqPf", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D", "Parameters": {}, "Used": [ @@ -154,7 +154,7 @@ { "@id": "urn:3dalline-LTjxwict", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run", "Parameters": {}, "Used": [ @@ -166,7 +166,7 @@ { "@id": "urn:3dalline-aadbI5yi", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run", "Parameters": {}, "Used": [ @@ -178,7 +178,7 @@ { "@id": "urn:3dtstat-y5G8BFbB", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc", "Parameters": {}, "Used": [ @@ -188,7 +188,7 @@ { "@id": "urn:cat-253bV9ng", "Label": "cat", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "cat dfile.r*.1D > dfile_rall.1D", "Parameters": {}, "Used": [ @@ -198,7 +198,7 @@ { "@id": "urn:3dcopy-XEa7vJeI", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents", "Parameters": {}, "Used": [ @@ -208,7 +208,7 @@ { "@id": "urn:3dcalc-1YvbY0PC", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg", "Parameters": {}, "Used": [ @@ -219,7 +219,7 @@ { "@id": "urn:3dcopy-dCftIe4a", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj", "Parameters": {}, "Used": [ @@ -229,7 +229,7 @@ { "@id": "urn:3dalline-UosLclnS", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped", "Parameters": {}, "Used": [ @@ -240,7 +240,7 @@ { "@id": "urn:3dmerge-Ne0kAscL", "Label": "3dmerge", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc", "Parameters": {}, "Used": [ @@ -251,7 +251,7 @@ { "@id": "urn:3dautoma-s2OEFl98", "Label": "3dAutomask", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -261,7 +261,7 @@ { "@id": "urn:3dmaskto-iHTEgBWH", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj", "Parameters": {}, "Used": [] @@ -269,7 +269,7 @@ { "@id": "urn:3dresamp-pocDgAWQ", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat", "Parameters": {}, "Used": [ @@ -280,7 +280,7 @@ { "@id": "urn:3dmaskto-vqzd0AtF", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj", "Parameters": {}, "Used": [ @@ -290,7 +290,7 @@ { "@id": "urn:3dabover-1xpPMyYj", "Label": "3dABoverlap", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt", "Parameters": {}, "Used": [ @@ -301,7 +301,7 @@ { "@id": "urn:3ddot-vG3Ho8HD", "Label": "3ddot", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt", "Parameters": {}, "Used": [ @@ -312,7 +312,7 @@ { "@id": "urn:3dresamp-ZykKjp5v", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/cmaumet/Softs/external/AFNI/macosx_10.7_Intel_64/TT_N27+tlrc", "Parameters": {}, "Used": [ @@ -323,7 +323,7 @@ { "@id": "urn:3dmaskto-zk5klqdp", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group", "Parameters": {}, "Used": [ @@ -333,7 +333,7 @@ { "@id": "urn:3dtstat-wkDlzccF", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -343,7 +343,7 @@ { "@id": "urn:3dcalc-ND3i7gG2", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale", "Parameters": {}, "Used": [ @@ -355,7 +355,7 @@ { "@id": "urn:1dtoolpy-jmVZrg5v", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D", "Parameters": {}, "Used": [ @@ -365,7 +365,7 @@ { "@id": "urn:1dtoolpy-WpZBMKSn", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D", "Parameters": {}, "Used": [ @@ -375,7 +375,7 @@ { "@id": "urn:1dtoolpy-qyqyePOj", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}", "Parameters": {}, "Used": [ @@ -385,7 +385,7 @@ { "@id": "urn:3ddeconv-lGWPUoyd", "Label": "3dDeconvolve", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'SPMG1(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj", "Parameters": {}, "Used": [ @@ -395,7 +395,7 @@ { "@id": "urn:1dtoolpy-7JKuHRGb", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt", "Parameters": {}, "Used": [ @@ -405,7 +405,7 @@ { "@id": "urn:3dtcat-VE6isJJF", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD", "Parameters": {}, "Used": [ @@ -415,7 +415,7 @@ { "@id": "urn:3dtstat-j6wPnIPn", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -425,7 +425,7 @@ { "@id": "urn:3dtstat-sL2ktdxz", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -435,7 +435,7 @@ { "@id": "urn:3dcalc-Mt6kd9m5", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj", "Parameters": {}, "Used": [ @@ -447,7 +447,7 @@ { "@id": "urn:3dtnorm-5j01dczD", "Label": "3dTnorm", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc", "Parameters": {}, "Used": [ @@ -457,7 +457,7 @@ { "@id": "urn:3dmaskav-oAcYVWNX", "Label": "3dmaskave", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D", "Parameters": {}, "Used": [ @@ -467,7 +467,7 @@ { "@id": "urn:3dtstat-aobd0oPt", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D", "Parameters": {}, "Used": [ @@ -477,7 +477,7 @@ { "@id": "urn:3dcalc-RnanHX9O", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP", "Parameters": {}, "Used": [ @@ -488,7 +488,7 @@ { "@id": "urn:3dtstat-qIVnovdP", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc", "Parameters": {}, "Used": [ @@ -498,7 +498,7 @@ { "@id": "urn:1dcat-YMqDTdmD", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D", "Parameters": {}, "Used": [ @@ -508,7 +508,7 @@ { "@id": "urn:1dcat-wxWuGyPa", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D", "Parameters": {}, "Used": [ @@ -518,7 +518,7 @@ { "@id": "urn:3dtstat-g09qekV2", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"", "Parameters": {}, "Used": [ @@ -528,7 +528,7 @@ { "@id": "urn:1dcat-rVexAwDh", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D", "Parameters": {}, "Used": [ @@ -538,7 +538,7 @@ { "@id": "urn:3dfwhmx-HbowdNMj", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D", "Parameters": {}, "Used": [ @@ -548,7 +548,7 @@ { "@id": "urn:3dfwhmx-AgcWE97u", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D", "Parameters": {}, "Used": [ @@ -558,7 +558,7 @@ { "@id": "urn:3dclusts-xWsyKiqb", "Label": "3dClustSim", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim", "Parameters": {}, "Used": [ @@ -568,7 +568,7 @@ { "@id": "urn:genepire-JDKTjSo7", "Label": "gen_epi_review.py", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD", "Parameters": {}, "Used": [ @@ -578,7 +578,7 @@ { "@id": "urn:genssrev-bLXWWzXw", "Label": "gen_ss_review_scripts.py", - "AssociatedWith": "urn:urn:afni-LuUPJG0l", + "AssociatedWith": "urn:afni-LuUPJG0l", "Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0", "Parameters": { "-mot_limit": "0.3", diff --git a/examples/from_parsers/afni/afni_hrf_gammadiff_proc.png b/examples/from_parsers/afni/afni_hrf_gammadiff_proc.png index 9d9ceb86..8c75b890 100644 Binary files a/examples/from_parsers/afni/afni_hrf_gammadiff_proc.png and b/examples/from_parsers/afni/afni_hrf_gammadiff_proc.png differ diff --git a/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.jsonld b/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.jsonld index c210ebfd..f9025140 100644 --- a/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.jsonld +++ b/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:autobloc-5KgJTiu3", "Label": "auto block: setup", - "AssociatedWith": "urn:urn:afni-ams3QlzR", + "AssociatedWith": "urn:afni-ams3QlzR", "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp /Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_onset_times.txt /Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy /Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/anat/sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ", "Used": [ "bids::/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_onset_times.txt", @@ -26,7 +26,7 @@ { "@id": "urn:autobloc-VH75Af2k", "Label": "auto block: tcat", - "AssociatedWith": "urn:urn:afni-ams3QlzR", + "AssociatedWith": "urn:afni-ams3QlzR", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat /Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ", "Used": [ "bids::/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'[0..$]'" @@ -35,7 +35,7 @@ { "@id": "urn:autobloc-Dev6mf7h", "Label": "auto block: outcount", - "AssociatedWith": "urn:urn:afni-ams3QlzR", + "AssociatedWith": "urn:afni-ams3QlzR", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig", @@ -45,7 +45,7 @@ { "@id": "urn:tshift-7nObZinu", "Label": "tshift", - "AssociatedWith": "urn:urn:afni-ams3QlzR", + "AssociatedWith": "urn:afni-ams3QlzR", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig" @@ -54,7 +54,7 @@ { "@id": "urn:align-8x9H6ddn", "Label": "align", - "AssociatedWith": "urn:urn:afni-ams3QlzR", + "AssociatedWith": "urn:afni-ams3QlzR", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ", "Used": [ "bids::pb01.$subj.r01.tshift+orig", @@ -64,7 +64,7 @@ { "@id": "urn:tlrc-YlBDOp0O", "Label": "tlrc", - "AssociatedWith": "urn:urn:afni-ams3QlzR", + "AssociatedWith": "urn:afni-ams3QlzR", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ", "Used": [ "bids::TT_N27+tlrc", @@ -75,7 +75,7 @@ { "@id": "urn:volreg-kb7kw99N", "Label": "volreg", - "AssociatedWith": "urn:urn:afni-ams3QlzR", + "AssociatedWith": "urn:afni-ams3QlzR", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ", "Used": [ "bids::pb01.$subj.r$run.tshift+orig", @@ -98,7 +98,7 @@ { "@id": "urn:blur-g3K2TO8T", "Label": "blur", - "AssociatedWith": "urn:urn:afni-ams3QlzR", + "AssociatedWith": "urn:afni-ams3QlzR", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ", "Used": [ "bids::pb02.$subj.r$run.volreg+tlrc", @@ -108,7 +108,7 @@ { "@id": "urn:mask-PfjxTDnW", "Label": "mask", - "AssociatedWith": "urn:urn:afni-ams3QlzR", + "AssociatedWith": "urn:afni-ams3QlzR", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/cmaumet/Softs/external/AFNI/macosx_10.7_Intel_64/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -127,7 +127,7 @@ { "@id": "urn:scale-W7kJCRkA", "Label": "scale", - "AssociatedWith": "urn:urn:afni-ams3QlzR", + "AssociatedWith": "urn:afni-ams3QlzR", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -139,7 +139,7 @@ { "@id": "urn:regress-ieJMqRzA", "Label": "regress", - "AssociatedWith": "urn:urn:afni-ams3QlzR", + "AssociatedWith": "urn:afni-ams3QlzR", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'SPMG1(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ", "Used": [ "bids::dfile_rall.1D", @@ -166,7 +166,7 @@ { "@id": "urn:bluresti-25XSZU9P", "Label": "blur estimation", - "AssociatedWith": "urn:urn:afni-ams3QlzR", + "AssociatedWith": "urn:afni-ams3QlzR", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ", "Used": [ "bids::full_mask.$subj+tlrc", @@ -177,7 +177,7 @@ { "@id": "urn:autobloc-mzC0nGoF", "Label": "auto block: generate review scripts", - "AssociatedWith": "urn:urn:afni-ams3QlzR", + "AssociatedWith": "urn:afni-ams3QlzR", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ", "Used": [ "bids::pb00.$subj.r*.tcat+orig.HEAD" diff --git a/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.png b/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.png index 8f137202..c651030d 100644 Binary files a/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.png and b/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.png differ diff --git a/examples/from_parsers/afni/afni_hrf_tent_proc.jsonld b/examples/from_parsers/afni/afni_hrf_tent_proc.jsonld index ca337ced..ecd6e548 100644 --- a/examples/from_parsers/afni/afni_hrf_tent_proc.jsonld +++ b/examples/from_parsers/afni/afni_hrf_tent_proc.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:makedire-rMBB43ru", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "mkdir $output_dir", "Parameters": {}, "Used": [] @@ -23,7 +23,7 @@ { "@id": "urn:makedire-pCcQt8Hm", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "mkdir $output_dir/stimuli", "Parameters": {}, "Used": [] @@ -31,7 +31,7 @@ { "@id": "urn:cp-4seTsodx", "Label": "cp", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "cp ./afni_tent_basis_function/tone_counting_onset_times.txt ./afni_tent_basis_function/tone_counting_probe_onsets.txt $output_dir/stimuli", "Parameters": {}, "Used": [ @@ -42,7 +42,7 @@ { "@id": "urn:3dcopy-YpRyxDa0", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dcopy ./afni_tent_basis_function/sub-01_T1w.nii.gz $output_dir/sub-01_T1w", "Parameters": {}, "Used": [ @@ -52,7 +52,7 @@ { "@id": "urn:3dtcat-FRtKXMIi", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_tent_basis_function/sub-01_task-tonecounting_bold.nii.gz'[0..$]'", "Parameters": {}, "Used": [ @@ -62,7 +62,7 @@ { "@id": "urn:3dtoutco-9zsBBDsR", "Label": "3dToutcount", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D", "Parameters": {}, "Used": [ @@ -72,7 +72,7 @@ { "@id": "urn:cat-kqzAufE3", "Label": "cat", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "cat outcount.r*.1D > outcount_rall.1D", "Parameters": {}, "Used": [ @@ -82,7 +82,7 @@ { "@id": "urn:3dtshift-6OSZ30P3", "Label": "3dTshift", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig", "Parameters": {}, "Used": [ @@ -92,7 +92,7 @@ { "@id": "urn:alignepi-TEeGO0Xs", "Label": "align_epi_anat.py", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off", "Parameters": {}, "Used": [ @@ -103,7 +103,7 @@ { "@id": "urn:autotlrc-nYCl29ey", "Label": "@auto_tlrc", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss", "Parameters": {}, "Used": [ @@ -114,7 +114,7 @@ { "@id": "urn:catmatve-DttU0PXp", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D", "Parameters": {}, "Used": [ @@ -124,7 +124,7 @@ { "@id": "urn:3dvolreg-Zl1YHCQi", "Label": "3dvolreg", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig", "Parameters": {}, "Used": [ @@ -134,7 +134,7 @@ { "@id": "urn:3dcalc-RS2awq0W", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1", "Parameters": {}, "Used": [ @@ -144,7 +144,7 @@ { "@id": "urn:catmatve-d1oJD0qG", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D", "Parameters": {}, "Used": [ @@ -154,7 +154,7 @@ { "@id": "urn:3dalline-TDVcAxMn", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run", "Parameters": {}, "Used": [ @@ -166,7 +166,7 @@ { "@id": "urn:3dalline-zUGfDpz1", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run", "Parameters": {}, "Used": [ @@ -178,7 +178,7 @@ { "@id": "urn:3dtstat-PDDSvUoK", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc", "Parameters": {}, "Used": [ @@ -188,7 +188,7 @@ { "@id": "urn:cat-V4HmPyNP", "Label": "cat", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "cat dfile.r*.1D > dfile_rall.1D", "Parameters": {}, "Used": [ @@ -198,7 +198,7 @@ { "@id": "urn:3dcopy-a49D5QLO", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents", "Parameters": {}, "Used": [ @@ -208,7 +208,7 @@ { "@id": "urn:3dcalc-UrcTwseN", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg", "Parameters": {}, "Used": [ @@ -219,7 +219,7 @@ { "@id": "urn:3dcopy-qsNxunE4", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj", "Parameters": {}, "Used": [ @@ -229,7 +229,7 @@ { "@id": "urn:3dalline-kygdvilF", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped", "Parameters": {}, "Used": [ @@ -240,7 +240,7 @@ { "@id": "urn:3dmerge-soXKeMFe", "Label": "3dmerge", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc", "Parameters": {}, "Used": [ @@ -251,7 +251,7 @@ { "@id": "urn:3dautoma-zXzILOFI", "Label": "3dAutomask", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -261,7 +261,7 @@ { "@id": "urn:3dmaskto-KORdJ9qp", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj", "Parameters": {}, "Used": [] @@ -269,7 +269,7 @@ { "@id": "urn:3dresamp-M7iURngw", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat", "Parameters": {}, "Used": [ @@ -280,7 +280,7 @@ { "@id": "urn:3dmaskto-hJBLuYfU", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj", "Parameters": {}, "Used": [ @@ -290,7 +290,7 @@ { "@id": "urn:3dabover-wyTw56Ux", "Label": "3dABoverlap", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt", "Parameters": {}, "Used": [ @@ -301,7 +301,7 @@ { "@id": "urn:3ddot-9UcoOjaJ", "Label": "3ddot", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt", "Parameters": {}, "Used": [ @@ -312,7 +312,7 @@ { "@id": "urn:3dresamp-KD4OLtse", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc", "Parameters": {}, "Used": [ @@ -323,7 +323,7 @@ { "@id": "urn:3dmaskto-r1L37Z4x", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group", "Parameters": {}, "Used": [ @@ -333,7 +333,7 @@ { "@id": "urn:3dtstat-90PVF6gg", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -343,7 +343,7 @@ { "@id": "urn:3dcalc-FaDTKvWb", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale", "Parameters": {}, "Used": [ @@ -355,7 +355,7 @@ { "@id": "urn:1dtoolpy-ZfaCxzZ6", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D", "Parameters": {}, "Used": [ @@ -365,7 +365,7 @@ { "@id": "urn:1dtoolpy-MZXwlLDw", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D", "Parameters": {}, "Used": [ @@ -375,7 +375,7 @@ { "@id": "urn:1dtoolpy-kv2PqQbU", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}", "Parameters": {}, "Used": [ @@ -385,7 +385,7 @@ { "@id": "urn:3ddeconv-hvXpUiR6", "Label": "3dDeconvolve", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'TENT(0,12,7)' -stim_label 1 tone_counting -stim_times 2 stimuli/tone_counting_probe_onsets.txt 'TENT(0,14,8)' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -iresp 1 iresp_tone_counting.$subj -iresp 2 iresp_probe.$subj -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj", "Parameters": {}, "Used": [ @@ -395,7 +395,7 @@ { "@id": "urn:1dtoolpy-EJgI912b", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt", "Parameters": {}, "Used": [ @@ -405,7 +405,7 @@ { "@id": "urn:timingto-MqFbTXF0", "Label": "timing_tool.py", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "timing_tool.py -multi_timing stimuli/tone_counting_onset_times.txt stimuli/tone_counting_probe_onsets.txt -tr 2.0 -warn_tr_stats |& tee out.TENT_warn.txt", "Parameters": { "-multi_timing": "stimuli/tone_counting_onset_times.txt", @@ -419,7 +419,7 @@ { "@id": "urn:3dtcat-nqcTZGqw", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD", "Parameters": {}, "Used": [ @@ -429,7 +429,7 @@ { "@id": "urn:3dtstat-6VWqNLos", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -439,7 +439,7 @@ { "@id": "urn:3dtstat-DWshRU94", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -449,7 +449,7 @@ { "@id": "urn:3dcalc-jnLuhj7l", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj", "Parameters": {}, "Used": [ @@ -461,7 +461,7 @@ { "@id": "urn:3dtnorm-LoxTEe0B", "Label": "3dTnorm", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc", "Parameters": {}, "Used": [ @@ -471,7 +471,7 @@ { "@id": "urn:3dmaskav-13pJnuBU", "Label": "3dmaskave", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D", "Parameters": {}, "Used": [ @@ -481,7 +481,7 @@ { "@id": "urn:3dtstat-b94l3K8y", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D", "Parameters": {}, "Used": [ @@ -491,7 +491,7 @@ { "@id": "urn:3dcalc-Zb2vG85e", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP", "Parameters": {}, "Used": [ @@ -502,7 +502,7 @@ { "@id": "urn:3dtstat-qIv85HKI", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc", "Parameters": {}, "Used": [ @@ -512,7 +512,7 @@ { "@id": "urn:3dtstat-vZlmpAJf", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"", "Parameters": {}, "Used": [ @@ -522,7 +522,7 @@ { "@id": "urn:1dcat-IjsgTPfv", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D", "Parameters": {}, "Used": [ @@ -532,7 +532,7 @@ { "@id": "urn:3dfwhmx-cZWCstBL", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D", "Parameters": {}, "Used": [ @@ -542,7 +542,7 @@ { "@id": "urn:3dfwhmx-CC6HkIhP", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D", "Parameters": {}, "Used": [ @@ -552,7 +552,7 @@ { "@id": "urn:3dclusts-a80eHKzD", "Label": "3dClustSim", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim", "Parameters": {}, "Used": [ @@ -562,7 +562,7 @@ { "@id": "urn:genepire-uCkxUTJ8", "Label": "gen_epi_review.py", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD", "Parameters": {}, "Used": [ @@ -572,7 +572,7 @@ { "@id": "urn:genssrev-v1XRw400", "Label": "gen_ss_review_scripts.py", - "AssociatedWith": "urn:urn:afni-KInB335j", + "AssociatedWith": "urn:afni-KInB335j", "Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0", "Parameters": { "-mot_limit": "0.3", diff --git a/examples/from_parsers/afni/afni_hrf_tent_proc.png b/examples/from_parsers/afni/afni_hrf_tent_proc.png index a15b03a7..7de99440 100644 Binary files a/examples/from_parsers/afni/afni_hrf_tent_proc.png and b/examples/from_parsers/afni/afni_hrf_tent_proc.png differ diff --git a/examples/from_parsers/afni/afni_hrf_tent_proc_block.jsonld b/examples/from_parsers/afni/afni_hrf_tent_proc_block.jsonld index b91ef8a6..63f146f2 100644 --- a/examples/from_parsers/afni/afni_hrf_tent_proc_block.jsonld +++ b/examples/from_parsers/afni/afni_hrf_tent_proc_block.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:autobloc-3YGfBr3I", "Label": "auto block: setup", - "AssociatedWith": "urn:urn:afni-uASy2GCl", + "AssociatedWith": "urn:afni-uASy2GCl", "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_tent_basis_function/tone_counting_onset_times.txt ./afni_tent_basis_function/tone_counting_probe_onsets.txt $output_dir/stimuli; 3dcopy ./afni_tent_basis_function/sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ", "Used": [ "bids::afni_tent_basis_function/tone_counting_onset_times.txt", @@ -26,7 +26,7 @@ { "@id": "urn:autobloc-phrCjl2z", "Label": "auto block: tcat", - "AssociatedWith": "urn:urn:afni-uASy2GCl", + "AssociatedWith": "urn:afni-uASy2GCl", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_tent_basis_function/sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ", "Used": [ "bids::afni_tent_basis_function/sub-01_task-tonecounting_bold.nii.gz'[0..$]'" @@ -35,7 +35,7 @@ { "@id": "urn:autobloc-5kWFbgC7", "Label": "auto block: outcount", - "AssociatedWith": "urn:urn:afni-uASy2GCl", + "AssociatedWith": "urn:afni-uASy2GCl", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig", @@ -45,7 +45,7 @@ { "@id": "urn:tshift-24rSnNu6", "Label": "tshift", - "AssociatedWith": "urn:urn:afni-uASy2GCl", + "AssociatedWith": "urn:afni-uASy2GCl", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig" @@ -54,7 +54,7 @@ { "@id": "urn:align-dHze0nqH", "Label": "align", - "AssociatedWith": "urn:urn:afni-uASy2GCl", + "AssociatedWith": "urn:afni-uASy2GCl", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ", "Used": [ "bids::pb01.$subj.r01.tshift+orig", @@ -64,7 +64,7 @@ { "@id": "urn:tlrc-0RmnlSoq", "Label": "tlrc", - "AssociatedWith": "urn:urn:afni-uASy2GCl", + "AssociatedWith": "urn:afni-uASy2GCl", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ", "Used": [ "bids::TT_N27+tlrc", @@ -75,7 +75,7 @@ { "@id": "urn:volreg-9AcKgwvI", "Label": "volreg", - "AssociatedWith": "urn:urn:afni-uASy2GCl", + "AssociatedWith": "urn:afni-uASy2GCl", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ", "Used": [ "bids::pb01.$subj.r$run.tshift+orig", @@ -98,7 +98,7 @@ { "@id": "urn:blur-XGkqFpmY", "Label": "blur", - "AssociatedWith": "urn:urn:afni-uASy2GCl", + "AssociatedWith": "urn:afni-uASy2GCl", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ", "Used": [ "bids::pb02.$subj.r$run.volreg+tlrc", @@ -108,7 +108,7 @@ { "@id": "urn:mask-3eXfLybE", "Label": "mask", - "AssociatedWith": "urn:urn:afni-uASy2GCl", + "AssociatedWith": "urn:afni-uASy2GCl", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -127,7 +127,7 @@ { "@id": "urn:scale-34hey5xA", "Label": "scale", - "AssociatedWith": "urn:urn:afni-uASy2GCl", + "AssociatedWith": "urn:afni-uASy2GCl", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -139,7 +139,7 @@ { "@id": "urn:regress-4r98WB2m", "Label": "regress", - "AssociatedWith": "urn:urn:afni-uASy2GCl", + "AssociatedWith": "urn:afni-uASy2GCl", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'TENT(0,12,7)' -stim_label 1 tone_counting -stim_times 2 stimuli/tone_counting_probe_onsets.txt 'TENT(0,14,8)' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -iresp 1 iresp_tone_counting.$subj -iresp 2 iresp_probe.$subj -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; timing_tool.py -multi_timing stimuli/tone_counting_onset_times.txt stimuli/tone_counting_probe_onsets.txt -tr 2.0 -warn_tr_stats |& tee out.TENT_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ", "Used": [ "bids::dfile_rall.1D", @@ -165,7 +165,7 @@ { "@id": "urn:bluresti-4mrz2v5M", "Label": "blur estimation", - "AssociatedWith": "urn:urn:afni-uASy2GCl", + "AssociatedWith": "urn:afni-uASy2GCl", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ", "Used": [ "bids::full_mask.$subj+tlrc", @@ -176,7 +176,7 @@ { "@id": "urn:autobloc-c0QvQZQU", "Label": "auto block: generate review scripts", - "AssociatedWith": "urn:urn:afni-uASy2GCl", + "AssociatedWith": "urn:afni-uASy2GCl", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ", "Used": [ "bids::pb00.$subj.r*.tcat+orig.HEAD" diff --git a/examples/from_parsers/afni/afni_hrf_tent_proc_block.png b/examples/from_parsers/afni/afni_hrf_tent_proc_block.png index c6b3bfc2..cd40a425 100644 Binary files a/examples/from_parsers/afni/afni_hrf_tent_proc_block.png and b/examples/from_parsers/afni/afni_hrf_tent_proc_block.png differ diff --git a/examples/from_parsers/afni/afni_other_template_proc.jsonld b/examples/from_parsers/afni/afni_other_template_proc.jsonld index a68038a9..a0464b8f 100644 --- a/examples/from_parsers/afni/afni_other_template_proc.jsonld +++ b/examples/from_parsers/afni/afni_other_template_proc.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:makedire-kLuppHkS", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "mkdir $output_dir", "Parameters": {}, "Used": [] @@ -23,7 +23,7 @@ { "@id": "urn:makedire-lTaUmSAd", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "mkdir $output_dir/stimuli", "Parameters": {}, "Used": [] @@ -31,7 +31,7 @@ { "@id": "urn:cp-dk0J9D1k", "Label": "cp", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "cp ./afni_other_template/tone_counting_onset_times.txt ./afni_other_template/tone_counting_probe_duration.txt $output_dir/stimuli", "Parameters": {}, "Used": [ @@ -42,7 +42,7 @@ { "@id": "urn:3dcopy-WCNzhSPt", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dcopy ./afni_other_template/sub-01_T1w.nii.gz $output_dir/sub-01_T1w", "Parameters": {}, "Used": [ @@ -52,7 +52,7 @@ { "@id": "urn:3dtcat-lB2O2RCN", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_other_template/sub-01_task-tonecounting_bold.nii.gz'[0..$]'", "Parameters": {}, "Used": [ @@ -62,7 +62,7 @@ { "@id": "urn:3dtoutco-deMvTxSG", "Label": "3dToutcount", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D", "Parameters": {}, "Used": [ @@ -72,7 +72,7 @@ { "@id": "urn:cat-eIpwJEgR", "Label": "cat", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "cat outcount.r*.1D > outcount_rall.1D", "Parameters": {}, "Used": [ @@ -82,7 +82,7 @@ { "@id": "urn:3dtshift-2qIKy4sQ", "Label": "3dTshift", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig", "Parameters": {}, "Used": [ @@ -92,7 +92,7 @@ { "@id": "urn:alignepi-henTELhM", "Label": "align_epi_anat.py", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off", "Parameters": {}, "Used": [ @@ -103,7 +103,7 @@ { "@id": "urn:autotlrc-7zuBWBEN", "Label": "@auto_tlrc", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "@auto_tlrc -base TT_icbm452+tlrc -input sub-01_T1w_ns+orig -no_ss", "Parameters": {}, "Used": [ @@ -114,7 +114,7 @@ { "@id": "urn:catmatve-FtabqVUy", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D", "Parameters": {}, "Used": [ @@ -124,7 +124,7 @@ { "@id": "urn:3dvolreg-tRffTRPI", "Label": "3dvolreg", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig", "Parameters": {}, "Used": [ @@ -134,7 +134,7 @@ { "@id": "urn:3dcalc-uliTn0Km", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1", "Parameters": {}, "Used": [ @@ -144,7 +144,7 @@ { "@id": "urn:catmatve-z3tnuXYu", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D", "Parameters": {}, "Used": [ @@ -154,7 +154,7 @@ { "@id": "urn:3dalline-q1cVmk64", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run", "Parameters": {}, "Used": [ @@ -166,7 +166,7 @@ { "@id": "urn:3dalline-s2NW7rWx", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run", "Parameters": {}, "Used": [ @@ -178,7 +178,7 @@ { "@id": "urn:3dtstat-UGtBTEHb", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc", "Parameters": {}, "Used": [ @@ -188,7 +188,7 @@ { "@id": "urn:cat-KcIw3qKJ", "Label": "cat", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "cat dfile.r*.1D > dfile_rall.1D", "Parameters": {}, "Used": [ @@ -198,7 +198,7 @@ { "@id": "urn:3dcopy-NOULEl6u", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents", "Parameters": {}, "Used": [ @@ -208,7 +208,7 @@ { "@id": "urn:3dcalc-VzmVGent", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg", "Parameters": {}, "Used": [ @@ -219,7 +219,7 @@ { "@id": "urn:3dcopy-vIF4FBjA", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj", "Parameters": {}, "Used": [ @@ -229,7 +229,7 @@ { "@id": "urn:3dalline-lN5R4jHH", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped", "Parameters": {}, "Used": [ @@ -240,7 +240,7 @@ { "@id": "urn:3dmerge-vYzWDJi5", "Label": "3dmerge", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc", "Parameters": {}, "Used": [ @@ -251,7 +251,7 @@ { "@id": "urn:3dautoma-4FNaiTgs", "Label": "3dAutomask", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -261,7 +261,7 @@ { "@id": "urn:3dmaskto-fja1GfuR", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj", "Parameters": {}, "Used": [] @@ -269,7 +269,7 @@ { "@id": "urn:3dresamp-ogTu8kZg", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat", "Parameters": {}, "Used": [ @@ -280,7 +280,7 @@ { "@id": "urn:3dmaskto-5803fP7R", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj", "Parameters": {}, "Used": [ @@ -290,7 +290,7 @@ { "@id": "urn:3dabover-UqFFmbFO", "Label": "3dABoverlap", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt", "Parameters": {}, "Used": [ @@ -301,7 +301,7 @@ { "@id": "urn:3ddot-owooRRUE", "Label": "3ddot", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt", "Parameters": {}, "Used": [ @@ -312,7 +312,7 @@ { "@id": "urn:3dresamp-iPUhLb1K", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_icbm452+tlrc", "Parameters": {}, "Used": [ @@ -323,7 +323,7 @@ { "@id": "urn:3dmaskto-vS1tRDqd", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group", "Parameters": {}, "Used": [ @@ -333,7 +333,7 @@ { "@id": "urn:3dtstat-Y5RmSFCv", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -343,7 +343,7 @@ { "@id": "urn:3dcalc-K4X4DN9L", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale", "Parameters": {}, "Used": [ @@ -355,7 +355,7 @@ { "@id": "urn:1dtoolpy-2AWzqdum", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D", "Parameters": {}, "Used": [ @@ -365,7 +365,7 @@ { "@id": "urn:1dtoolpy-SGulyxie", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D", "Parameters": {}, "Used": [ @@ -375,7 +375,7 @@ { "@id": "urn:1dtoolpy-NB1SjVzV", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}", "Parameters": {}, "Used": [ @@ -385,7 +385,7 @@ { "@id": "urn:3ddeconv-OoMAmZgE", "Label": "3dDeconvolve", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj", "Parameters": {}, "Used": [ @@ -395,7 +395,7 @@ { "@id": "urn:1dtoolpy-so1G4GNe", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt", "Parameters": {}, "Used": [ @@ -405,7 +405,7 @@ { "@id": "urn:3dtcat-iIu57VXs", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD", "Parameters": {}, "Used": [ @@ -415,7 +415,7 @@ { "@id": "urn:3dtstat-7859jRZO", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -425,7 +425,7 @@ { "@id": "urn:3dtstat-DkShidOa", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -435,7 +435,7 @@ { "@id": "urn:3dcalc-2J9dUflw", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj", "Parameters": {}, "Used": [ @@ -447,7 +447,7 @@ { "@id": "urn:3dtnorm-pMUJuYjw", "Label": "3dTnorm", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc", "Parameters": {}, "Used": [ @@ -457,7 +457,7 @@ { "@id": "urn:3dmaskav-dvsD2epu", "Label": "3dmaskave", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D", "Parameters": {}, "Used": [ @@ -467,7 +467,7 @@ { "@id": "urn:3dtstat-ktjNDoNF", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D", "Parameters": {}, "Used": [ @@ -477,7 +477,7 @@ { "@id": "urn:3dcalc-SnxiqcDb", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP", "Parameters": {}, "Used": [ @@ -488,7 +488,7 @@ { "@id": "urn:3dtstat-TQOy4xl8", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc", "Parameters": {}, "Used": [ @@ -498,7 +498,7 @@ { "@id": "urn:1dcat-4G6OUj2l", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D", "Parameters": {}, "Used": [ @@ -508,7 +508,7 @@ { "@id": "urn:1dcat-gLkoyvOA", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D", "Parameters": {}, "Used": [ @@ -518,7 +518,7 @@ { "@id": "urn:3dtstat-2ERP6fmu", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"", "Parameters": {}, "Used": [ @@ -528,7 +528,7 @@ { "@id": "urn:1dcat-utdtUqJM", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D", "Parameters": {}, "Used": [ @@ -538,7 +538,7 @@ { "@id": "urn:3dfwhmx-5IqPC8kh", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D", "Parameters": {}, "Used": [ @@ -548,7 +548,7 @@ { "@id": "urn:3dfwhmx-NkxUKdaX", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D", "Parameters": {}, "Used": [ @@ -558,7 +558,7 @@ { "@id": "urn:3dclusts-l5YDzEfr", "Label": "3dClustSim", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim", "Parameters": {}, "Used": [ @@ -568,7 +568,7 @@ { "@id": "urn:genepire-29FksSzA", "Label": "gen_epi_review.py", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD", "Parameters": {}, "Used": [ @@ -578,7 +578,7 @@ { "@id": "urn:genssrev-n8NqP2Tq", "Label": "gen_ss_review_scripts.py", - "AssociatedWith": "urn:urn:afni-OtBYYGL9", + "AssociatedWith": "urn:afni-OtBYYGL9", "Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0", "Parameters": { "-mot_limit": "0.3", diff --git a/examples/from_parsers/afni/afni_other_template_proc.png b/examples/from_parsers/afni/afni_other_template_proc.png index 494e35b4..260db6ad 100644 Binary files a/examples/from_parsers/afni/afni_other_template_proc.png and b/examples/from_parsers/afni/afni_other_template_proc.png differ diff --git a/examples/from_parsers/afni/afni_other_template_proc_block.jsonld b/examples/from_parsers/afni/afni_other_template_proc_block.jsonld index 54b37828..e50c0638 100644 --- a/examples/from_parsers/afni/afni_other_template_proc_block.jsonld +++ b/examples/from_parsers/afni/afni_other_template_proc_block.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:autobloc-NCfx652N", "Label": "auto block: setup", - "AssociatedWith": "urn:urn:afni-YYVukVUa", + "AssociatedWith": "urn:afni-YYVukVUa", "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_other_template/tone_counting_onset_times.txt ./afni_other_template/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy ./afni_other_template/sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ", "Used": [ "bids::afni_other_template/tone_counting_onset_times.txt", @@ -26,7 +26,7 @@ { "@id": "urn:autobloc-1lc3rowI", "Label": "auto block: tcat", - "AssociatedWith": "urn:urn:afni-YYVukVUa", + "AssociatedWith": "urn:afni-YYVukVUa", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_other_template/sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ", "Used": [ "bids::afni_other_template/sub-01_task-tonecounting_bold.nii.gz'[0..$]'" @@ -35,7 +35,7 @@ { "@id": "urn:autobloc-4CqOaPM0", "Label": "auto block: outcount", - "AssociatedWith": "urn:urn:afni-YYVukVUa", + "AssociatedWith": "urn:afni-YYVukVUa", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig", @@ -45,7 +45,7 @@ { "@id": "urn:tshift-iPalhda0", "Label": "tshift", - "AssociatedWith": "urn:urn:afni-YYVukVUa", + "AssociatedWith": "urn:afni-YYVukVUa", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig" @@ -54,7 +54,7 @@ { "@id": "urn:align-iJXWvura", "Label": "align", - "AssociatedWith": "urn:urn:afni-YYVukVUa", + "AssociatedWith": "urn:afni-YYVukVUa", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ", "Used": [ "bids::pb01.$subj.r01.tshift+orig", @@ -64,7 +64,7 @@ { "@id": "urn:tlrc-KjPkMBFn", "Label": "tlrc", - "AssociatedWith": "urn:urn:afni-YYVukVUa", + "AssociatedWith": "urn:afni-YYVukVUa", "Command": "@auto_tlrc -base TT_icbm452+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ", "Used": [ "bids::TT_icbm452+tlrc", @@ -75,7 +75,7 @@ { "@id": "urn:volreg-GdAJQq8f", "Label": "volreg", - "AssociatedWith": "urn:urn:afni-YYVukVUa", + "AssociatedWith": "urn:afni-YYVukVUa", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ", "Used": [ "bids::pb01.$subj.r$run.tshift+orig", @@ -98,7 +98,7 @@ { "@id": "urn:blur-s3bO7HKu", "Label": "blur", - "AssociatedWith": "urn:urn:afni-YYVukVUa", + "AssociatedWith": "urn:afni-YYVukVUa", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ", "Used": [ "bids::pb02.$subj.r$run.volreg+tlrc", @@ -108,7 +108,7 @@ { "@id": "urn:mask-j7YojExy", "Label": "mask", - "AssociatedWith": "urn:urn:afni-YYVukVUa", + "AssociatedWith": "urn:afni-YYVukVUa", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_icbm452+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -127,7 +127,7 @@ { "@id": "urn:scale-Tm1YtRxv", "Label": "scale", - "AssociatedWith": "urn:urn:afni-YYVukVUa", + "AssociatedWith": "urn:afni-YYVukVUa", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -139,7 +139,7 @@ { "@id": "urn:regress-fsFkOQmi", "Label": "regress", - "AssociatedWith": "urn:urn:afni-YYVukVUa", + "AssociatedWith": "urn:afni-YYVukVUa", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ", "Used": [ "bids::dfile_rall.1D", @@ -166,7 +166,7 @@ { "@id": "urn:bluresti-a9WkYy7D", "Label": "blur estimation", - "AssociatedWith": "urn:urn:afni-YYVukVUa", + "AssociatedWith": "urn:afni-YYVukVUa", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ", "Used": [ "bids::full_mask.$subj+tlrc", @@ -177,7 +177,7 @@ { "@id": "urn:autobloc-iR03faH6", "Label": "auto block: generate review scripts", - "AssociatedWith": "urn:urn:afni-YYVukVUa", + "AssociatedWith": "urn:afni-YYVukVUa", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ", "Used": [ "bids::pb00.$subj.r*.tcat+orig.HEAD" diff --git a/examples/from_parsers/afni/afni_other_template_proc_block.png b/examples/from_parsers/afni/afni_other_template_proc_block.png index deed1e5c..a34fc0dc 100644 Binary files a/examples/from_parsers/afni/afni_other_template_proc_block.png and b/examples/from_parsers/afni/afni_other_template_proc_block.png differ diff --git a/examples/from_parsers/afni/afni_thr_clustfwep05_proc.jsonld b/examples/from_parsers/afni/afni_thr_clustfwep05_proc.jsonld index 8dd89933..9d756931 100644 --- a/examples/from_parsers/afni/afni_thr_clustfwep05_proc.jsonld +++ b/examples/from_parsers/afni/afni_thr_clustfwep05_proc.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:makedire-FbjuNWop", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "mkdir $output_dir", "Parameters": {}, "Used": [] @@ -23,7 +23,7 @@ { "@id": "urn:makedire-zEcKY7Zg", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "mkdir $output_dir/stimuli", "Parameters": {}, "Used": [] @@ -31,7 +31,7 @@ { "@id": "urn:cp-tfse5Zds", "Label": "cp", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "cp ./afni_clusterwise_fwe/tone_counting_onset_times.txt ./afni_clusterwise_fwe/tone_counting_probe_duration.txt $output_dir/stimuli", "Parameters": {}, "Used": [ @@ -42,7 +42,7 @@ { "@id": "urn:3dcopy-eaJ6SNxb", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w", "Parameters": {}, "Used": [ @@ -52,7 +52,7 @@ { "@id": "urn:3dtcat-FiDxPQrL", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'", "Parameters": {}, "Used": [ @@ -62,7 +62,7 @@ { "@id": "urn:3dtoutco-4UtqD6kx", "Label": "3dToutcount", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D", "Parameters": {}, "Used": [ @@ -72,7 +72,7 @@ { "@id": "urn:cat-ZhJDXyQD", "Label": "cat", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "cat outcount.r*.1D > outcount_rall.1D", "Parameters": {}, "Used": [ @@ -82,7 +82,7 @@ { "@id": "urn:3dtshift-nIE1uBeo", "Label": "3dTshift", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig", "Parameters": {}, "Used": [ @@ -92,7 +92,7 @@ { "@id": "urn:alignepi-MMhnKpbM", "Label": "align_epi_anat.py", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off", "Parameters": {}, "Used": [ @@ -103,7 +103,7 @@ { "@id": "urn:autotlrc-mKudz3sg", "Label": "@auto_tlrc", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss", "Parameters": {}, "Used": [ @@ -114,7 +114,7 @@ { "@id": "urn:catmatve-sPOMH5oj", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D", "Parameters": {}, "Used": [ @@ -124,7 +124,7 @@ { "@id": "urn:3dvolreg-jfUxbOBp", "Label": "3dvolreg", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig", "Parameters": {}, "Used": [ @@ -134,7 +134,7 @@ { "@id": "urn:3dcalc-AcOCVbkr", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1", "Parameters": {}, "Used": [ @@ -144,7 +144,7 @@ { "@id": "urn:catmatve-X27tWZ8o", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D", "Parameters": {}, "Used": [ @@ -154,7 +154,7 @@ { "@id": "urn:3dalline-qZCRq4GK", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run", "Parameters": {}, "Used": [ @@ -166,7 +166,7 @@ { "@id": "urn:3dalline-L1ZeQ8Oe", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run", "Parameters": {}, "Used": [ @@ -178,7 +178,7 @@ { "@id": "urn:3dtstat-ibSidOtG", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc", "Parameters": {}, "Used": [ @@ -188,7 +188,7 @@ { "@id": "urn:cat-qgu5dC3S", "Label": "cat", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "cat dfile.r*.1D > dfile_rall.1D", "Parameters": {}, "Used": [ @@ -198,7 +198,7 @@ { "@id": "urn:3dcopy-lIVz7ZE9", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents", "Parameters": {}, "Used": [ @@ -208,7 +208,7 @@ { "@id": "urn:3dcalc-zltI9Eku", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg", "Parameters": {}, "Used": [ @@ -219,7 +219,7 @@ { "@id": "urn:3dcopy-JHnQ1OV4", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj", "Parameters": {}, "Used": [ @@ -229,7 +229,7 @@ { "@id": "urn:3dalline-mIklOZRC", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped", "Parameters": {}, "Used": [ @@ -240,7 +240,7 @@ { "@id": "urn:3dmerge-t6gYVDK8", "Label": "3dmerge", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc", "Parameters": {}, "Used": [ @@ -251,7 +251,7 @@ { "@id": "urn:3dautoma-Ix0vEWru", "Label": "3dAutomask", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -261,7 +261,7 @@ { "@id": "urn:3dmaskto-nMSxv6HR", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj", "Parameters": {}, "Used": [] @@ -269,7 +269,7 @@ { "@id": "urn:3dresamp-oQ0wyYBD", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat", "Parameters": {}, "Used": [ @@ -280,7 +280,7 @@ { "@id": "urn:3dmaskto-fTiVoRLQ", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj", "Parameters": {}, "Used": [ @@ -290,7 +290,7 @@ { "@id": "urn:3dabover-i33bsMQT", "Label": "3dABoverlap", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt", "Parameters": {}, "Used": [ @@ -301,7 +301,7 @@ { "@id": "urn:3ddot-X0Yb6q0Q", "Label": "3ddot", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt", "Parameters": {}, "Used": [ @@ -312,7 +312,7 @@ { "@id": "urn:3dresamp-wHMlxr6g", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc", "Parameters": {}, "Used": [ @@ -323,7 +323,7 @@ { "@id": "urn:3dmaskto-VdtzEJFq", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group", "Parameters": {}, "Used": [ @@ -333,7 +333,7 @@ { "@id": "urn:3dtstat-N8h8WI8V", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -343,7 +343,7 @@ { "@id": "urn:3dcalc-awdhVElk", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale", "Parameters": {}, "Used": [ @@ -355,7 +355,7 @@ { "@id": "urn:1dtoolpy-fGZjwTxy", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D", "Parameters": {}, "Used": [ @@ -365,7 +365,7 @@ { "@id": "urn:1dtoolpy-CyMrv5Xy", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D", "Parameters": {}, "Used": [ @@ -375,7 +375,7 @@ { "@id": "urn:1dtoolpy-MUeVb72K", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}", "Parameters": {}, "Used": [ @@ -385,7 +385,7 @@ { "@id": "urn:3ddeconv-LAzXsF8t", "Label": "3dDeconvolve", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj", "Parameters": {}, "Used": [ @@ -395,7 +395,7 @@ { "@id": "urn:1dtoolpy-AhNNeewD", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt", "Parameters": {}, "Used": [ @@ -405,7 +405,7 @@ { "@id": "urn:3dtcat-1dvxRp0t", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD", "Parameters": {}, "Used": [ @@ -415,7 +415,7 @@ { "@id": "urn:3dtstat-29NCbF5Q", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -425,7 +425,7 @@ { "@id": "urn:3dtstat-p1OOFx5l", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -435,7 +435,7 @@ { "@id": "urn:3dcalc-vxkvWYQt", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj", "Parameters": {}, "Used": [ @@ -447,7 +447,7 @@ { "@id": "urn:3dtnorm-plidluuV", "Label": "3dTnorm", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc", "Parameters": {}, "Used": [ @@ -457,7 +457,7 @@ { "@id": "urn:3dmaskav-dCMQaRZ0", "Label": "3dmaskave", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D", "Parameters": {}, "Used": [ @@ -467,7 +467,7 @@ { "@id": "urn:3dtstat-zRHxYgiC", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D", "Parameters": {}, "Used": [ @@ -477,7 +477,7 @@ { "@id": "urn:3dcalc-yAknuXpJ", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP", "Parameters": {}, "Used": [ @@ -488,7 +488,7 @@ { "@id": "urn:3dtstat-6wWrCL7Q", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc", "Parameters": {}, "Used": [ @@ -498,7 +498,7 @@ { "@id": "urn:1dcat-l087IEw3", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D", "Parameters": {}, "Used": [ @@ -508,7 +508,7 @@ { "@id": "urn:1dcat-LyoM8qes", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D", "Parameters": {}, "Used": [ @@ -518,7 +518,7 @@ { "@id": "urn:3dtstat-zaJyNlVp", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"", "Parameters": {}, "Used": [ @@ -528,7 +528,7 @@ { "@id": "urn:1dcat-xgxysZLI", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D", "Parameters": {}, "Used": [ @@ -538,7 +538,7 @@ { "@id": "urn:3dfwhmx-6mRpHZer", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D", "Parameters": {}, "Used": [ @@ -548,7 +548,7 @@ { "@id": "urn:3dfwhmx-j8xguQBu", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D", "Parameters": {}, "Used": [ @@ -558,7 +558,7 @@ { "@id": "urn:3dclusts-H3H37Ejv", "Label": "3dClustSim", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim", "Parameters": {}, "Used": [ @@ -568,7 +568,7 @@ { "@id": "urn:genepire-AENVIknc", "Label": "gen_epi_review.py", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD", "Parameters": {}, "Used": [ @@ -578,7 +578,7 @@ { "@id": "urn:genssrev-OSEn5lXu", "Label": "gen_ss_review_scripts.py", - "AssociatedWith": "urn:urn:afni-mcH6dZNr", + "AssociatedWith": "urn:afni-mcH6dZNr", "Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0", "Parameters": { "-mot_limit": "0.3", diff --git a/examples/from_parsers/afni/afni_thr_clustfwep05_proc.png b/examples/from_parsers/afni/afni_thr_clustfwep05_proc.png index 081ce957..ebb01e8f 100644 Binary files a/examples/from_parsers/afni/afni_thr_clustfwep05_proc.png and b/examples/from_parsers/afni/afni_thr_clustfwep05_proc.png differ diff --git a/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.jsonld b/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.jsonld index f5618d35..3e410278 100644 --- a/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.jsonld +++ b/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:autobloc-O2EAcJPK", "Label": "auto block: setup", - "AssociatedWith": "urn:urn:afni-XB2LYpvU", + "AssociatedWith": "urn:afni-XB2LYpvU", "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_clusterwise_fwe/tone_counting_onset_times.txt ./afni_clusterwise_fwe/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ", "Used": [ "bids::afni_clusterwise_fwe/tone_counting_onset_times.txt", @@ -26,7 +26,7 @@ { "@id": "urn:autobloc-K8cP1HXJ", "Label": "auto block: tcat", - "AssociatedWith": "urn:urn:afni-XB2LYpvU", + "AssociatedWith": "urn:afni-XB2LYpvU", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ", "Used": [ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'" @@ -35,7 +35,7 @@ { "@id": "urn:autobloc-A9ob1Zdf", "Label": "auto block: outcount", - "AssociatedWith": "urn:urn:afni-XB2LYpvU", + "AssociatedWith": "urn:afni-XB2LYpvU", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig", @@ -45,7 +45,7 @@ { "@id": "urn:tshift-os3rZrwr", "Label": "tshift", - "AssociatedWith": "urn:urn:afni-XB2LYpvU", + "AssociatedWith": "urn:afni-XB2LYpvU", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig" @@ -54,7 +54,7 @@ { "@id": "urn:align-YJumoEmQ", "Label": "align", - "AssociatedWith": "urn:urn:afni-XB2LYpvU", + "AssociatedWith": "urn:afni-XB2LYpvU", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ", "Used": [ "bids::pb01.$subj.r01.tshift+orig", @@ -64,7 +64,7 @@ { "@id": "urn:tlrc-XYGehrKJ", "Label": "tlrc", - "AssociatedWith": "urn:urn:afni-XB2LYpvU", + "AssociatedWith": "urn:afni-XB2LYpvU", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ", "Used": [ "bids::TT_N27+tlrc", @@ -75,7 +75,7 @@ { "@id": "urn:volreg-byFDcmEp", "Label": "volreg", - "AssociatedWith": "urn:urn:afni-XB2LYpvU", + "AssociatedWith": "urn:afni-XB2LYpvU", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ", "Used": [ "bids::pb01.$subj.r$run.tshift+orig", @@ -98,7 +98,7 @@ { "@id": "urn:blur-8RPMY4qi", "Label": "blur", - "AssociatedWith": "urn:urn:afni-XB2LYpvU", + "AssociatedWith": "urn:afni-XB2LYpvU", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ", "Used": [ "bids::pb02.$subj.r$run.volreg+tlrc", @@ -108,7 +108,7 @@ { "@id": "urn:mask-RISCfneZ", "Label": "mask", - "AssociatedWith": "urn:urn:afni-XB2LYpvU", + "AssociatedWith": "urn:afni-XB2LYpvU", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -127,7 +127,7 @@ { "@id": "urn:scale-TtlMGQiE", "Label": "scale", - "AssociatedWith": "urn:urn:afni-XB2LYpvU", + "AssociatedWith": "urn:afni-XB2LYpvU", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -139,7 +139,7 @@ { "@id": "urn:regress-SE5Q0bej", "Label": "regress", - "AssociatedWith": "urn:urn:afni-XB2LYpvU", + "AssociatedWith": "urn:afni-XB2LYpvU", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ", "Used": [ "bids::dfile_rall.1D", @@ -166,7 +166,7 @@ { "@id": "urn:bluresti-LQzLcXWZ", "Label": "blur estimation", - "AssociatedWith": "urn:urn:afni-XB2LYpvU", + "AssociatedWith": "urn:afni-XB2LYpvU", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ", "Used": [ "bids::full_mask.$subj+tlrc", @@ -177,7 +177,7 @@ { "@id": "urn:autobloc-Wk5QBdUZ", "Label": "auto block: generate review scripts", - "AssociatedWith": "urn:urn:afni-XB2LYpvU", + "AssociatedWith": "urn:afni-XB2LYpvU", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ", "Used": [ "bids::pb00.$subj.r*.tcat+orig.HEAD" diff --git a/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.png b/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.png index 62bc6a06..6db69fc9 100644 Binary files a/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.png and b/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.png differ diff --git a/examples/from_parsers/afni/afni_thr_clustunck10_proc.jsonld b/examples/from_parsers/afni/afni_thr_clustunck10_proc.jsonld index 0cf46301..5cee2746 100644 --- a/examples/from_parsers/afni/afni_thr_clustunck10_proc.jsonld +++ b/examples/from_parsers/afni/afni_thr_clustunck10_proc.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:makedire-OY6SE0Gy", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "mkdir $output_dir", "Parameters": {}, "Used": [] @@ -23,7 +23,7 @@ { "@id": "urn:makedire-VjI1qbRf", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "mkdir $output_dir/stimuli", "Parameters": {}, "Used": [] @@ -31,7 +31,7 @@ { "@id": "urn:cp-JaVdQoMW", "Label": "cp", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "cp ./afni_cluster_k10/tone_counting_onset_times.txt ./afni_cluster_k10/tone_counting_probe_duration.txt $output_dir/stimuli", "Parameters": {}, "Used": [ @@ -42,7 +42,7 @@ { "@id": "urn:3dcopy-xF0uDGm7", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w", "Parameters": {}, "Used": [ @@ -52,7 +52,7 @@ { "@id": "urn:3dtcat-xQIY5D9z", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'", "Parameters": {}, "Used": [ @@ -62,7 +62,7 @@ { "@id": "urn:3dtoutco-3pmrFtyf", "Label": "3dToutcount", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D", "Parameters": {}, "Used": [ @@ -72,7 +72,7 @@ { "@id": "urn:cat-SMezXh8B", "Label": "cat", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "cat outcount.r*.1D > outcount_rall.1D", "Parameters": {}, "Used": [ @@ -82,7 +82,7 @@ { "@id": "urn:3dtshift-iXx5fsUq", "Label": "3dTshift", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig", "Parameters": {}, "Used": [ @@ -92,7 +92,7 @@ { "@id": "urn:alignepi-b6S1htVH", "Label": "align_epi_anat.py", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off", "Parameters": {}, "Used": [ @@ -103,7 +103,7 @@ { "@id": "urn:autotlrc-A74FNMle", "Label": "@auto_tlrc", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss", "Parameters": {}, "Used": [ @@ -114,7 +114,7 @@ { "@id": "urn:catmatve-GL1r7ATk", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D", "Parameters": {}, "Used": [ @@ -124,7 +124,7 @@ { "@id": "urn:3dvolreg-NBrMfK1y", "Label": "3dvolreg", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig", "Parameters": {}, "Used": [ @@ -134,7 +134,7 @@ { "@id": "urn:3dcalc-bycui7e4", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1", "Parameters": {}, "Used": [ @@ -144,7 +144,7 @@ { "@id": "urn:catmatve-bmNwpYtV", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D", "Parameters": {}, "Used": [ @@ -154,7 +154,7 @@ { "@id": "urn:3dalline-1xNOZt2X", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run", "Parameters": {}, "Used": [ @@ -166,7 +166,7 @@ { "@id": "urn:3dalline-lTu4iPLW", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run", "Parameters": {}, "Used": [ @@ -178,7 +178,7 @@ { "@id": "urn:3dtstat-zffgHJ5p", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc", "Parameters": {}, "Used": [ @@ -188,7 +188,7 @@ { "@id": "urn:cat-e3C1aNZg", "Label": "cat", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "cat dfile.r*.1D > dfile_rall.1D", "Parameters": {}, "Used": [ @@ -198,7 +198,7 @@ { "@id": "urn:3dcopy-vvTaRlWw", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents", "Parameters": {}, "Used": [ @@ -208,7 +208,7 @@ { "@id": "urn:3dcalc-uVIWlPiD", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg", "Parameters": {}, "Used": [ @@ -219,7 +219,7 @@ { "@id": "urn:3dcopy-Dzjz2HnL", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj", "Parameters": {}, "Used": [ @@ -229,7 +229,7 @@ { "@id": "urn:3dalline-k1TXBknG", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped", "Parameters": {}, "Used": [ @@ -240,7 +240,7 @@ { "@id": "urn:3dmerge-NNfu6hxa", "Label": "3dmerge", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc", "Parameters": {}, "Used": [ @@ -251,7 +251,7 @@ { "@id": "urn:3dautoma-Dlp8THpI", "Label": "3dAutomask", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -261,7 +261,7 @@ { "@id": "urn:3dmaskto-IeXPRJi8", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj", "Parameters": {}, "Used": [] @@ -269,7 +269,7 @@ { "@id": "urn:3dresamp-24JIQmw1", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat", "Parameters": {}, "Used": [ @@ -280,7 +280,7 @@ { "@id": "urn:3dmaskto-QPPysgL0", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj", "Parameters": {}, "Used": [ @@ -290,7 +290,7 @@ { "@id": "urn:3dabover-4tTtcN3O", "Label": "3dABoverlap", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt", "Parameters": {}, "Used": [ @@ -301,7 +301,7 @@ { "@id": "urn:3ddot-U2YcbixB", "Label": "3ddot", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt", "Parameters": {}, "Used": [ @@ -312,7 +312,7 @@ { "@id": "urn:3dresamp-uVnI1DWZ", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc", "Parameters": {}, "Used": [ @@ -323,7 +323,7 @@ { "@id": "urn:3dmaskto-xd2PfRzE", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group", "Parameters": {}, "Used": [ @@ -333,7 +333,7 @@ { "@id": "urn:3dtstat-17thIIuc", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -343,7 +343,7 @@ { "@id": "urn:3dcalc-zTQ3B910", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale", "Parameters": {}, "Used": [ @@ -355,7 +355,7 @@ { "@id": "urn:1dtoolpy-J7rvb59O", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D", "Parameters": {}, "Used": [ @@ -365,7 +365,7 @@ { "@id": "urn:1dtoolpy-povM5av3", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D", "Parameters": {}, "Used": [ @@ -375,7 +375,7 @@ { "@id": "urn:1dtoolpy-ssHLOGUR", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}", "Parameters": {}, "Used": [ @@ -385,7 +385,7 @@ { "@id": "urn:3ddeconv-fML2IpFp", "Label": "3dDeconvolve", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj", "Parameters": {}, "Used": [ @@ -395,7 +395,7 @@ { "@id": "urn:1dtoolpy-eMfyeIYj", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt", "Parameters": {}, "Used": [ @@ -405,7 +405,7 @@ { "@id": "urn:3dtcat-DQwVr0Uo", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD", "Parameters": {}, "Used": [ @@ -415,7 +415,7 @@ { "@id": "urn:3dtstat-uDZRncVM", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -425,7 +425,7 @@ { "@id": "urn:3dtstat-r7lNHPYE", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -435,7 +435,7 @@ { "@id": "urn:3dcalc-Y84nz2OI", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj", "Parameters": {}, "Used": [ @@ -447,7 +447,7 @@ { "@id": "urn:3dtnorm-N3ej7CkG", "Label": "3dTnorm", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc", "Parameters": {}, "Used": [ @@ -457,7 +457,7 @@ { "@id": "urn:3dmaskav-TMgsSY8d", "Label": "3dmaskave", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D", "Parameters": {}, "Used": [ @@ -467,7 +467,7 @@ { "@id": "urn:3dtstat-r4WfRcQO", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D", "Parameters": {}, "Used": [ @@ -477,7 +477,7 @@ { "@id": "urn:3dcalc-Diz78Vi7", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP", "Parameters": {}, "Used": [ @@ -488,7 +488,7 @@ { "@id": "urn:3dtstat-YBxYvXSr", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc", "Parameters": {}, "Used": [ @@ -498,7 +498,7 @@ { "@id": "urn:1dcat-mKOV8OBk", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D", "Parameters": {}, "Used": [ @@ -508,7 +508,7 @@ { "@id": "urn:1dcat-ik7pWJJu", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D", "Parameters": {}, "Used": [ @@ -518,7 +518,7 @@ { "@id": "urn:3dtstat-KMyBshB8", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"", "Parameters": {}, "Used": [ @@ -528,7 +528,7 @@ { "@id": "urn:1dcat-BYaIlWxZ", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D", "Parameters": {}, "Used": [ @@ -538,7 +538,7 @@ { "@id": "urn:3dfwhmx-Ud3U0uO1", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D", "Parameters": {}, "Used": [ @@ -548,7 +548,7 @@ { "@id": "urn:3dfwhmx-5rR4o8zi", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D", "Parameters": {}, "Used": [ @@ -558,7 +558,7 @@ { "@id": "urn:3dclusts-yn5oKahn", "Label": "3dClustSim", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim", "Parameters": {}, "Used": [ @@ -568,7 +568,7 @@ { "@id": "urn:genepire-EZvDz1cD", "Label": "gen_epi_review.py", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD", "Parameters": {}, "Used": [ @@ -578,7 +578,7 @@ { "@id": "urn:genssrev-F0b9dXGV", "Label": "gen_ss_review_scripts.py", - "AssociatedWith": "urn:urn:afni-hJIahMsr", + "AssociatedWith": "urn:afni-hJIahMsr", "Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0", "Parameters": { "-mot_limit": "0.3", diff --git a/examples/from_parsers/afni/afni_thr_clustunck10_proc.png b/examples/from_parsers/afni/afni_thr_clustunck10_proc.png index 0015793f..0655e98b 100644 Binary files a/examples/from_parsers/afni/afni_thr_clustunck10_proc.png and b/examples/from_parsers/afni/afni_thr_clustunck10_proc.png differ diff --git a/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.jsonld b/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.jsonld index ce5cad2f..381f84f6 100644 --- a/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.jsonld +++ b/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:autobloc-LgDQ5Cau", "Label": "auto block: setup", - "AssociatedWith": "urn:urn:afni-Ie70nH53", + "AssociatedWith": "urn:afni-Ie70nH53", "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_cluster_k10/tone_counting_onset_times.txt ./afni_cluster_k10/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ", "Used": [ "bids::afni_cluster_k10/tone_counting_onset_times.txt", @@ -26,7 +26,7 @@ { "@id": "urn:autobloc-gGJDCSg9", "Label": "auto block: tcat", - "AssociatedWith": "urn:urn:afni-Ie70nH53", + "AssociatedWith": "urn:afni-Ie70nH53", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ", "Used": [ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'" @@ -35,7 +35,7 @@ { "@id": "urn:autobloc-BxTtH4fF", "Label": "auto block: outcount", - "AssociatedWith": "urn:urn:afni-Ie70nH53", + "AssociatedWith": "urn:afni-Ie70nH53", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig", @@ -45,7 +45,7 @@ { "@id": "urn:tshift-XMM25khJ", "Label": "tshift", - "AssociatedWith": "urn:urn:afni-Ie70nH53", + "AssociatedWith": "urn:afni-Ie70nH53", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig" @@ -54,7 +54,7 @@ { "@id": "urn:align-bsB9poRV", "Label": "align", - "AssociatedWith": "urn:urn:afni-Ie70nH53", + "AssociatedWith": "urn:afni-Ie70nH53", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ", "Used": [ "bids::pb01.$subj.r01.tshift+orig", @@ -64,7 +64,7 @@ { "@id": "urn:tlrc-J1B4oPWF", "Label": "tlrc", - "AssociatedWith": "urn:urn:afni-Ie70nH53", + "AssociatedWith": "urn:afni-Ie70nH53", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ", "Used": [ "bids::TT_N27+tlrc", @@ -75,7 +75,7 @@ { "@id": "urn:volreg-QASdhVdj", "Label": "volreg", - "AssociatedWith": "urn:urn:afni-Ie70nH53", + "AssociatedWith": "urn:afni-Ie70nH53", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ", "Used": [ "bids::pb01.$subj.r$run.tshift+orig", @@ -98,7 +98,7 @@ { "@id": "urn:blur-Ij61bOyL", "Label": "blur", - "AssociatedWith": "urn:urn:afni-Ie70nH53", + "AssociatedWith": "urn:afni-Ie70nH53", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ", "Used": [ "bids::pb02.$subj.r$run.volreg+tlrc", @@ -108,7 +108,7 @@ { "@id": "urn:mask-d0J0X9W5", "Label": "mask", - "AssociatedWith": "urn:urn:afni-Ie70nH53", + "AssociatedWith": "urn:afni-Ie70nH53", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -127,7 +127,7 @@ { "@id": "urn:scale-tqb4fi1p", "Label": "scale", - "AssociatedWith": "urn:urn:afni-Ie70nH53", + "AssociatedWith": "urn:afni-Ie70nH53", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -139,7 +139,7 @@ { "@id": "urn:regress-QBMi7uo8", "Label": "regress", - "AssociatedWith": "urn:urn:afni-Ie70nH53", + "AssociatedWith": "urn:afni-Ie70nH53", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ", "Used": [ "bids::dfile_rall.1D", @@ -166,7 +166,7 @@ { "@id": "urn:bluresti-a7rUmMml", "Label": "blur estimation", - "AssociatedWith": "urn:urn:afni-Ie70nH53", + "AssociatedWith": "urn:afni-Ie70nH53", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ", "Used": [ "bids::full_mask.$subj+tlrc", @@ -177,7 +177,7 @@ { "@id": "urn:autobloc-olTmkcM4", "Label": "auto block: generate review scripts", - "AssociatedWith": "urn:urn:afni-Ie70nH53", + "AssociatedWith": "urn:afni-Ie70nH53", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ", "Used": [ "bids::pb00.$subj.r*.tcat+orig.HEAD" diff --git a/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.png b/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.png index 9bba86e8..cdcf2806 100644 Binary files a/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.png and b/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.png differ diff --git a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.jsonld b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.jsonld index 6c4c6aa0..0197e4aa 100644 --- a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.jsonld +++ b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:makedire-xHouasWb", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "mkdir $output_dir", "Parameters": {}, "Used": [] @@ -23,7 +23,7 @@ { "@id": "urn:makedire-ikqUgOGP", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "mkdir $output_dir/stimuli", "Parameters": {}, "Used": [] @@ -31,7 +31,7 @@ { "@id": "urn:cp-6qkwf0q0", "Label": "cp", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "cp ./afni_voxelwise_fdr_p005/tone_counting_onset_times.txt ./afni_voxelwise_fdr_p005/tone_counting_probe_duration.txt $output_dir/stimuli", "Parameters": {}, "Used": [ @@ -42,7 +42,7 @@ { "@id": "urn:3dcopy-8N2iEpYo", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w", "Parameters": {}, "Used": [ @@ -52,7 +52,7 @@ { "@id": "urn:3dtcat-zECB7UZU", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'", "Parameters": {}, "Used": [ @@ -62,7 +62,7 @@ { "@id": "urn:3dtoutco-zhAFS3NH", "Label": "3dToutcount", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D", "Parameters": {}, "Used": [ @@ -72,7 +72,7 @@ { "@id": "urn:cat-pNK8q7O6", "Label": "cat", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "cat outcount.r*.1D > outcount_rall.1D", "Parameters": {}, "Used": [ @@ -82,7 +82,7 @@ { "@id": "urn:3dtshift-CbynrLCD", "Label": "3dTshift", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig", "Parameters": {}, "Used": [ @@ -92,7 +92,7 @@ { "@id": "urn:alignepi-NMFGrarO", "Label": "align_epi_anat.py", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off", "Parameters": {}, "Used": [ @@ -103,7 +103,7 @@ { "@id": "urn:autotlrc-TSlycvih", "Label": "@auto_tlrc", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss", "Parameters": {}, "Used": [ @@ -114,7 +114,7 @@ { "@id": "urn:catmatve-HCS5IUyZ", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D", "Parameters": {}, "Used": [ @@ -124,7 +124,7 @@ { "@id": "urn:3dvolreg-vv7XX0yk", "Label": "3dvolreg", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig", "Parameters": {}, "Used": [ @@ -134,7 +134,7 @@ { "@id": "urn:3dcalc-Cxm5xD74", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1", "Parameters": {}, "Used": [ @@ -144,7 +144,7 @@ { "@id": "urn:catmatve-3uuUHbaW", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D", "Parameters": {}, "Used": [ @@ -154,7 +154,7 @@ { "@id": "urn:3dalline-jEXn2s4t", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run", "Parameters": {}, "Used": [ @@ -166,7 +166,7 @@ { "@id": "urn:3dalline-p9hWi9Rx", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run", "Parameters": {}, "Used": [ @@ -178,7 +178,7 @@ { "@id": "urn:3dtstat-42xTJb5v", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc", "Parameters": {}, "Used": [ @@ -188,7 +188,7 @@ { "@id": "urn:cat-QxDklpDH", "Label": "cat", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "cat dfile.r*.1D > dfile_rall.1D", "Parameters": {}, "Used": [ @@ -198,7 +198,7 @@ { "@id": "urn:3dcopy-YqLNlgfd", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents", "Parameters": {}, "Used": [ @@ -208,7 +208,7 @@ { "@id": "urn:3dcalc-nwnpdeD8", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg", "Parameters": {}, "Used": [ @@ -219,7 +219,7 @@ { "@id": "urn:3dcopy-sWazpmol", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj", "Parameters": {}, "Used": [ @@ -229,7 +229,7 @@ { "@id": "urn:3dalline-Gkr9wZce", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped", "Parameters": {}, "Used": [ @@ -240,7 +240,7 @@ { "@id": "urn:3dmerge-DuWTIduU", "Label": "3dmerge", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc", "Parameters": {}, "Used": [ @@ -251,7 +251,7 @@ { "@id": "urn:3dautoma-9uASZijc", "Label": "3dAutomask", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -261,7 +261,7 @@ { "@id": "urn:3dmaskto-sfwNoLLZ", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj", "Parameters": {}, "Used": [] @@ -269,7 +269,7 @@ { "@id": "urn:3dresamp-xA6d9Uf6", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat", "Parameters": {}, "Used": [ @@ -280,7 +280,7 @@ { "@id": "urn:3dmaskto-ZfejqHaM", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj", "Parameters": {}, "Used": [ @@ -290,7 +290,7 @@ { "@id": "urn:3dabover-vvyh4Nym", "Label": "3dABoverlap", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt", "Parameters": {}, "Used": [ @@ -301,7 +301,7 @@ { "@id": "urn:3ddot-Yg3gmlJA", "Label": "3ddot", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt", "Parameters": {}, "Used": [ @@ -312,7 +312,7 @@ { "@id": "urn:3dresamp-XCEnyeM1", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc", "Parameters": {}, "Used": [ @@ -323,7 +323,7 @@ { "@id": "urn:3dmaskto-MkN1j1sE", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group", "Parameters": {}, "Used": [ @@ -333,7 +333,7 @@ { "@id": "urn:3dtstat-44rAL5NV", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -343,7 +343,7 @@ { "@id": "urn:3dcalc-9DYdW41e", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale", "Parameters": {}, "Used": [ @@ -355,7 +355,7 @@ { "@id": "urn:1dtoolpy-3LqsoK7f", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D", "Parameters": {}, "Used": [ @@ -365,7 +365,7 @@ { "@id": "urn:1dtoolpy-EJ9CJXoE", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D", "Parameters": {}, "Used": [ @@ -375,7 +375,7 @@ { "@id": "urn:1dtoolpy-gqPPMiGB", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}", "Parameters": {}, "Used": [ @@ -385,7 +385,7 @@ { "@id": "urn:3ddeconv-zxISCpbR", "Label": "3dDeconvolve", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj", "Parameters": {}, "Used": [ @@ -395,7 +395,7 @@ { "@id": "urn:1dtoolpy-VMxL9qLW", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt", "Parameters": {}, "Used": [ @@ -405,7 +405,7 @@ { "@id": "urn:3dtcat-bXpUL2kv", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD", "Parameters": {}, "Used": [ @@ -415,7 +415,7 @@ { "@id": "urn:3dtstat-IKAKcmGw", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -425,7 +425,7 @@ { "@id": "urn:3dtstat-GTXQ0NaI", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -435,7 +435,7 @@ { "@id": "urn:3dcalc-5aWFRDAY", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj", "Parameters": {}, "Used": [ @@ -447,7 +447,7 @@ { "@id": "urn:3dtnorm-C8LjardN", "Label": "3dTnorm", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc", "Parameters": {}, "Used": [ @@ -457,7 +457,7 @@ { "@id": "urn:3dmaskav-PGPxFIWj", "Label": "3dmaskave", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D", "Parameters": {}, "Used": [ @@ -467,7 +467,7 @@ { "@id": "urn:3dtstat-U3O8J2lt", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D", "Parameters": {}, "Used": [ @@ -477,7 +477,7 @@ { "@id": "urn:3dcalc-dnHEfxzV", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP", "Parameters": {}, "Used": [ @@ -488,7 +488,7 @@ { "@id": "urn:3dtstat-o7tC0mIS", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc", "Parameters": {}, "Used": [ @@ -498,7 +498,7 @@ { "@id": "urn:1dcat-vWKWYGl9", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D", "Parameters": {}, "Used": [ @@ -508,7 +508,7 @@ { "@id": "urn:1dcat-LuD2LyAl", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D", "Parameters": {}, "Used": [ @@ -518,7 +518,7 @@ { "@id": "urn:3dtstat-dbJoftKk", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"", "Parameters": {}, "Used": [ @@ -528,7 +528,7 @@ { "@id": "urn:1dcat-JsZglSmL", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D", "Parameters": {}, "Used": [ @@ -538,7 +538,7 @@ { "@id": "urn:3dfwhmx-GscTV8E7", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D", "Parameters": {}, "Used": [ @@ -548,7 +548,7 @@ { "@id": "urn:3dfwhmx-tozyQ3za", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D", "Parameters": {}, "Used": [ @@ -558,7 +558,7 @@ { "@id": "urn:3dclusts-pDD8OMkd", "Label": "3dClustSim", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim", "Parameters": {}, "Used": [ @@ -568,7 +568,7 @@ { "@id": "urn:genepire-JofLi2Iv", "Label": "gen_epi_review.py", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD", "Parameters": {}, "Used": [ @@ -578,7 +578,7 @@ { "@id": "urn:genssrev-6zZrgJp6", "Label": "gen_ss_review_scripts.py", - "AssociatedWith": "urn:urn:afni-tLT3AXf7", + "AssociatedWith": "urn:afni-tLT3AXf7", "Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0", "Parameters": { "-mot_limit": "0.3", diff --git a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.png b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.png index b777126c..64037be1 100644 Binary files a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.png and b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.png differ diff --git a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.jsonld b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.jsonld index 7545b0f9..9d6700ce 100644 --- a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.jsonld +++ b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:autobloc-Lb7mU4cg", "Label": "auto block: setup", - "AssociatedWith": "urn:urn:afni-bx6q4Oas", + "AssociatedWith": "urn:afni-bx6q4Oas", "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_voxelwise_fdr_p005/tone_counting_onset_times.txt ./afni_voxelwise_fdr_p005/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ", "Used": [ "bids::afni_voxelwise_fdr_p005/tone_counting_onset_times.txt", @@ -26,7 +26,7 @@ { "@id": "urn:autobloc-rUFvnhtZ", "Label": "auto block: tcat", - "AssociatedWith": "urn:urn:afni-bx6q4Oas", + "AssociatedWith": "urn:afni-bx6q4Oas", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ", "Used": [ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'" @@ -35,7 +35,7 @@ { "@id": "urn:autobloc-MMJBhghb", "Label": "auto block: outcount", - "AssociatedWith": "urn:urn:afni-bx6q4Oas", + "AssociatedWith": "urn:afni-bx6q4Oas", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig", @@ -45,7 +45,7 @@ { "@id": "urn:tshift-9jkHUP80", "Label": "tshift", - "AssociatedWith": "urn:urn:afni-bx6q4Oas", + "AssociatedWith": "urn:afni-bx6q4Oas", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig" @@ -54,7 +54,7 @@ { "@id": "urn:align-j9wdpba6", "Label": "align", - "AssociatedWith": "urn:urn:afni-bx6q4Oas", + "AssociatedWith": "urn:afni-bx6q4Oas", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ", "Used": [ "bids::pb01.$subj.r01.tshift+orig", @@ -64,7 +64,7 @@ { "@id": "urn:tlrc-D1HWOqFx", "Label": "tlrc", - "AssociatedWith": "urn:urn:afni-bx6q4Oas", + "AssociatedWith": "urn:afni-bx6q4Oas", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ", "Used": [ "bids::TT_N27+tlrc", @@ -75,7 +75,7 @@ { "@id": "urn:volreg-z9mTiN6d", "Label": "volreg", - "AssociatedWith": "urn:urn:afni-bx6q4Oas", + "AssociatedWith": "urn:afni-bx6q4Oas", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ", "Used": [ "bids::pb01.$subj.r$run.tshift+orig", @@ -98,7 +98,7 @@ { "@id": "urn:blur-ZFrDByJZ", "Label": "blur", - "AssociatedWith": "urn:urn:afni-bx6q4Oas", + "AssociatedWith": "urn:afni-bx6q4Oas", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ", "Used": [ "bids::pb02.$subj.r$run.volreg+tlrc", @@ -108,7 +108,7 @@ { "@id": "urn:mask-2jbzY0kR", "Label": "mask", - "AssociatedWith": "urn:urn:afni-bx6q4Oas", + "AssociatedWith": "urn:afni-bx6q4Oas", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -127,7 +127,7 @@ { "@id": "urn:scale-3YoozkFZ", "Label": "scale", - "AssociatedWith": "urn:urn:afni-bx6q4Oas", + "AssociatedWith": "urn:afni-bx6q4Oas", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -139,7 +139,7 @@ { "@id": "urn:regress-TUuT4CNb", "Label": "regress", - "AssociatedWith": "urn:urn:afni-bx6q4Oas", + "AssociatedWith": "urn:afni-bx6q4Oas", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ", "Used": [ "bids::dfile_rall.1D", @@ -166,7 +166,7 @@ { "@id": "urn:bluresti-0pPC1AJS", "Label": "blur estimation", - "AssociatedWith": "urn:urn:afni-bx6q4Oas", + "AssociatedWith": "urn:afni-bx6q4Oas", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ", "Used": [ "bids::full_mask.$subj+tlrc", @@ -177,7 +177,7 @@ { "@id": "urn:autobloc-3hupkewz", "Label": "auto block: generate review scripts", - "AssociatedWith": "urn:urn:afni-bx6q4Oas", + "AssociatedWith": "urn:afni-bx6q4Oas", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ", "Used": [ "bids::pb00.$subj.r*.tcat+orig.HEAD" diff --git a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.png b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.png index 64e326c9..6233fc35 100644 Binary files a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.png and b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.png differ diff --git a/examples/from_parsers/afni/afni_thr_voxelunct4_proc.jsonld b/examples/from_parsers/afni/afni_thr_voxelunct4_proc.jsonld index 038017c6..7a4e6d3f 100644 --- a/examples/from_parsers/afni/afni_thr_voxelunct4_proc.jsonld +++ b/examples/from_parsers/afni/afni_thr_voxelunct4_proc.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:makedire-iFdm4p5Y", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "mkdir $output_dir", "Parameters": {}, "Used": [] @@ -23,7 +23,7 @@ { "@id": "urn:makedire-7b1I4rvH", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "mkdir $output_dir/stimuli", "Parameters": {}, "Used": [] @@ -31,7 +31,7 @@ { "@id": "urn:cp-ca6PNsvH", "Label": "cp", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "cp ./afni_voxelwise_t4/tone_counting_onset_times.txt ./afni_voxelwise_t4/tone_counting_probe_duration.txt $output_dir/stimuli", "Parameters": {}, "Used": [ @@ -42,7 +42,7 @@ { "@id": "urn:3dcopy-9k58WpVo", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w", "Parameters": {}, "Used": [ @@ -52,7 +52,7 @@ { "@id": "urn:3dtcat-0ZxXYorR", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'", "Parameters": {}, "Used": [ @@ -62,7 +62,7 @@ { "@id": "urn:3dtoutco-ik1bRskW", "Label": "3dToutcount", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D", "Parameters": {}, "Used": [ @@ -72,7 +72,7 @@ { "@id": "urn:cat-pkAOeENL", "Label": "cat", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "cat outcount.r*.1D > outcount_rall.1D", "Parameters": {}, "Used": [ @@ -82,7 +82,7 @@ { "@id": "urn:3dtshift-1s3mZhmF", "Label": "3dTshift", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig", "Parameters": {}, "Used": [ @@ -92,7 +92,7 @@ { "@id": "urn:alignepi-dTIk7nk3", "Label": "align_epi_anat.py", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off", "Parameters": {}, "Used": [ @@ -103,7 +103,7 @@ { "@id": "urn:autotlrc-mvmK1Bz8", "Label": "@auto_tlrc", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss", "Parameters": {}, "Used": [ @@ -114,7 +114,7 @@ { "@id": "urn:catmatve-IJzNefhm", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D", "Parameters": {}, "Used": [ @@ -124,7 +124,7 @@ { "@id": "urn:3dvolreg-O6tLmVdq", "Label": "3dvolreg", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig", "Parameters": {}, "Used": [ @@ -134,7 +134,7 @@ { "@id": "urn:3dcalc-abvVqlYS", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1", "Parameters": {}, "Used": [ @@ -144,7 +144,7 @@ { "@id": "urn:catmatve-O5GbwUs0", "Label": "cat_matvec", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D", "Parameters": {}, "Used": [ @@ -154,7 +154,7 @@ { "@id": "urn:3dalline-D00HrQEK", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run", "Parameters": {}, "Used": [ @@ -166,7 +166,7 @@ { "@id": "urn:3dalline-MSx3Xfbr", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run", "Parameters": {}, "Used": [ @@ -178,7 +178,7 @@ { "@id": "urn:3dtstat-gdzMud8a", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc", "Parameters": {}, "Used": [ @@ -188,7 +188,7 @@ { "@id": "urn:cat-kWtH0mNC", "Label": "cat", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "cat dfile.r*.1D > dfile_rall.1D", "Parameters": {}, "Used": [ @@ -198,7 +198,7 @@ { "@id": "urn:3dcopy-IAV4FmmX", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents", "Parameters": {}, "Used": [ @@ -208,7 +208,7 @@ { "@id": "urn:3dcalc-gllFh2IY", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg", "Parameters": {}, "Used": [ @@ -219,7 +219,7 @@ { "@id": "urn:3dcopy-mWiPsmH7", "Label": "3dcopy", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj", "Parameters": {}, "Used": [ @@ -229,7 +229,7 @@ { "@id": "urn:3dalline-y5OXIUGU", "Label": "3dAllineate", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped", "Parameters": {}, "Used": [ @@ -240,7 +240,7 @@ { "@id": "urn:3dmerge-i0saPomM", "Label": "3dmerge", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc", "Parameters": {}, "Used": [ @@ -251,7 +251,7 @@ { "@id": "urn:3dautoma-QrU9lY5P", "Label": "3dAutomask", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -261,7 +261,7 @@ { "@id": "urn:3dmaskto-Aeh3ucUx", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj", "Parameters": {}, "Used": [] @@ -269,7 +269,7 @@ { "@id": "urn:3dresamp-SwGWI41p", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat", "Parameters": {}, "Used": [ @@ -280,7 +280,7 @@ { "@id": "urn:3dmaskto-mRybVZG4", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj", "Parameters": {}, "Used": [ @@ -290,7 +290,7 @@ { "@id": "urn:3dabover-lHAbRJGu", "Label": "3dABoverlap", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt", "Parameters": {}, "Used": [ @@ -301,7 +301,7 @@ { "@id": "urn:3ddot-FMfjPWlg", "Label": "3ddot", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt", "Parameters": {}, "Used": [ @@ -312,7 +312,7 @@ { "@id": "urn:3dresamp-8r8ElSpK", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc", "Parameters": {}, "Used": [ @@ -323,7 +323,7 @@ { "@id": "urn:3dmaskto-G8eA3DDQ", "Label": "3dmask_tool", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group", "Parameters": {}, "Used": [ @@ -333,7 +333,7 @@ { "@id": "urn:3dtstat-SCph0awI", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc", "Parameters": {}, "Used": [ @@ -343,7 +343,7 @@ { "@id": "urn:3dcalc-neUl0mA2", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale", "Parameters": {}, "Used": [ @@ -355,7 +355,7 @@ { "@id": "urn:1dtoolpy-L9OtMQxy", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D", "Parameters": {}, "Used": [ @@ -365,7 +365,7 @@ { "@id": "urn:1dtoolpy-VrRbA8c5", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D", "Parameters": {}, "Used": [ @@ -375,7 +375,7 @@ { "@id": "urn:1dtoolpy-AIN7Of4w", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}", "Parameters": {}, "Used": [ @@ -385,7 +385,7 @@ { "@id": "urn:3ddeconv-IjQMt3QN", "Label": "3dDeconvolve", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj", "Parameters": {}, "Used": [ @@ -395,7 +395,7 @@ { "@id": "urn:1dtoolpy-J0cOwMKf", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt", "Parameters": {}, "Used": [ @@ -405,7 +405,7 @@ { "@id": "urn:3dtcat-llsqdBCU", "Label": "3dTcat", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD", "Parameters": {}, "Used": [ @@ -415,7 +415,7 @@ { "@id": "urn:3dtstat-t3hTw7tN", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -425,7 +425,7 @@ { "@id": "urn:3dtstat-n6gcZwl0", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"", "Parameters": {}, "Used": [ @@ -435,7 +435,7 @@ { "@id": "urn:3dcalc-6uQ9g5pA", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj", "Parameters": {}, "Used": [ @@ -447,7 +447,7 @@ { "@id": "urn:3dtnorm-JskZiYfq", "Label": "3dTnorm", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc", "Parameters": {}, "Used": [ @@ -457,7 +457,7 @@ { "@id": "urn:3dmaskav-Y2YKe8wv", "Label": "3dmaskave", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D", "Parameters": {}, "Used": [ @@ -467,7 +467,7 @@ { "@id": "urn:3dtstat-0Gkaz1x2", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D", "Parameters": {}, "Used": [ @@ -477,7 +477,7 @@ { "@id": "urn:3dcalc-Uxphk1Ou", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP", "Parameters": {}, "Used": [ @@ -488,7 +488,7 @@ { "@id": "urn:3dtstat-Or9t5EsD", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc", "Parameters": {}, "Used": [ @@ -498,7 +498,7 @@ { "@id": "urn:1dcat-9pGZCsRu", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D", "Parameters": {}, "Used": [ @@ -508,7 +508,7 @@ { "@id": "urn:1dcat-Bh8sgUNo", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D", "Parameters": {}, "Used": [ @@ -518,7 +518,7 @@ { "@id": "urn:3dtstat-BDL1Mvqp", "Label": "3dTstat", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"", "Parameters": {}, "Used": [ @@ -528,7 +528,7 @@ { "@id": "urn:1dcat-1H6PkvZy", "Label": "1dcat", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D", "Parameters": {}, "Used": [ @@ -538,7 +538,7 @@ { "@id": "urn:3dfwhmx-0bHZEnGq", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D", "Parameters": {}, "Used": [ @@ -548,7 +548,7 @@ { "@id": "urn:3dfwhmx-aUiJXUtM", "Label": "3dFWHMx", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D", "Parameters": {}, "Used": [ @@ -558,7 +558,7 @@ { "@id": "urn:3dclusts-Zh1od73U", "Label": "3dClustSim", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim", "Parameters": {}, "Used": [ @@ -568,7 +568,7 @@ { "@id": "urn:genepire-pYUpG6e9", "Label": "gen_epi_review.py", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD", "Parameters": {}, "Used": [ @@ -578,7 +578,7 @@ { "@id": "urn:genssrev-3Wv3HhIo", "Label": "gen_ss_review_scripts.py", - "AssociatedWith": "urn:urn:afni-SFNElAFI", + "AssociatedWith": "urn:afni-SFNElAFI", "Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0", "Parameters": { "-mot_limit": "0.3", diff --git a/examples/from_parsers/afni/afni_thr_voxelunct4_proc.png b/examples/from_parsers/afni/afni_thr_voxelunct4_proc.png index 81f61326..3887c231 100644 Binary files a/examples/from_parsers/afni/afni_thr_voxelunct4_proc.png and b/examples/from_parsers/afni/afni_thr_voxelunct4_proc.png differ diff --git a/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.jsonld b/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.jsonld index 05c7c803..3092341d 100644 --- a/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.jsonld +++ b/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:autobloc-XPw5Ibf6", "Label": "auto block: setup", - "AssociatedWith": "urn:urn:afni-Azo4OHIC", + "AssociatedWith": "urn:afni-Azo4OHIC", "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_voxelwise_t4/tone_counting_onset_times.txt ./afni_voxelwise_t4/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ", "Used": [ "bids::afni_voxelwise_t4/tone_counting_onset_times.txt", @@ -26,7 +26,7 @@ { "@id": "urn:autobloc-Xsbsvk4k", "Label": "auto block: tcat", - "AssociatedWith": "urn:urn:afni-Azo4OHIC", + "AssociatedWith": "urn:afni-Azo4OHIC", "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ", "Used": [ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'" @@ -35,7 +35,7 @@ { "@id": "urn:autobloc-8DXvAoHU", "Label": "auto block: outcount", - "AssociatedWith": "urn:urn:afni-Azo4OHIC", + "AssociatedWith": "urn:afni-Azo4OHIC", "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig", @@ -45,7 +45,7 @@ { "@id": "urn:tshift-4PWunAHR", "Label": "tshift", - "AssociatedWith": "urn:urn:afni-Azo4OHIC", + "AssociatedWith": "urn:afni-Azo4OHIC", "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ", "Used": [ "bids::pb00.$subj.r$run.tcat+orig" @@ -54,7 +54,7 @@ { "@id": "urn:align-H9dKW59q", "Label": "align", - "AssociatedWith": "urn:urn:afni-Azo4OHIC", + "AssociatedWith": "urn:afni-Azo4OHIC", "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ", "Used": [ "bids::pb01.$subj.r01.tshift+orig", @@ -64,7 +64,7 @@ { "@id": "urn:tlrc-8Ob4ZRGu", "Label": "tlrc", - "AssociatedWith": "urn:urn:afni-Azo4OHIC", + "AssociatedWith": "urn:afni-Azo4OHIC", "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ", "Used": [ "bids::TT_N27+tlrc", @@ -75,7 +75,7 @@ { "@id": "urn:volreg-XniyBbVH", "Label": "volreg", - "AssociatedWith": "urn:urn:afni-Azo4OHIC", + "AssociatedWith": "urn:afni-Azo4OHIC", "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ", "Used": [ "bids::pb01.$subj.r$run.tshift+orig", @@ -98,7 +98,7 @@ { "@id": "urn:blur-5nvxP9to", "Label": "blur", - "AssociatedWith": "urn:urn:afni-Azo4OHIC", + "AssociatedWith": "urn:afni-Azo4OHIC", "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ", "Used": [ "bids::pb02.$subj.r$run.volreg+tlrc", @@ -108,7 +108,7 @@ { "@id": "urn:mask-6s6g20Wz", "Label": "mask", - "AssociatedWith": "urn:urn:afni-Azo4OHIC", + "AssociatedWith": "urn:afni-Azo4OHIC", "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -127,7 +127,7 @@ { "@id": "urn:scale-CYGvfYfG", "Label": "scale", - "AssociatedWith": "urn:urn:afni-Azo4OHIC", + "AssociatedWith": "urn:afni-Azo4OHIC", "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ", "Used": [ "bids::pb03.$subj.r$run.blur+tlrc", @@ -139,7 +139,7 @@ { "@id": "urn:regress-tLkm9uCW", "Label": "regress", - "AssociatedWith": "urn:urn:afni-Azo4OHIC", + "AssociatedWith": "urn:afni-Azo4OHIC", "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ", "Used": [ "bids::dfile_rall.1D", @@ -166,7 +166,7 @@ { "@id": "urn:bluresti-u8JJjV7y", "Label": "blur estimation", - "AssociatedWith": "urn:urn:afni-Azo4OHIC", + "AssociatedWith": "urn:afni-Azo4OHIC", "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ", "Used": [ "bids::full_mask.$subj+tlrc", @@ -177,7 +177,7 @@ { "@id": "urn:autobloc-cE18tebx", "Label": "auto block: generate review scripts", - "AssociatedWith": "urn:urn:afni-Azo4OHIC", + "AssociatedWith": "urn:afni-Azo4OHIC", "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ", "Used": [ "bids::pb00.$subj.r*.tcat+orig.HEAD" diff --git a/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.png b/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.png index 2b22a4e7..d13519b8 100644 Binary files a/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.png and b/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.png differ diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld b/examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld index 70a432c7..b568809a 100644 --- a/examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld +++ b/examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:3dpc-zSEKMSc5", "Label": "3dpc", - "AssociatedWith": "urn:urn:afni-ZvsAtHNd", + "AssociatedWith": "urn:afni-ZvsAtHNd", "Command": "3dpc -overwrite -mask ${dset_mask} -pcsave 5 -prefix ${dir_hyp}/PC_hyp${num} ${grp_dset}", "Parameters": {}, "Used": [ @@ -26,7 +26,7 @@ { "@id": "urn:3dresamp-xAJr0qAP", "Label": "3dresample", - "AssociatedWith": "urn:urn:afni-ZvsAtHNd", + "AssociatedWith": "urn:afni-ZvsAtHNd", "Command": "3dresample -overwrite -prefix tmp_REF_DSET.nii.gz -master ${dset_mask} -input \"${ref_dset}\"", "Parameters": {}, "Used": [ @@ -37,7 +37,7 @@ { "@id": "urn:3dmatch-0E3O84FA", "Label": "3dMatch", - "AssociatedWith": "urn:urn:afni-ZvsAtHNd", + "AssociatedWith": "urn:afni-ZvsAtHNd", "Command": "3dMatch -echo_edu -overwrite -mask ${dset_mask} -refset ${dir_hyp}/PC_hyp${num}+tlrc -inset tmp_REF_DSET.nii.gz -prefix tmp_MATCHED", "Parameters": {}, "Used": [ @@ -49,7 +49,7 @@ { "@id": "urn:3dcalc-NJBuzmnS", "Label": "3dcalc", - "AssociatedWith": "urn:urn:afni-ZvsAtHNd", + "AssociatedWith": "urn:afni-ZvsAtHNd", "Command": "3dcalc -echo_edu -overwrite -a ${dir_hyp}/PC_hyp${num}+tlrc -expr \"${signum}*a\" -prefix ${dir_hyp}/PC_hyp${num}_sign0.nii.gz", "Parameters": {}, "Used": [ diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0.png b/examples/from_parsers/afni/narps_do_02_pc_with_sign0.png index e79c10da..1e47294a 100644 Binary files a/examples/from_parsers/afni/narps_do_02_pc_with_sign0.png and b/examples/from_parsers/afni/narps_do_02_pc_with_sign0.png differ diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.jsonld b/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.jsonld index 5f9033dd..ae34d788 100644 --- a/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.jsonld +++ b/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:-2wgEiing", "Label": "", - "AssociatedWith": "urn:urn:afni-oHzJ5GRz", + "AssociatedWith": "urn:afni-oHzJ5GRz", "Command": "3dpc -overwrite -mask ${dset_mask} -pcsave 5 -prefix ${dir_hyp}/PC_hyp${num} ${grp_dset}; ", "Used": [ "bids::$%7Bdset_mask%7D", @@ -25,7 +25,7 @@ { "@id": "urn:block-qU0Fey8I", "Label": "block ...", - "AssociatedWith": "urn:urn:afni-oHzJ5GRz", + "AssociatedWith": "urn:afni-oHzJ5GRz", "Command": "3dresample -overwrite -prefix tmp_REF_DSET.nii.gz -master ${dset_mask} -input \"${ref_dset}\"; 3dMatch -echo_edu -overwrite -mask ${dset_mask} -refset ${dir_hyp}/PC_hyp${num}+tlrc -inset tmp_REF_DSET.nii.gz -prefix tmp_MATCHED; 3dcalc -echo_edu -overwrite -a ${dir_hyp}/PC_hyp${num}+tlrc -expr \"${signum}*a\" -prefix ${dir_hyp}/PC_hyp${num}_sign0.nii.gz; ", "Used": [ "bids::$%7Bdset_mask%7D", diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.png b/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.png index e39f5da0..56f1d1d1 100644 Binary files a/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.png and b/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.png differ diff --git a/examples/from_parsers/afni/narps_do_04_make_imgs_A.jsonld b/examples/from_parsers/afni/narps_do_04_make_imgs_A.jsonld index a306aaf6..7043e2f1 100644 --- a/examples/from_parsers/afni/narps_do_04_make_imgs_A.jsonld +++ b/examples/from_parsers/afni/narps_do_04_make_imgs_A.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:makedire-yn1TxmnM", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-jIIjAQ4i", + "AssociatedWith": "urn:afni-jIIjAQ4i", "Command": "\\mkdir ${odir}", "Parameters": {}, "Used": [] @@ -23,7 +23,7 @@ { "@id": "urn:chauffeu-vqfOC3c7", "Label": "@chauffeur_afni", - "AssociatedWith": "urn:urn:afni-jIIjAQ4i", + "AssociatedWith": "urn:afni-jIIjAQ4i", "Command": "@chauffeur_afni -ulay ${ref} -ulay_range \"2%\" \"110%\" -olay ${ff} -set_subbricks -1 0 0 -func_range 5 -thr_olay 3 -cbar Reds_and_Blues_Inv -olay_alpha Linear -olay_boxed Yes -opacity 7 -prefix ${odir}/img_${nnn}_alpha_${iid} -montx 1 -monty 1 -set_dicom_xyz 5 18 18 -set_xhairs OFF -label_string \"::${iid}\" -label_mode 1 -label_size 3 -do_clean", "Parameters": {}, "Used": [ @@ -33,7 +33,7 @@ { "@id": "urn:chauffeu-oq80JGUT", "Label": "@chauffeur_afni", - "AssociatedWith": "urn:urn:afni-jIIjAQ4i", + "AssociatedWith": "urn:afni-jIIjAQ4i", "Command": "@chauffeur_afni -ulay ${ref} -ulay_range \"2%\" \"110%\" -olay ${ff} -set_subbricks -1 0 0 -func_range 5 -thr_olay 3 -cbar Reds_and_Blues_Inv -olay_alpha No -olay_boxed No -opacity 7 -prefix ${odir}/img_${nnn}_psi_${iid} -montx 1 -monty 1 -set_dicom_xyz 5 18 18 -set_xhairs OFF -label_string \"::${iid}\" -label_mode 1 -label_size 3 -do_clean", "Parameters": {}, "Used": [ @@ -43,7 +43,7 @@ { "@id": "urn:adjunctc-i20W9Yge", "Label": "adjunct_calc_mont_dims.py", - "AssociatedWith": "urn:urn:afni-jIIjAQ4i", + "AssociatedWith": "urn:afni-jIIjAQ4i", "Command": "adjunct_calc_mont_dims.py ${nallbase} __tmp_${hyp}", "Parameters": {}, "Used": [ @@ -53,7 +53,7 @@ { "@id": "urn:2dcat-OgarwyZa", "Label": "2dcat", - "AssociatedWith": "urn:urn:afni-jIIjAQ4i", + "AssociatedWith": "urn:afni-jIIjAQ4i", "Command": "2dcat -echo_edu -gap 5 -gap_col ${lcol} -ny ${dims[4]} -nx ${dims[3]} -zero_wrap -prefix ${odir}/ALL_alpha_${hyp}_sview_${ss}.jpg ${odir}/img_*_alpha*${ss}*", "Parameters": {}, "Used": [ @@ -63,7 +63,7 @@ { "@id": "urn:2dcat-9kS1gW3n", "Label": "2dcat", - "AssociatedWith": "urn:urn:afni-jIIjAQ4i", + "AssociatedWith": "urn:afni-jIIjAQ4i", "Command": "2dcat -echo_edu -gap 5 -gap_col ${lcol} -ny ${dims[4]} -nx ${dims[3]} -zero_wrap -prefix ${odir}/ALL_psi_${hyp}_sview_${ss}.jpg ${odir}/img_*_psi*${ss}*", "Parameters": {}, "Used": [ diff --git a/examples/from_parsers/afni/narps_do_04_make_imgs_A.png b/examples/from_parsers/afni/narps_do_04_make_imgs_A.png index 115a6212..cff9094e 100644 Binary files a/examples/from_parsers/afni/narps_do_04_make_imgs_A.png and b/examples/from_parsers/afni/narps_do_04_make_imgs_A.png differ diff --git a/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.jsonld b/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.jsonld index 30fdac0c..cf6a8d0e 100644 --- a/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.jsonld +++ b/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.jsonld @@ -15,14 +15,14 @@ { "@id": "urn:-NU4cG5f8", "Label": "", - "AssociatedWith": "urn:urn:afni-VLZIevJh", + "AssociatedWith": "urn:afni-VLZIevJh", "Command": "\\mkdir ${odir}; ", "Used": [] }, { "@id": "urn:block-jBYVWSxh", "Label": "block ...", - "AssociatedWith": "urn:urn:afni-VLZIevJh", + "AssociatedWith": "urn:afni-VLZIevJh", "Command": "@chauffeur_afni -ulay ${ref} -ulay_range \"2%\" \"110%\" -olay ${ff} -set_subbricks -1 0 0 -func_range 5 -thr_olay 3 -cbar Reds_and_Blues_Inv -olay_alpha Linear -olay_boxed Yes -opacity 7 -prefix ${odir}/img_${nnn}_alpha_${iid} -montx 1 -monty 1 -set_dicom_xyz 5 18 18 -set_xhairs OFF -label_string \"::${iid}\" -label_mode 1 -label_size 3 -do_clean; @chauffeur_afni -ulay ${ref} -ulay_range \"2%\" \"110%\" -olay ${ff} -set_subbricks -1 0 0 -func_range 5 -thr_olay 3 -cbar Reds_and_Blues_Inv -olay_alpha No -olay_boxed No -opacity 7 -prefix ${odir}/img_${nnn}_psi_${iid} -montx 1 -monty 1 -set_dicom_xyz 5 18 18 -set_xhairs OFF -label_string \"::${iid}\" -label_mode 1 -label_size 3 -do_clean; adjunct_calc_mont_dims.py ${nallbase} __tmp_${hyp}; 2dcat -echo_edu -gap 5 -gap_col ${lcol} -ny ${dims[4]} -nx ${dims[3]} -zero_wrap -prefix ${odir}/ALL_alpha_${hyp}_sview_${ss}.jpg ${odir}/img_*_alpha*${ss}*; 2dcat -echo_edu -gap 5 -gap_col ${lcol} -ny ${dims[4]} -nx ${dims[3]} -zero_wrap -prefix ${odir}/ALL_psi_${hyp}_sview_${ss}.jpg ${odir}/img_*_psi*${ss}*; ", "Used": [ "bids::$%7Bref%7D", diff --git a/examples/from_parsers/afni/narps_do_13_view_zoom.jsonld b/examples/from_parsers/afni/narps_do_13_view_zoom.jsonld index 10cb68cb..ee5ddeb5 100644 --- a/examples/from_parsers/afni/narps_do_13_view_zoom.jsonld +++ b/examples/from_parsers/afni/narps_do_13_view_zoom.jsonld @@ -15,7 +15,7 @@ { "@id": "urn:makedire-zyl0QmyL", "Label": "Make directory", - "AssociatedWith": "urn:urn:afni-wiCVuDES", + "AssociatedWith": "urn:afni-wiCVuDES", "Command": "mkdir -p ${odir}", "Parameters": {}, "Used": [] @@ -23,7 +23,7 @@ { "@id": "urn:isosurfa-6HaOfiy0", "Label": "IsoSurface", - "AssociatedWith": "urn:urn:afni-wiCVuDES", + "AssociatedWith": "urn:afni-wiCVuDES", "Command": "IsoSurface -overwrite -isorois+dsets -input ${ivol} -o_gii cc_${pref_surf} -Tsmooth 0 0 -remesh 1", "Parameters": {}, "Used": [] @@ -31,7 +31,7 @@ { "@id": "urn:1dtoolpy-duovL16A", "Label": "1d_tool.py", - "AssociatedWith": "urn:urn:afni-wiCVuDES", + "AssociatedWith": "urn:afni-wiCVuDES", "Command": "1d_tool.py -csim_pthr ${pthr} -csim_alpha ${alpha} -infile ${file_1D}", "Parameters": {}, "Used": [ @@ -41,7 +41,7 @@ { "@id": "urn:plugoutd-Mi2Op0t1", "Label": "plugout_drive", - "AssociatedWith": "urn:urn:afni-wiCVuDES", + "AssociatedWith": "urn:afni-wiCVuDES", "Command": "plugout_drive -echo_edu -npb $portnum -com \"SWITCH_UNDERLAY ${dset_ref:t}\" -com \"SWITCH_OVERLAY ${dset_ttest:t}\" -com \"SET_XHAIRS OFF\" -com \"SET_SUBBRICKS ${subbb}\" -com \"SET_PBAR_ALL -99 1.0 ${cbar}\" -com \"SET_FUNC_ALPHA ${olay_alpha}\" -com \"SET_FUNC_BOXED ${olay_boxed}\" -com \"$coor_type $coors\" -com \"SET_THRESHNEW ${thr}\" -com \"SET_FUNC_VISIBLE +\" -com \"SET_FUNC_RANGE $frange\" -com \"$OW sagittalimage ifrac=${ifrac} opacity=${opac} mont=${mx}x${my}:${gapord[1]}:${mgap}:${mcolor}\" -com \"$OW coronalimage ifrac=${ifrac} opacity=${opac} mont=${mx}x${my}:${gapord[2]}:${mgap}:${mcolor}\" -com \"$OW axialimage ifrac=${ifrac} opacity=${opac} mont=${mx}x${my}:${gapord[3]}:${mgap}:${mcolor}\" &", "Parameters": { "-echo_edu": true, @@ -56,7 +56,7 @@ { "@id": "urn:suma-l1dTtGBm", "Label": "suma", - "AssociatedWith": "urn:urn:afni-wiCVuDES", + "AssociatedWith": "urn:afni-wiCVuDES", "Command": "suma -echo_edu -npb $portnum -onestate -niml -i cc*.k*.gii -vol ${dset_ref} -sv ${dset_ref} &", "Parameters": {}, "Used": [ @@ -66,7 +66,7 @@ { "@id": "urn:drivesum-urGoHOyw", "Label": "DriveSuma", - "AssociatedWith": "urn:urn:afni-wiCVuDES", + "AssociatedWith": "urn:afni-wiCVuDES", "Command": "DriveSuma -npb $portnum -com viewer_cont -key \"t\" -key \".\" &", "Parameters": { "-npb": "$portnum", diff --git a/examples/from_parsers/afni/narps_do_13_view_zoom.png b/examples/from_parsers/afni/narps_do_13_view_zoom.png index 645f4f79..9c6a266b 100644 Binary files a/examples/from_parsers/afni/narps_do_13_view_zoom.png and b/examples/from_parsers/afni/narps_do_13_view_zoom.png differ diff --git a/examples/from_parsers/afni/narps_do_13_view_zoom_block.jsonld b/examples/from_parsers/afni/narps_do_13_view_zoom_block.jsonld index 4df66547..96d85560 100644 --- a/examples/from_parsers/afni/narps_do_13_view_zoom_block.jsonld +++ b/examples/from_parsers/afni/narps_do_13_view_zoom_block.jsonld @@ -15,14 +15,14 @@ { "@id": "urn:-XCHU0CSU", "Label": "", - "AssociatedWith": "urn:urn:afni-UTYTzyNw", + "AssociatedWith": "urn:afni-UTYTzyNw", "Command": "mkdir -p ${odir}; ", "Used": [] }, { "@id": "urn:block-8SCS9Ax3", "Label": "block ...", - "AssociatedWith": "urn:urn:afni-UTYTzyNw", + "AssociatedWith": "urn:afni-UTYTzyNw", "Command": "IsoSurface -overwrite -isorois+dsets -input ${ivol} -o_gii cc_${pref_surf} -Tsmooth 0 0 -remesh 1; 1d_tool.py -csim_pthr ${pthr} -csim_alpha ${alpha} -infile ${file_1D}; plugout_drive -echo_edu -npb $portnum -com \"SWITCH_UNDERLAY ${dset_ref:t}\" -com \"SWITCH_OVERLAY ${dset_ttest:t}\" -com \"SET_XHAIRS OFF\" -com \"SET_SUBBRICKS ${subbb}\" -com \"SET_PBAR_ALL -99 1.0 ${cbar}\" -com \"SET_FUNC_ALPHA ${olay_alpha}\" -com \"SET_FUNC_BOXED ${olay_boxed}\" -com \"$coor_type $coors\" -com \"SET_THRESHNEW ${thr}\" -com \"SET_FUNC_VISIBLE +\" -com \"SET_FUNC_RANGE $frange\" -com \"$OW sagittalimage ifrac=${ifrac} opacity=${opac} mont=${mx}x${my}:${gapord[1]}:${mgap}:${mcolor}\" -com \"$OW coronalimage ifrac=${ifrac} opacity=${opac} mont=${mx}x${my}:${gapord[2]}:${mgap}:${mcolor}\" -com \"$OW axialimage ifrac=${ifrac} opacity=${opac} mont=${mx}x${my}:${gapord[3]}:${mgap}:${mcolor}\" &; suma -echo_edu -npb $portnum -onestate -niml -i cc*.k*.gii -vol ${dset_ref} -sv ${dset_ref} &; DriveSuma -npb $portnum -com viewer_cont -key \"t\" -key \".\" &; ", "Used": [ "bids::$%7Bfile_1D%7D", diff --git a/examples/from_parsers/afni/narps_do_13_view_zoom_block.png b/examples/from_parsers/afni/narps_do_13_view_zoom_block.png index 5a34064b..d27ec2b7 100644 Binary files a/examples/from_parsers/afni/narps_do_13_view_zoom_block.png and b/examples/from_parsers/afni/narps_do_13_view_zoom_block.png differ diff --git a/examples/from_parsers/context_2024_10_03_14h17m13s.txt b/examples/from_parsers/context_2024_10_04_12h28m38s.txt similarity index 98% rename from examples/from_parsers/context_2024_10_03_14h17m13s.txt rename to examples/from_parsers/context_2024_10_04_12h28m38s.txt index b0c095a0..d1bda5cc 100644 --- a/examples/from_parsers/context_2024_10_03_14h17m13s.txt +++ b/examples/from_parsers/context_2024_10_04_12h28m38s.txt @@ -1,4 +1,4 @@ -Date : 2024_10_03_14h17m13s +Date : 2024_10_04_12h28m38s Processing files... file= nidmresults-examples/afni_alt_onesided_proc.sub_001 file= nidmresults-examples/afni_alt_onesided_proc.sub_001 @@ -69,4 +69,4 @@ Processing files... file= nidmresults-examples/spm_thr_voxelfdrp05_batch.m file= nidmresults-examples/spm_thr_voxelfwep05_batch.m file= nidmresults-examples/spm_thr_voxelunct4_batch.m -End of processed files. Results in dir : 'examples/from_parsers'. Time required: 0:01:07.444562 +End of processed files. Results in dir : 'examples/from_parsers'. Time required: 0:01:09.558909 diff --git a/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.html b/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.html index 9c688d67..d79bee5e 100644 --- a/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.html +++ b/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.html @@ -35,14 +35,14 @@

Progress Report / Log

/usr/local/packages/fsl-5.0.8/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
 
-/usr/local/packages/fsl-5.0.8/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/example_func.nii.gz  -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
+/usr/local/packages/fsl-5.0.8/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/example_func.nii.gz  -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
 Option -F ( FEAT version parameter ) selected with  argument "6.00"
 Option -d ( output directory ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat"
 Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/logs/feat2_pre"
 Option -R ( html unwarping report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_unwarp.html"
 Option -r ( html registration report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_reg.html"
 Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with  argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
 Option -w ( highres dof ) selected with  argument "BBR"
 Option -x ( highres search ) selected with  argument "90"
 Option -s ( standard image ) selected with  argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -53,10 +53,10 @@ 
Progress Report / Log

 /bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/reg
 
 
-/usr/local/packages/fsl-5.0.8/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.8/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
 
 
-/usr/local/packages/fsl-5.0.8/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain  highres_head
+/usr/local/packages/fsl-5.0.8/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain  highres_head
 
 
 /usr/local/packages/fsl-5.0.8/bin/fslmaths /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain standard
@@ -151,9 +151,9 @@ 
Progress Report / Log

 /bin/rm -rf prefiltered_func_data*
Stats
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.8/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.8/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.8/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.8/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
 
 /usr/local/packages/fsl-5.0.8/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts  
 Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.jsonld b/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.jsonld
index 70c68a07..d25d87e2 100644
--- a/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.jsonld
@@ -15,7 +15,7 @@
       {
         "@id": "urn:fslmaths-X40sMWOm",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths /home/tommaullin/Documents/Data/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
         "Used": [
           "bids::/home/tommaullin/Documents/Data/ds011/sub-01/func/sub-01_task-tonecounting_bold"
@@ -24,7 +24,7 @@
       {
         "@id": "urn:fslroi-oh19ScPe",
         "Label": "fslroi",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslroi prefiltered_func_data example_func 52 1",
         "Used": [
           "bids::prefiltered_func_data"
@@ -33,43 +33,43 @@
       {
         "@id": "urn:mainfeat-aTrcG3Fx",
         "Label": "mainfeatreg",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
-        "Command": "/usr/local/packages/fsl-5.0.8/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
+        "Command": "/usr/local/packages/fsl-5.0.8/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
           "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/example_func.nii.gz",
-          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
+          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:makedire-3zzI0Agw",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/reg",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-w3sXEcK0",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
-        "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
+        "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:fslmaths-QEpXdgnq",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
-        "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres_head",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
+        "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres_head",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:fslmaths-pZHZsQhS",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain standard",
         "Used": [
           "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -78,7 +78,7 @@
       {
         "@id": "urn:epireg-fHxZonCr",
         "Label": "epi_reg",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
         "Used": [
           "bids::example_func",
@@ -89,7 +89,7 @@
       {
         "@id": "urn:convertx-hYXi1Bs2",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
         "Used": [
           "bids::example_func2highres.mat"
@@ -98,7 +98,7 @@
       {
         "@id": "urn:slicer-sVwU0TQP",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -108,7 +108,7 @@
       {
         "@id": "urn:pngappen-3fyJh6cv",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
         "Used": [
           "bids::sla.png",
@@ -128,7 +128,7 @@
       {
         "@id": "urn:slicer-IZBDalQP",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -138,7 +138,7 @@
       {
         "@id": "urn:pngappen-zkTzwqDN",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
         "Used": [
           "bids::sla.png",
@@ -158,7 +158,7 @@
       {
         "@id": "urn:pngappen-vIamPDjN",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
         "Used": [
           "bids::example_func2highres1.png",
@@ -168,7 +168,7 @@
       {
         "@id": "urn:rm-OKQx0V46",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/bin/rm -f sl?.png example_func2highres2.png",
         "Used": [
           "bids::example_func2highres2.png",
@@ -178,7 +178,7 @@
       {
         "@id": "urn:rm-YNr6d9hV",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/bin/rm example_func2highres1.png",
         "Used": [
           "bids::example_func2highres1.png"
@@ -187,7 +187,7 @@
       {
         "@id": "urn:flirt-3JDHmTy3",
         "Label": "flirt",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/flirt -in highres -ref standard -out highres2standard -omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear",
         "Used": [
           "bids::highres",
@@ -197,7 +197,7 @@
       {
         "@id": "urn:convertx-4mENLjfA",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat",
         "Used": [
           "bids::highres2standard.mat"
@@ -206,7 +206,7 @@
       {
         "@id": "urn:slicer-9X1OkKJ1",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/slicer highres2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::highres2standard",
@@ -216,7 +216,7 @@
       {
         "@id": "urn:pngappen-dBq2Zzk0",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png highres2standard1.png",
         "Used": [
           "bids::sla.png",
@@ -236,7 +236,7 @@
       {
         "@id": "urn:slicer-Ll7VbI1E",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/slicer standard highres2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::highres2standard",
@@ -246,7 +246,7 @@
       {
         "@id": "urn:pngappen-smb7ArFx",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png highres2standard2.png",
         "Used": [
           "bids::sla.png",
@@ -266,7 +266,7 @@
       {
         "@id": "urn:pngappen-JKK6GHt6",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend highres2standard1.png highres2standard2.png highres2standard.png",
         "Used": [
           "bids::highres2standard1.png",
@@ -276,7 +276,7 @@
       {
         "@id": "urn:rm-MB1AOON1",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/bin/rm -f sl?.png highres2standard2.png",
         "Used": [
           "bids::highres2standard2.png",
@@ -286,7 +286,7 @@
       {
         "@id": "urn:rm-GgsgGxnu",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/bin/rm highres2standard1.png",
         "Used": [
           "bids::highres2standard1.png"
@@ -295,7 +295,7 @@
       {
         "@id": "urn:convertx-SQmLkvOL",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat",
         "Used": [
           "bids::example_func2highres.mat"
@@ -304,7 +304,7 @@
       {
         "@id": "urn:flirt-Mfdaj8tY",
         "Label": "flirt",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear",
         "Used": [
           "bids::example_func",
@@ -315,7 +315,7 @@
       {
         "@id": "urn:convertx-a3Wz3MSn",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat",
         "Used": [
           "bids::example_func2standard.mat"
@@ -324,7 +324,7 @@
       {
         "@id": "urn:slicer-Nj4PlX7k",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/slicer example_func2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2standard",
@@ -334,7 +334,7 @@
       {
         "@id": "urn:pngappen-ZTsccGHu",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2standard1.png",
         "Used": [
           "bids::sla.png",
@@ -354,7 +354,7 @@
       {
         "@id": "urn:slicer-XFKi41kx",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/slicer standard example_func2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2standard",
@@ -364,7 +364,7 @@
       {
         "@id": "urn:pngappen-95KxztEE",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2standard2.png",
         "Used": [
           "bids::sla.png",
@@ -384,7 +384,7 @@
       {
         "@id": "urn:pngappen-Emkbpxnn",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend example_func2standard1.png example_func2standard2.png example_func2standard.png",
         "Used": [
           "bids::example_func2standard1.png",
@@ -394,7 +394,7 @@
       {
         "@id": "urn:rm-PwA8gtun",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/bin/rm -f sl?.png example_func2standard2.png",
         "Used": [
           "bids::example_func2standard2.png",
@@ -404,7 +404,7 @@
       {
         "@id": "urn:mcflirt-RhkfkZU8",
         "Label": "mcflirt",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
         "Used": [
           "bids::prefiltered_func_data"
@@ -413,14 +413,14 @@
       {
         "@id": "urn:makedire-L9bykLV3",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/bin/mkdir -p mc",
         "Used": []
       },
       {
         "@id": "urn:mv-Dezd134K",
         "Label": "mv",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
         "Used": [
           "bids::prefiltered_func_data_mcf.mat",
@@ -434,7 +434,7 @@
       {
         "@id": "urn:fsltsplo-GHWIXd10",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -443,7 +443,7 @@
       {
         "@id": "urn:fsltsplo-FjkHHTOt",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -452,7 +452,7 @@
       {
         "@id": "urn:fsltsplo-1AOZD9Ii",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
         "Used": [
           "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
@@ -461,7 +461,7 @@
       {
         "@id": "urn:fslmaths-hWzoSr4S",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -470,7 +470,7 @@
       {
         "@id": "urn:bet2-cTeUPlvL",
         "Label": "bet2",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/bet2 mean_func mask -f 0.3 -n -m",
         "Used": [
           "bids::mean_func"
@@ -479,7 +479,7 @@
       {
         "@id": "urn:immv-XjUkbn2U",
         "Label": "immv",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/immv mask_mask mask",
         "Used": [
           "bids::mask_mask"
@@ -488,7 +488,7 @@
       {
         "@id": "urn:fslmaths-EV2GCd4j",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
         "Used": [
           "bids::mask",
@@ -498,7 +498,7 @@
       {
         "@id": "urn:fslstats-WuQ9EvLs",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -507,7 +507,7 @@
       {
         "@id": "urn:fslmaths-HQvvGkr3",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -516,7 +516,7 @@
       {
         "@id": "urn:fslstats-X9E18DJd",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -525,7 +525,7 @@
       {
         "@id": "urn:fslmaths-6dbK2akr",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths mask -dilF mask",
         "Used": [
           "bids::mask"
@@ -534,7 +534,7 @@
       {
         "@id": "urn:fslmaths-LhcU1kaU",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
         "Used": [
           "bids::mask",
@@ -544,7 +544,7 @@
       {
         "@id": "urn:fslmaths-8vlKApk2",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -553,7 +553,7 @@
       {
         "@id": "urn:susan-UxYIP1lX",
         "Label": "susan",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -562,7 +562,7 @@
       {
         "@id": "urn:fslmaths-iFvYKT4p",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
         "Used": [
           "bids::mask",
@@ -572,7 +572,7 @@
       {
         "@id": "urn:fslmaths-4pYyDrcL",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
         "Used": [
           "bids::prefiltered_func_data_smooth"
@@ -581,7 +581,7 @@
       {
         "@id": "urn:fslmaths-wLkyGtTj",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
         "Used": [
           "bids::prefiltered_func_data_intnorm"
@@ -590,7 +590,7 @@
       {
         "@id": "urn:fslmaths-kSriC40g",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
         "Used": [
           "bids::prefiltered_func_data_intnorm",
@@ -600,7 +600,7 @@
       {
         "@id": "urn:imrm-PJYzYkv0",
         "Label": "imrm",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/imrm tempMean",
         "Used": [
           "bids::tempMean"
@@ -609,7 +609,7 @@
       {
         "@id": "urn:fslmaths-x2Mvt4OA",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
         "Used": [
           "bids::prefiltered_func_data_tempfilt"
@@ -618,7 +618,7 @@
       {
         "@id": "urn:fslmaths-o6vpI5Id",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths filtered_func_data -Tmean mean_func",
         "Used": [
           "bids::filtered_func_data"
@@ -627,7 +627,7 @@
       {
         "@id": "urn:rm-Hj8YxGgj",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/bin/rm -rf prefiltered_func_data*",
         "Used": [
           "bids::prefiltered_func_data*"
@@ -636,39 +636,39 @@
       {
         "@id": "urn:makedire-RDOOlycE",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-3PXP67h4",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
-        "Command": "/usr/local/packages/fsl-5.0.8/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
+        "Command": "/usr/local/packages/fsl-5.0.8/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
         ]
       },
       {
         "@id": "urn:makedire-RrxzWAED",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-f9DuphuI",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
-        "Command": "/usr/local/packages/fsl-5.0.8/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
+        "Command": "/usr/local/packages/fsl-5.0.8/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
         ]
       },
       {
         "@id": "urn:filmgls-xpjNuWUs",
         "Label": "film_gls",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts",
         "Used": [
           "bids::design.con",
@@ -681,7 +681,7 @@
       {
         "@id": "urn:smoothes-VTT9rn8N",
         "Label": "smoothest",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
         "Used": [
           "bids::mask",
@@ -691,7 +691,7 @@
       {
         "@id": "urn:fslmaths-wxrzYlhL",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
         "Used": [
           "bids::mask",
@@ -701,14 +701,14 @@
       {
         "@id": "urn:echo-IbMksC8P",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "echo 38352 > thresh_zstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-2YQYb7ln",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2",
         "Used": [
           "bids::mask",
@@ -718,14 +718,14 @@
       {
         "@id": "urn:echo-OIwar3Jw",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "echo 38352 > thresh_zstat2.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-mUk1TnwY",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths stats/zfstat1 -mas mask thresh_zfstat1",
         "Used": [
           "bids::mask",
@@ -735,14 +735,14 @@
       {
         "@id": "urn:echo-yGvpKaqD",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "echo 38352 > thresh_zfstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-VTzvv2bx",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths stats/zfstat2 -mas mask thresh_zfstat2",
         "Used": [
           "bids::mask",
@@ -752,14 +752,14 @@
       {
         "@id": "urn:echo-u8ZXMJhB",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "echo 38352 > thresh_zfstat2.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-OZbfjxwh",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths stats/zfstat3 -mas mask thresh_zfstat3",
         "Used": [
           "bids::mask",
@@ -769,21 +769,21 @@
       {
         "@id": "urn:echo-W1LSESgK",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "echo 38352 > thresh_zfstat3.vol",
         "Used": []
       },
       {
         "@id": "urn:ptoz-C9rpj6iK",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-6EgN0K4y",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
         "Used": [
           "bids::stats/cope1",
@@ -793,7 +793,7 @@
       {
         "@id": "urn:cluster2-1Slnt5f5",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zstat1",
         "Used": [
           "bids::cluster_zstat1"
@@ -802,14 +802,14 @@
       {
         "@id": "urn:ptoz-pdPBHfty",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-3VvOdnac",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
         "Used": [
           "bids::stats/cope2",
@@ -819,7 +819,7 @@
       {
         "@id": "urn:cluster2-SUXY6x29",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zstat2",
         "Used": [
           "bids::cluster_zstat2"
@@ -828,14 +828,14 @@
       {
         "@id": "urn:ptoz-nAQkKuoV",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-se2emGpz",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat1 -t 3.090232 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z --voxuncthresh > cluster_zfstat1.txt",
         "Used": [
           "bids::thresh_zfstat1"
@@ -844,7 +844,7 @@
       {
         "@id": "urn:cluster2-isaWHcwc",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat1",
         "Used": [
           "bids::cluster_zfstat1"
@@ -853,14 +853,14 @@
       {
         "@id": "urn:ptoz-GMJ6r1Ua",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-0M7QqJvZ",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat2 -t 3.090232 --othresh=thresh_zfstat2 -o cluster_mask_zfstat2 --connectivity=26 --olmax=lmax_zfstat2.txt --scalarname=Z --voxuncthresh > cluster_zfstat2.txt",
         "Used": [
           "bids::thresh_zfstat2"
@@ -869,7 +869,7 @@
       {
         "@id": "urn:cluster2-89Uqgluc",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat2",
         "Used": [
           "bids::cluster_zfstat2"
@@ -878,14 +878,14 @@
       {
         "@id": "urn:ptoz-HswgvjMt",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-OF94q1Q7",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat3 -t 3.090232 --othresh=thresh_zfstat3 -o cluster_mask_zfstat3 --connectivity=26 --olmax=lmax_zfstat3.txt --scalarname=Z --voxuncthresh > cluster_zfstat3.txt",
         "Used": [
           "bids::thresh_zfstat3"
@@ -894,7 +894,7 @@
       {
         "@id": "urn:cluster2-NX555VWz",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat3",
         "Used": [
           "bids::cluster_zfstat3"
@@ -903,14 +903,14 @@
       {
         "@id": "urn:ptoz-Vl4IyDA0",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-iGFpF9oV",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat1_std.txt --scalarname=Z --voxuncthresh > cluster_zstat1_std.txt",
         "Used": [
           "bids::stats/cope1",
@@ -920,7 +920,7 @@
       {
         "@id": "urn:cluster2-aPqs0IQH",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zstat1 -std",
         "Used": [
           "bids::cluster_zstat1"
@@ -929,7 +929,7 @@
       {
         "@id": "urn:cluster-CUsyPhtO",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zstat2 -c stats/cope2 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat2_std.txt --scalarname=Z --voxuncthresh > cluster_zstat2_std.txt",
         "Used": [
           "bids::stats/cope2",
@@ -939,7 +939,7 @@
       {
         "@id": "urn:cluster2-1MwzcECw",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zstat2 -std",
         "Used": [
           "bids::cluster_zstat2"
@@ -948,7 +948,7 @@
       {
         "@id": "urn:cluster-PFSC1Nv3",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat1 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zfstat1_std.txt --scalarname=Z --voxuncthresh > cluster_zfstat1_std.txt",
         "Used": [
           "bids::thresh_zfstat1"
@@ -957,7 +957,7 @@
       {
         "@id": "urn:cluster2-ioZKXTRb",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat1 -std",
         "Used": [
           "bids::cluster_zfstat1"
@@ -966,7 +966,7 @@
       {
         "@id": "urn:cluster-Gzi0hcGl",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat2 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zfstat2_std.txt --scalarname=Z --voxuncthresh > cluster_zfstat2_std.txt",
         "Used": [
           "bids::thresh_zfstat2"
@@ -975,7 +975,7 @@
       {
         "@id": "urn:cluster2-YswmVVvl",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat2 -std",
         "Used": [
           "bids::cluster_zfstat2"
@@ -984,7 +984,7 @@
       {
         "@id": "urn:cluster-AbETZMSV",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat3 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zfstat3_std.txt --scalarname=Z --voxuncthresh > cluster_zfstat3_std.txt",
         "Used": [
           "bids::thresh_zfstat3"
@@ -993,7 +993,7 @@
       {
         "@id": "urn:cluster2-NoOJS8aG",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat3 -std",
         "Used": [
           "bids::cluster_zfstat3"
@@ -1002,7 +1002,7 @@
       {
         "@id": "urn:fslstats-P85DXb3S",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat1"
@@ -1011,7 +1011,7 @@
       {
         "@id": "urn:fslstats-MzAH9rNz",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslstats thresh_zstat2 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat2"
@@ -1020,7 +1020,7 @@
       {
         "@id": "urn:fslstats-1niR35ux",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslstats thresh_zfstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zfstat1"
@@ -1029,7 +1029,7 @@
       {
         "@id": "urn:fslstats-iwrasjHL",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslstats thresh_zfstat2 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zfstat2"
@@ -1038,7 +1038,7 @@
       {
         "@id": "urn:fslstats-yZ4wfefH",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/fslstats thresh_zfstat3 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zfstat3"
@@ -1047,14 +1047,14 @@
       {
         "@id": "urn:overlay-AEeSiJRN",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/overlay 1 0 example_func -a thresh_zstat1 3.090250 7.488793 rendered_thresh_zstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-gUWrtCQu",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
         "Used": [
           "bids::rendered_thresh_zstat1"
@@ -1063,7 +1063,7 @@
       {
         "@id": "urn:cp-XWedD4a4",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/bin/cp /usr/local/packages/fsl-5.0.8/etc/luts/ramp.gif .ramp.gif",
         "Used": [
           "bids::/usr/local/packages/fsl-5.0.8/etc/luts/ramp.gif"
@@ -1072,14 +1072,14 @@
       {
         "@id": "urn:overlay-CTlqYESD",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/overlay 1 0 example_func -a thresh_zstat2 3.090250 7.488793 rendered_thresh_zstat2",
         "Used": []
       },
       {
         "@id": "urn:slicer-fmz6vzFn",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/slicer rendered_thresh_zstat2 -A 750 rendered_thresh_zstat2.png",
         "Used": [
           "bids::rendered_thresh_zstat2"
@@ -1088,14 +1088,14 @@
       {
         "@id": "urn:overlay-7HYmK5zG",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/overlay 1 0 example_func -a thresh_zfstat1 3.090250 7.488793 rendered_thresh_zfstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-NyAy9pUv",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/slicer rendered_thresh_zfstat1 -A 750 rendered_thresh_zfstat1.png",
         "Used": [
           "bids::rendered_thresh_zfstat1"
@@ -1104,14 +1104,14 @@
       {
         "@id": "urn:overlay-ilPFUrlv",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/overlay 1 0 example_func -a thresh_zfstat2 3.090250 7.488793 rendered_thresh_zfstat2",
         "Used": []
       },
       {
         "@id": "urn:slicer-zwdZ7Um5",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/slicer rendered_thresh_zfstat2 -A 750 rendered_thresh_zfstat2.png",
         "Used": [
           "bids::rendered_thresh_zfstat2"
@@ -1120,14 +1120,14 @@
       {
         "@id": "urn:overlay-8fyKCoI9",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/overlay 1 0 example_func -a thresh_zfstat3 3.090250 7.488793 rendered_thresh_zfstat3",
         "Used": []
       },
       {
         "@id": "urn:slicer-mmdzsZLM",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/slicer rendered_thresh_zfstat3 -A 750 rendered_thresh_zfstat3.png",
         "Used": [
           "bids::rendered_thresh_zfstat3"
@@ -1136,14 +1136,14 @@
       {
         "@id": "urn:makedire-vZc4wsey",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "mkdir -p tsplot",
         "Used": []
       },
       {
         "@id": "urn:tsplot-qwfDtqRW",
         "Label": "tsplot",
-        "AssociatedWith": "urn:urn:fsl-RWQkET6j",
+        "AssociatedWith": "urn:fsl-RWQkET6j",
         "Command": "/usr/local/packages/fsl-5.0.8/bin/tsplot . -f filtered_func_data -o tsplot",
         "Used": []
       }
@@ -1184,11 +1184,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "Label": "sub-01_T1w_brain",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "digest": {
-          "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
+          "sha256": "8f1ae7ba69869c79b2cc5a83ce4ca24a7d666187256c2aa4d61a952b903b05b0"
         }
       },
       {
@@ -2329,11 +2329,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "Label": "sub-01_tone_counting.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "digest": {
-          "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+          "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
         }
       },
       {
@@ -2352,11 +2352,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "Label": "sub-01_tone_counting_probe.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "digest": {
-          "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+          "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
         }
       },
       {
diff --git a/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.png b/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.png
index 51fa7eea..0ff7c23c 100644
Binary files a/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.png and b/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_con_f_report_log.html b/examples/from_parsers/fsl/fsl_con_f_report_log.html
index e7cc0973..11a7422b 100644
--- a/examples/from_parsers/fsl/fsl_con_f_report_log.html
+++ b/examples/from_parsers/fsl/fsl_con_f_report_log.html
@@ -35,20 +35,20 @@ 
Progress Report / Log

 326895
Initialisation
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
 Total original volumes = 104
 
 /usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
 
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/example_func.nii.gz  -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/example_func.nii.gz  -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
 Option -F ( FEAT version parameter ) selected with  argument "6.00"
 Option -d ( output directory ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat"
 Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/logs/feat2_pre"
 Option -R ( html unwarping report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_unwarp.html"
 Option -r ( html registration report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_reg.html"
 Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with  argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
 Option -w ( highres dof ) selected with  argument "BBR"
 Option -x ( highres search ) selected with  argument "90"
 Option -s ( standard image ) selected with  argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ 
Progress Report / Log

 /bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/reg
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
 
 did not find file: example_func2highres.mat. Generating transform.
 
@@ -128,9 +128,9 @@ 
Progress Report / Log

 /bin/rm -rf prefiltered_func_data*
Stats
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
 
 /usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts  
 Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_con_f_report_log.jsonld b/examples/from_parsers/fsl/fsl_con_f_report_log.jsonld
index dcc710bb..1db9f141 100644
--- a/examples/from_parsers/fsl/fsl_con_f_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_con_f_report_log.jsonld
@@ -15,16 +15,16 @@
       {
         "@id": "urn:fslmaths-oc14GKDP",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold"
+          "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
         ]
       },
       {
         "@id": "urn:fslroi-6k5pLepL",
         "Label": "fslroi",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
         "Used": [
           "bids::prefiltered_func_data"
@@ -33,43 +33,43 @@
       {
         "@id": "urn:mainfeat-jJrIyjtr",
         "Label": "mainfeatreg",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
           "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/example_func.nii.gz",
-          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
+          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:makedire-h9dkEsGr",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/reg",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-rkVMg3eS",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:fslmaths-y3rdENXm",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
         ]
       },
       {
         "@id": "urn:epireg-SrLJqoNK",
         "Label": "epi_reg",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
         "Used": [
           "bids::example_func",
@@ -80,7 +80,7 @@
       {
         "@id": "urn:convertx-0XwNnwAf",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
         "Used": [
           "bids::example_func2highres.mat"
@@ -89,7 +89,7 @@
       {
         "@id": "urn:slicer-oYAWwQEK",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -99,7 +99,7 @@
       {
         "@id": "urn:pngappen-ea6vl3HF",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
         "Used": [
           "bids::sla.png",
@@ -119,7 +119,7 @@
       {
         "@id": "urn:slicer-NaQlNrU9",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -129,7 +129,7 @@
       {
         "@id": "urn:pngappen-KHqutS7T",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
         "Used": [
           "bids::sla.png",
@@ -149,7 +149,7 @@
       {
         "@id": "urn:pngappen-buPbtlmN",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
         "Used": [
           "bids::example_func2highres1.png",
@@ -159,7 +159,7 @@
       {
         "@id": "urn:rm-G2QoZwJo",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/bin/rm -f sl?.png example_func2highres2.png",
         "Used": [
           "bids::example_func2highres2.png",
@@ -169,7 +169,7 @@
       {
         "@id": "urn:rm-4GTCd5W3",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/bin/rm example_func2highres1.png",
         "Used": [
           "bids::example_func2highres1.png"
@@ -178,7 +178,7 @@
       {
         "@id": "urn:mcflirt-nb93z6pl",
         "Label": "mcflirt",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
         "Used": [
           "bids::prefiltered_func_data"
@@ -187,14 +187,14 @@
       {
         "@id": "urn:makedire-BdY1mJzW",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/bin/mkdir -p mc",
         "Used": []
       },
       {
         "@id": "urn:mv-MwSL31tw",
         "Label": "mv",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
         "Used": [
           "bids::prefiltered_func_data_mcf.mat",
@@ -208,7 +208,7 @@
       {
         "@id": "urn:fsltsplo-CmX0rhkg",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -217,7 +217,7 @@
       {
         "@id": "urn:fsltsplo-xZvlJGJR",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -226,7 +226,7 @@
       {
         "@id": "urn:fsltsplo-y1QUR534",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
         "Used": [
           "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
@@ -235,7 +235,7 @@
       {
         "@id": "urn:fslmaths-b0cbKTer",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -244,7 +244,7 @@
       {
         "@id": "urn:bet2-xVedVR2i",
         "Label": "bet2",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
         "Used": [
           "bids::mean_func"
@@ -253,7 +253,7 @@
       {
         "@id": "urn:immv-XyQRaHT9",
         "Label": "immv",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
         "Used": [
           "bids::mask_mask"
@@ -262,7 +262,7 @@
       {
         "@id": "urn:fslmaths-6R9f17aP",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
         "Used": [
           "bids::mask",
@@ -272,7 +272,7 @@
       {
         "@id": "urn:fslstats-ETmNlzhi",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -281,7 +281,7 @@
       {
         "@id": "urn:fslmaths-zvMwGcMe",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -290,7 +290,7 @@
       {
         "@id": "urn:fslstats-9pVn8GVH",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -299,7 +299,7 @@
       {
         "@id": "urn:fslmaths-JXsIsq2q",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
         "Used": [
           "bids::mask"
@@ -308,7 +308,7 @@
       {
         "@id": "urn:fslmaths-i1BTSETh",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
         "Used": [
           "bids::mask",
@@ -318,7 +318,7 @@
       {
         "@id": "urn:fslmaths-QNoJTpOa",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -327,7 +327,7 @@
       {
         "@id": "urn:susan-j7lDL1a2",
         "Label": "susan",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -336,7 +336,7 @@
       {
         "@id": "urn:fslmaths-eaHPEfI0",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
         "Used": [
           "bids::mask",
@@ -346,7 +346,7 @@
       {
         "@id": "urn:fslmaths-TViFxxjT",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
         "Used": [
           "bids::prefiltered_func_data_smooth"
@@ -355,7 +355,7 @@
       {
         "@id": "urn:fslmaths-NSt9V9sw",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
         "Used": [
           "bids::prefiltered_func_data_intnorm"
@@ -364,7 +364,7 @@
       {
         "@id": "urn:fslmaths-eZHX1jve",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
         "Used": [
           "bids::prefiltered_func_data_intnorm",
@@ -374,7 +374,7 @@
       {
         "@id": "urn:imrm-6AsWFoz1",
         "Label": "imrm",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
         "Used": [
           "bids::tempMean"
@@ -383,7 +383,7 @@
       {
         "@id": "urn:fslmaths-KbrkJIBY",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
         "Used": [
           "bids::prefiltered_func_data_tempfilt"
@@ -392,7 +392,7 @@
       {
         "@id": "urn:fslmaths-TFy9OeDH",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
         "Used": [
           "bids::filtered_func_data"
@@ -401,7 +401,7 @@
       {
         "@id": "urn:rm-S5y4JiDJ",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/bin/rm -rf prefiltered_func_data*",
         "Used": [
           "bids::prefiltered_func_data*"
@@ -410,39 +410,39 @@
       {
         "@id": "urn:makedire-CYU7q463",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-dpO7fTvF",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
         ]
       },
       {
         "@id": "urn:makedire-LmNQcVed",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-Ru3257Bq",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
         ]
       },
       {
         "@id": "urn:filmgls-sDjcg2z9",
         "Label": "film_gls",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts",
         "Used": [
           "bids::design.con",
@@ -455,7 +455,7 @@
       {
         "@id": "urn:smoothes-xNwolFhT",
         "Label": "smoothest",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
         "Used": [
           "bids::mask",
@@ -465,7 +465,7 @@
       {
         "@id": "urn:fslmaths-C7DZCLIJ",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
         "Used": [
           "bids::mask",
@@ -475,14 +475,14 @@
       {
         "@id": "urn:echo-1sAApjLG",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "echo 38352 > thresh_zstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-O3riA05d",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zfstat1 -mas mask thresh_zfstat1",
         "Used": [
           "bids::mask",
@@ -492,21 +492,21 @@
       {
         "@id": "urn:echo-MZ1h05oO",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "echo 38352 > thresh_zfstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:ptoz-ia1Ulg5h",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-q85r87w0",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
         "Used": [
           "bids::stats/cope1",
@@ -516,7 +516,7 @@
       {
         "@id": "urn:cluster2-j4o3usk6",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
         "Used": [
           "bids::cluster_zstat1"
@@ -525,14 +525,14 @@
       {
         "@id": "urn:ptoz-jqsGIdOl",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-MRZWM656",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zfstat1 -t 3.090232 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z --voxuncthresh > cluster_zfstat1.txt",
         "Used": [
           "bids::thresh_zfstat1"
@@ -541,7 +541,7 @@
       {
         "@id": "urn:cluster2-FSBIpyPU",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zfstat1",
         "Used": [
           "bids::cluster_zfstat1"
@@ -550,7 +550,7 @@
       {
         "@id": "urn:fslstats-dowWh0hs",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat1"
@@ -559,7 +559,7 @@
       {
         "@id": "urn:fslstats-SgHefAry",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zfstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zfstat1"
@@ -568,14 +568,14 @@
       {
         "@id": "urn:overlay-MzJgJACL",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090250 7.488793 rendered_thresh_zstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-3wFnCCy8",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
         "Used": [
           "bids::rendered_thresh_zstat1"
@@ -584,7 +584,7 @@
       {
         "@id": "urn:cp-SPUZKjCU",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
         "Used": [
           "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
@@ -593,14 +593,14 @@
       {
         "@id": "urn:overlay-4KIeCJr6",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zfstat1 3.090250 7.488793 rendered_thresh_zfstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-WhXfy3dQ",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zfstat1 -A 750 rendered_thresh_zfstat1.png",
         "Used": [
           "bids::rendered_thresh_zfstat1"
@@ -609,25 +609,25 @@
       {
         "@id": "urn:makedire-Rbuz4y5j",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "mkdir -p tsplot",
         "Used": []
       },
       {
         "@id": "urn:tsplot-ex5pJZVe",
         "Label": "tsplot",
-        "AssociatedWith": "urn:urn:fsl-IhAeexzD",
+        "AssociatedWith": "urn:fsl-IhAeexzD",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
         "Used": []
       }
     ],
     "Entities": [
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "Label": "sub-01_task-tonecounting_bold",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "digest": {
-          "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
+          "sha256": "33501604ae140e58832facff473a9578d5a549403bdbec53107d2b3eaab898ee"
         }
       },
       {
@@ -657,11 +657,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "Label": "sub-01_T1w_brain",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "digest": {
-          "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
+          "sha256": "8f1ae7ba69869c79b2cc5a83ce4ca24a7d666187256c2aa4d61a952b903b05b0"
         }
       },
       {
@@ -697,11 +697,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "Label": "sub-01_T1w",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "digest": {
-          "sha256": "3be6c69338e200d2a286a56cd9a0030539cf50201f412c910ade833e18354d27"
+          "sha256": "8dd4893a9c9500ce8c516f1a9845abf887087d00c2c47fc3524a17d924e78acf"
         }
       },
       {
@@ -1261,11 +1261,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "Label": "sub-01_tone_counting.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "digest": {
-          "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+          "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
         }
       },
       {
@@ -1284,11 +1284,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "Label": "sub-01_tone_counting_probe.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "digest": {
-          "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+          "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
         }
       },
       {
diff --git a/examples/from_parsers/fsl/fsl_con_f_report_log.png b/examples/from_parsers/fsl/fsl_con_f_report_log.png
index 8485e158..aa30bfd9 100644
Binary files a/examples/from_parsers/fsl/fsl_con_f_report_log.png and b/examples/from_parsers/fsl/fsl_con_f_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_contrast_mask_report_log.html b/examples/from_parsers/fsl/fsl_contrast_mask_report_log.html
index 18017d46..0c14551a 100644
--- a/examples/from_parsers/fsl/fsl_contrast_mask_report_log.html
+++ b/examples/from_parsers/fsl/fsl_contrast_mask_report_log.html
@@ -35,20 +35,20 @@ 
Progress Report / Log

 326900
Initialisation
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
 Total original volumes = 104
 
 /usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
 
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/example_func.nii.gz  -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/example_func.nii.gz  -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
 Option -F ( FEAT version parameter ) selected with  argument "6.00"
 Option -d ( output directory ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat"
 Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/logs/feat2_pre"
 Option -R ( html unwarping report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_unwarp.html"
 Option -r ( html registration report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_reg.html"
 Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with  argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
 Option -w ( highres dof ) selected with  argument "BBR"
 Option -x ( highres search ) selected with  argument "90"
 Option -s ( standard image ) selected with  argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ 
Progress Report / Log

 /bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/reg
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
 
 did not find file: example_func2highres.mat. Generating transform.
 
@@ -128,9 +128,9 @@ 
Progress Report / Log

 /bin/rm -rf prefiltered_func_data*
Stats
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
 
 /usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con  
 Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_contrast_mask_report_log.jsonld b/examples/from_parsers/fsl/fsl_contrast_mask_report_log.jsonld
index eebc71c3..c0c031cb 100644
--- a/examples/from_parsers/fsl/fsl_contrast_mask_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_contrast_mask_report_log.jsonld
@@ -15,16 +15,16 @@
       {
         "@id": "urn:fslmaths-Xuyim67B",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold"
+          "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
         ]
       },
       {
         "@id": "urn:fslroi-3d5HkXKh",
         "Label": "fslroi",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
         "Used": [
           "bids::prefiltered_func_data"
@@ -33,43 +33,43 @@
       {
         "@id": "urn:mainfeat-uc29xqXi",
         "Label": "mainfeatreg",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
           "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/example_func.nii.gz",
-          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
+          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:makedire-HB3mMbwP",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/reg",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-YiN6wsRz",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:fslmaths-YCDMAWXA",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
         ]
       },
       {
         "@id": "urn:epireg-JxbV7pkT",
         "Label": "epi_reg",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
         "Used": [
           "bids::example_func",
@@ -80,7 +80,7 @@
       {
         "@id": "urn:convertx-BjiVbzit",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
         "Used": [
           "bids::example_func2highres.mat"
@@ -89,7 +89,7 @@
       {
         "@id": "urn:slicer-bEbtJCop",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -99,7 +99,7 @@
       {
         "@id": "urn:pngappen-m18AYAi4",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
         "Used": [
           "bids::sla.png",
@@ -119,7 +119,7 @@
       {
         "@id": "urn:slicer-XbZXqIgv",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -129,7 +129,7 @@
       {
         "@id": "urn:pngappen-epl9TLVc",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
         "Used": [
           "bids::sla.png",
@@ -149,7 +149,7 @@
       {
         "@id": "urn:pngappen-10ldR3vU",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
         "Used": [
           "bids::example_func2highres1.png",
@@ -159,7 +159,7 @@
       {
         "@id": "urn:rm-wWRksZcv",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/bin/rm -f sl?.png example_func2highres2.png",
         "Used": [
           "bids::example_func2highres2.png",
@@ -169,7 +169,7 @@
       {
         "@id": "urn:rm-sJLZbIki",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/bin/rm example_func2highres1.png",
         "Used": [
           "bids::example_func2highres1.png"
@@ -178,7 +178,7 @@
       {
         "@id": "urn:mcflirt-yfIrHolT",
         "Label": "mcflirt",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
         "Used": [
           "bids::prefiltered_func_data"
@@ -187,14 +187,14 @@
       {
         "@id": "urn:makedire-8o9UTCSS",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/bin/mkdir -p mc",
         "Used": []
       },
       {
         "@id": "urn:mv-563E2MPP",
         "Label": "mv",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
         "Used": [
           "bids::prefiltered_func_data_mcf.mat",
@@ -208,7 +208,7 @@
       {
         "@id": "urn:fsltsplo-fxUJXTgT",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -217,7 +217,7 @@
       {
         "@id": "urn:fsltsplo-UxjDo0NZ",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -226,7 +226,7 @@
       {
         "@id": "urn:fsltsplo-mRcnuaAd",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
         "Used": [
           "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
@@ -235,7 +235,7 @@
       {
         "@id": "urn:fslmaths-SKesHBPT",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -244,7 +244,7 @@
       {
         "@id": "urn:bet2-z8jTqNMY",
         "Label": "bet2",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
         "Used": [
           "bids::mean_func"
@@ -253,7 +253,7 @@
       {
         "@id": "urn:immv-2Aycx2Pp",
         "Label": "immv",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
         "Used": [
           "bids::mask_mask"
@@ -262,7 +262,7 @@
       {
         "@id": "urn:fslmaths-WLFMXeqd",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
         "Used": [
           "bids::mask",
@@ -272,7 +272,7 @@
       {
         "@id": "urn:fslstats-Sxs64kSH",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -281,7 +281,7 @@
       {
         "@id": "urn:fslmaths-eHWA2R63",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -290,7 +290,7 @@
       {
         "@id": "urn:fslstats-Nute5Xvq",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -299,7 +299,7 @@
       {
         "@id": "urn:fslmaths-pyfyjzeh",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
         "Used": [
           "bids::mask"
@@ -308,7 +308,7 @@
       {
         "@id": "urn:fslmaths-uF6O4TLB",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
         "Used": [
           "bids::mask",
@@ -318,7 +318,7 @@
       {
         "@id": "urn:fslmaths-W7rvUch0",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -327,7 +327,7 @@
       {
         "@id": "urn:susan-bgDTUD0R",
         "Label": "susan",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -336,7 +336,7 @@
       {
         "@id": "urn:fslmaths-BZVuhqW9",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
         "Used": [
           "bids::mask",
@@ -346,7 +346,7 @@
       {
         "@id": "urn:fslmaths-5gSV2JIW",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
         "Used": [
           "bids::prefiltered_func_data_smooth"
@@ -355,7 +355,7 @@
       {
         "@id": "urn:fslmaths-of0s39J8",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
         "Used": [
           "bids::prefiltered_func_data_intnorm"
@@ -364,7 +364,7 @@
       {
         "@id": "urn:fslmaths-0Yxn67qj",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
         "Used": [
           "bids::prefiltered_func_data_intnorm",
@@ -374,7 +374,7 @@
       {
         "@id": "urn:imrm-ZIinjJYn",
         "Label": "imrm",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
         "Used": [
           "bids::tempMean"
@@ -383,7 +383,7 @@
       {
         "@id": "urn:fslmaths-zQn78yon",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
         "Used": [
           "bids::prefiltered_func_data_tempfilt"
@@ -392,7 +392,7 @@
       {
         "@id": "urn:fslmaths-AoENJ4vu",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
         "Used": [
           "bids::filtered_func_data"
@@ -401,7 +401,7 @@
       {
         "@id": "urn:rm-F8kdvqWr",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/bin/rm -rf prefiltered_func_data*",
         "Used": [
           "bids::prefiltered_func_data*"
@@ -410,39 +410,39 @@
       {
         "@id": "urn:makedire-BNU0v0w6",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-gPWYR3x8",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
         ]
       },
       {
         "@id": "urn:makedire-fqvNCFv9",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-6BH43olN",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
         ]
       },
       {
         "@id": "urn:filmgls-hnXGCyIa",
         "Label": "film_gls",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
         "Used": [
           "bids::design.con",
@@ -454,7 +454,7 @@
       {
         "@id": "urn:smoothes-HqoKWOFV",
         "Label": "smoothest",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
         "Used": [
           "bids::mask",
@@ -464,7 +464,7 @@
       {
         "@id": "urn:fslmaths-BRCsyWxk",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
         "Used": [
           "bids::mask",
@@ -474,14 +474,14 @@
       {
         "@id": "urn:echo-yV2rC6mn",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "echo 38352 > thresh_zstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-5zja6ybF",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2",
         "Used": [
           "bids::mask",
@@ -491,21 +491,21 @@
       {
         "@id": "urn:echo-I9XfYCFO",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "echo 38352 > thresh_zstat2.vol",
         "Used": []
       },
       {
         "@id": "urn:ptoz-gSLlUd7H",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-KIgiCoyq",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
         "Used": [
           "bids::stats/cope1",
@@ -515,7 +515,7 @@
       {
         "@id": "urn:cluster2-mHF7PeTK",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
         "Used": [
           "bids::cluster_zstat1"
@@ -524,14 +524,14 @@
       {
         "@id": "urn:ptoz-EzAWsACC",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-MRFJ9REm",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
         "Used": [
           "bids::stats/cope2",
@@ -541,7 +541,7 @@
       {
         "@id": "urn:cluster2-fL0yiugD",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat2",
         "Used": [
           "bids::cluster_zstat2"
@@ -550,14 +550,14 @@
       {
         "@id": "urn:makedire-7qR7aS7n",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "mkdir -p conmask",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-l6gT6VDx",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths thresh_zstat1 -mas thresh_zstat2 conmask/thresh_zstat1",
         "Used": [
           "bids::thresh_zstat1",
@@ -567,7 +567,7 @@
       {
         "@id": "urn:mv-cM6i4hre",
         "Label": "mv",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/bin/mv -f conmask/* .",
         "Used": [
           "bids::conmask/*"
@@ -576,7 +576,7 @@
       {
         "@id": "urn:rmdir-MvjZDLjS",
         "Label": "rmdir",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "rmdir conmask",
         "Used": [
           "bids::conmask"
@@ -585,14 +585,14 @@
       {
         "@id": "urn:ptoz-jEOVCEWD",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-KSF2yOj5",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z > cluster_zstat1.txt",
         "Used": [
           "bids::stats/cope1",
@@ -602,7 +602,7 @@
       {
         "@id": "urn:cluster2-6ftEMoV3",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
         "Used": [
           "bids::cluster_zstat1"
@@ -611,7 +611,7 @@
       {
         "@id": "urn:cluster-9sTEgQIH",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -c stats/cope2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z > cluster_zstat2.txt",
         "Used": [
           "bids::stats/cope2",
@@ -621,7 +621,7 @@
       {
         "@id": "urn:cluster2-RcKazPNN",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat2",
         "Used": [
           "bids::cluster_zstat2"
@@ -630,7 +630,7 @@
       {
         "@id": "urn:fslstats-3g7Su0HS",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat1"
@@ -639,7 +639,7 @@
       {
         "@id": "urn:fslstats-l5TuOakI",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat2 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat2"
@@ -648,14 +648,14 @@
       {
         "@id": "urn:overlay-N8rFrcHs",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090262 7.488793 rendered_thresh_zstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-yKHiTJ8J",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
         "Used": [
           "bids::rendered_thresh_zstat1"
@@ -664,7 +664,7 @@
       {
         "@id": "urn:cp-NwMvSfas",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
         "Used": [
           "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
@@ -673,14 +673,14 @@
       {
         "@id": "urn:overlay-7Z2044QX",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat2 3.090262 7.488793 rendered_thresh_zstat2",
         "Used": []
       },
       {
         "@id": "urn:slicer-uH9J1HCB",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat2 -A 750 rendered_thresh_zstat2.png",
         "Used": [
           "bids::rendered_thresh_zstat2"
@@ -689,25 +689,25 @@
       {
         "@id": "urn:makedire-1Dvf4Uew",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "mkdir -p tsplot",
         "Used": []
       },
       {
         "@id": "urn:tsplot-7pwv5ldO",
         "Label": "tsplot",
-        "AssociatedWith": "urn:urn:fsl-JIPD22pA",
+        "AssociatedWith": "urn:fsl-JIPD22pA",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
         "Used": []
       }
     ],
     "Entities": [
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "Label": "sub-01_task-tonecounting_bold",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "digest": {
-          "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
+          "sha256": "33501604ae140e58832facff473a9578d5a549403bdbec53107d2b3eaab898ee"
         }
       },
       {
@@ -737,11 +737,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "Label": "sub-01_T1w_brain",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "digest": {
-          "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
+          "sha256": "8f1ae7ba69869c79b2cc5a83ce4ca24a7d666187256c2aa4d61a952b903b05b0"
         }
       },
       {
@@ -777,11 +777,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "Label": "sub-01_T1w",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "digest": {
-          "sha256": "3be6c69338e200d2a286a56cd9a0030539cf50201f412c910ade833e18354d27"
+          "sha256": "8dd4893a9c9500ce8c516f1a9845abf887087d00c2c47fc3524a17d924e78acf"
         }
       },
       {
@@ -1341,11 +1341,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "Label": "sub-01_tone_counting.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "digest": {
-          "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+          "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
         }
       },
       {
@@ -1364,11 +1364,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "Label": "sub-01_tone_counting_probe.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "digest": {
-          "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+          "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
         }
       },
       {
diff --git a/examples/from_parsers/fsl/fsl_contrast_mask_report_log.png b/examples/from_parsers/fsl/fsl_contrast_mask_report_log.png
index bee8399f..f36b91cc 100644
Binary files a/examples/from_parsers/fsl/fsl_contrast_mask_report_log.png and b/examples/from_parsers/fsl/fsl_contrast_mask_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_default_report_log.html b/examples/from_parsers/fsl/fsl_default_report_log.html
index 9fa11fc8..72b140ae 100644
--- a/examples/from_parsers/fsl/fsl_default_report_log.html
+++ b/examples/from_parsers/fsl/fsl_default_report_log.html
@@ -35,20 +35,20 @@ 
Progress Report / Log

 326905
Initialisation
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
 Total original volumes = 104
 
 /usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
 
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/example_func.nii.gz  -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/example_func.nii.gz  -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
 Option -F ( FEAT version parameter ) selected with  argument "6.00"
 Option -d ( output directory ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat"
 Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/logs/feat2_pre"
 Option -R ( html unwarping report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_unwarp.html"
 Option -r ( html registration report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_reg.html"
 Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with  argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
 Option -w ( highres dof ) selected with  argument "BBR"
 Option -x ( highres search ) selected with  argument "90"
 Option -s ( standard image ) selected with  argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ 
Progress Report / Log

 /bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/reg
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
 
 did not find file: example_func2highres.mat. Generating transform.
 
@@ -128,9 +128,9 @@ 
Progress Report / Log

 /bin/rm -rf prefiltered_func_data*
Stats
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
 
 /usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con  
 Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_default_report_log.jsonld b/examples/from_parsers/fsl/fsl_default_report_log.jsonld
index 4f92b39f..08e5cbd5 100644
--- a/examples/from_parsers/fsl/fsl_default_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_default_report_log.jsonld
@@ -15,16 +15,16 @@
       {
         "@id": "urn:fslmaths-fcSIwVMX",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold"
+          "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
         ]
       },
       {
         "@id": "urn:fslroi-OG3P6KqD",
         "Label": "fslroi",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
         "Used": [
           "bids::prefiltered_func_data"
@@ -33,43 +33,43 @@
       {
         "@id": "urn:mainfeat-DMP0PTOA",
         "Label": "mainfeatreg",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
           "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/example_func.nii.gz",
-          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
+          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:makedire-BYrQI1M0",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/reg",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-wMZbWTyd",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:fslmaths-Ddt8tGbY",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
         ]
       },
       {
         "@id": "urn:epireg-H7ZIk7pS",
         "Label": "epi_reg",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
         "Used": [
           "bids::example_func",
@@ -80,7 +80,7 @@
       {
         "@id": "urn:convertx-yjHkcYPz",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
         "Used": [
           "bids::example_func2highres.mat"
@@ -89,7 +89,7 @@
       {
         "@id": "urn:slicer-FHEZSaNt",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -99,7 +99,7 @@
       {
         "@id": "urn:pngappen-SFkxyMJz",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
         "Used": [
           "bids::sla.png",
@@ -119,7 +119,7 @@
       {
         "@id": "urn:slicer-sJLXpGr2",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -129,7 +129,7 @@
       {
         "@id": "urn:pngappen-RUvG0ImG",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
         "Used": [
           "bids::sla.png",
@@ -149,7 +149,7 @@
       {
         "@id": "urn:pngappen-FtOA4j1l",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
         "Used": [
           "bids::example_func2highres1.png",
@@ -159,7 +159,7 @@
       {
         "@id": "urn:rm-wjUAGwJx",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/bin/rm -f sl?.png example_func2highres2.png",
         "Used": [
           "bids::example_func2highres2.png",
@@ -169,7 +169,7 @@
       {
         "@id": "urn:rm-WsyCazgR",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/bin/rm example_func2highres1.png",
         "Used": [
           "bids::example_func2highres1.png"
@@ -178,7 +178,7 @@
       {
         "@id": "urn:mcflirt-psopAuVm",
         "Label": "mcflirt",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
         "Used": [
           "bids::prefiltered_func_data"
@@ -187,14 +187,14 @@
       {
         "@id": "urn:makedire-4wMbJbeY",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/bin/mkdir -p mc",
         "Used": []
       },
       {
         "@id": "urn:mv-5vMsPN6O",
         "Label": "mv",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
         "Used": [
           "bids::prefiltered_func_data_mcf.mat",
@@ -208,7 +208,7 @@
       {
         "@id": "urn:fsltsplo-VAnxKfBU",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -217,7 +217,7 @@
       {
         "@id": "urn:fsltsplo-mhaEcLEl",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -226,7 +226,7 @@
       {
         "@id": "urn:fsltsplo-kJvjcgIP",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
         "Used": [
           "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
@@ -235,7 +235,7 @@
       {
         "@id": "urn:fslmaths-xN4svDa6",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -244,7 +244,7 @@
       {
         "@id": "urn:bet2-dCRCwC4Q",
         "Label": "bet2",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
         "Used": [
           "bids::mean_func"
@@ -253,7 +253,7 @@
       {
         "@id": "urn:immv-rj6XOp5N",
         "Label": "immv",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
         "Used": [
           "bids::mask_mask"
@@ -262,7 +262,7 @@
       {
         "@id": "urn:fslmaths-uHMcxkxd",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
         "Used": [
           "bids::mask",
@@ -272,7 +272,7 @@
       {
         "@id": "urn:fslstats-v3Akthn6",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -281,7 +281,7 @@
       {
         "@id": "urn:fslmaths-9NPek5gf",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -290,7 +290,7 @@
       {
         "@id": "urn:fslstats-xvXfXEBP",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -299,7 +299,7 @@
       {
         "@id": "urn:fslmaths-OgFigMP9",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
         "Used": [
           "bids::mask"
@@ -308,7 +308,7 @@
       {
         "@id": "urn:fslmaths-JDkXh2Ek",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
         "Used": [
           "bids::mask",
@@ -318,7 +318,7 @@
       {
         "@id": "urn:fslmaths-6tB3QPvV",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -327,7 +327,7 @@
       {
         "@id": "urn:susan-yEISM3Bq",
         "Label": "susan",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -336,7 +336,7 @@
       {
         "@id": "urn:fslmaths-i8mmZH4R",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
         "Used": [
           "bids::mask",
@@ -346,7 +346,7 @@
       {
         "@id": "urn:fslmaths-8mVq8ArW",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
         "Used": [
           "bids::prefiltered_func_data_smooth"
@@ -355,7 +355,7 @@
       {
         "@id": "urn:fslmaths-PxrisfAb",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
         "Used": [
           "bids::prefiltered_func_data_intnorm"
@@ -364,7 +364,7 @@
       {
         "@id": "urn:fslmaths-dEwDEqMs",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
         "Used": [
           "bids::prefiltered_func_data_intnorm",
@@ -374,7 +374,7 @@
       {
         "@id": "urn:imrm-9EqLmaK5",
         "Label": "imrm",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
         "Used": [
           "bids::tempMean"
@@ -383,7 +383,7 @@
       {
         "@id": "urn:fslmaths-ZNc1S4EG",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
         "Used": [
           "bids::prefiltered_func_data_tempfilt"
@@ -392,7 +392,7 @@
       {
         "@id": "urn:fslmaths-b1QMiBd0",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
         "Used": [
           "bids::filtered_func_data"
@@ -401,7 +401,7 @@
       {
         "@id": "urn:rm-HbfJKC7Y",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/bin/rm -rf prefiltered_func_data*",
         "Used": [
           "bids::prefiltered_func_data*"
@@ -410,39 +410,39 @@
       {
         "@id": "urn:makedire-nIMQRQkl",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-bHzmy5Rc",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
         ]
       },
       {
         "@id": "urn:makedire-uK8ar6PC",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-UK3whvWC",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
         ]
       },
       {
         "@id": "urn:filmgls-4inTDGsm",
         "Label": "film_gls",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
         "Used": [
           "bids::design.con",
@@ -454,7 +454,7 @@
       {
         "@id": "urn:smoothes-y9B7AsN0",
         "Label": "smoothest",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
         "Used": [
           "bids::mask",
@@ -464,7 +464,7 @@
       {
         "@id": "urn:fslmaths-AOfrEHao",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
         "Used": [
           "bids::mask",
@@ -474,21 +474,21 @@
       {
         "@id": "urn:echo-mE5BoYda",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "echo 38352 > thresh_zstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:ptoz-PLLGjThF",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-UwBXCmUj",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
         "Used": [
           "bids::stats/cope1",
@@ -498,7 +498,7 @@
       {
         "@id": "urn:cluster2-0MFqmsA1",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
         "Used": [
           "bids::cluster_zstat1"
@@ -507,7 +507,7 @@
       {
         "@id": "urn:fslstats-96CGPa1j",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat1"
@@ -516,14 +516,14 @@
       {
         "@id": "urn:overlay-0XOXZytD",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090524 7.488793 rendered_thresh_zstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-naOf7SVy",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
         "Used": [
           "bids::rendered_thresh_zstat1"
@@ -532,7 +532,7 @@
       {
         "@id": "urn:cp-oC4qeHWI",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
         "Used": [
           "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
@@ -541,25 +541,25 @@
       {
         "@id": "urn:makedire-0SY3kjho",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "mkdir -p tsplot",
         "Used": []
       },
       {
         "@id": "urn:tsplot-BPGsLPU3",
         "Label": "tsplot",
-        "AssociatedWith": "urn:urn:fsl-E4ALjxdM",
+        "AssociatedWith": "urn:fsl-E4ALjxdM",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
         "Used": []
       }
     ],
     "Entities": [
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "Label": "sub-01_task-tonecounting_bold",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "digest": {
-          "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
+          "sha256": "33501604ae140e58832facff473a9578d5a549403bdbec53107d2b3eaab898ee"
         }
       },
       {
@@ -589,11 +589,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "Label": "sub-01_T1w_brain",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "digest": {
-          "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
+          "sha256": "8f1ae7ba69869c79b2cc5a83ce4ca24a7d666187256c2aa4d61a952b903b05b0"
         }
       },
       {
@@ -629,11 +629,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "Label": "sub-01_T1w",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "digest": {
-          "sha256": "3be6c69338e200d2a286a56cd9a0030539cf50201f412c910ade833e18354d27"
+          "sha256": "8dd4893a9c9500ce8c516f1a9845abf887087d00c2c47fc3524a17d924e78acf"
         }
       },
       {
@@ -1193,11 +1193,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "Label": "sub-01_tone_counting.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "digest": {
-          "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+          "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
         }
       },
       {
@@ -1216,11 +1216,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "Label": "sub-01_tone_counting_probe.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "digest": {
-          "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+          "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
         }
       },
       {
diff --git a/examples/from_parsers/fsl/fsl_default_report_log.png b/examples/from_parsers/fsl/fsl_default_report_log.png
index 6989171d..1178741f 100644
Binary files a/examples/from_parsers/fsl/fsl_default_report_log.png and b/examples/from_parsers/fsl/fsl_default_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_full_examples001_report_log.jsonld b/examples/from_parsers/fsl/fsl_full_examples001_report_log.jsonld
index 9946481a..f1821fc1 100644
--- a/examples/from_parsers/fsl/fsl_full_examples001_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_full_examples001_report_log.jsonld
@@ -15,7 +15,7 @@
       {
         "@id": "urn:fslmaths-b1MGvYNo",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslmaths /Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/fmri prefiltered_func_data -odt float",
         "Used": [
           "bids::/Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/fmri"
@@ -24,7 +24,7 @@
       {
         "@id": "urn:fslroi-pEfBZwC1",
         "Label": "fslroi",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslroi prefiltered_func_data example_func 53 1",
         "Used": [
           "bids::prefiltered_func_data"
@@ -33,7 +33,7 @@
       {
         "@id": "urn:mcflirt-KeW71fTO",
         "Label": "mcflirt",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs",
         "Used": [
           "bids::prefiltered_func_data"
@@ -42,14 +42,14 @@
       {
         "@id": "urn:makedire-QsOZPp7d",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/bin/mkdir -p mc",
         "Used": []
       },
       {
         "@id": "urn:mv-iaHeHtFC",
         "Label": "mv",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
         "Used": [
           "bids::prefiltered_func_data_mcf.mat",
@@ -63,7 +63,7 @@
       {
         "@id": "urn:fsltsplo-B4QqMADr",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -72,7 +72,7 @@
       {
         "@id": "urn:fsltsplo-PBP7q6Mm",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -81,7 +81,7 @@
       {
         "@id": "urn:fsltsplo-FRGlfszX",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
         "Used": [
           "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
@@ -90,7 +90,7 @@
       {
         "@id": "urn:fslmaths-TFXrmtg1",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -99,7 +99,7 @@
       {
         "@id": "urn:bet2-906V4kHT",
         "Label": "bet2",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/bet2 mean_func mask -f 0.3 -n -m",
         "Used": [
           "bids::mean_func"
@@ -108,7 +108,7 @@
       {
         "@id": "urn:immv-vs9RHb6O",
         "Label": "immv",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/immv mask_mask mask",
         "Used": [
           "bids::mask_mask"
@@ -117,7 +117,7 @@
       {
         "@id": "urn:fslmaths-4fMxR2bm",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
         "Used": [
           "bids::mask",
@@ -127,7 +127,7 @@
       {
         "@id": "urn:fslstats-4kMoZNWn",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -136,7 +136,7 @@
       {
         "@id": "urn:fslmaths-ZT26rDzN",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_bet -thr 978.24375 -Tmin -bin mask -odt char",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -145,7 +145,7 @@
       {
         "@id": "urn:fslstats-C4Vkq7YG",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -154,7 +154,7 @@
       {
         "@id": "urn:fslmaths-x3vBn14T",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslmaths mask -dilF mask",
         "Used": [
           "bids::mask"
@@ -163,7 +163,7 @@
       {
         "@id": "urn:fslmaths-Ug4rV82p",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
         "Used": [
           "bids::mask",
@@ -173,7 +173,7 @@
       {
         "@id": "urn:fslmaths-FtnR53jV",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -182,7 +182,7 @@
       {
         "@id": "urn:susan-FiFaiCkb",
         "Label": "susan",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/susan prefiltered_func_data_thresh 5646.963501 2.97239915074 3 1 1 mean_func 5646.963501 prefiltered_func_data_smooth",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -191,7 +191,7 @@
       {
         "@id": "urn:fslmaths-USD6zrsf",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
         "Used": [
           "bids::mask",
@@ -201,7 +201,7 @@
       {
         "@id": "urn:fslmaths-DFXryZ4N",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mul 1.32814741917 prefiltered_func_data_intnorm",
         "Used": [
           "bids::prefiltered_func_data_smooth"
@@ -210,7 +210,7 @@
       {
         "@id": "urn:fslmaths-YuhXjVaO",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_intnorm -bptf 227.142867456 -1 prefiltered_func_data_tempfilt",
         "Used": [
           "bids::prefiltered_func_data_intnorm"
@@ -219,7 +219,7 @@
       {
         "@id": "urn:fslmaths-xst3I97I",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
         "Used": [
           "bids::prefiltered_func_data_tempfilt"
@@ -228,7 +228,7 @@
       {
         "@id": "urn:fslmaths-YKjFeGPL",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslmaths filtered_func_data -Tmean mean_func",
         "Used": [
           "bids::filtered_func_data"
@@ -237,7 +237,7 @@
       {
         "@id": "urn:rm-KPKJQj8H",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/bin/rm -rf prefiltered_func_data*",
         "Used": [
           "bids::prefiltered_func_data*"
@@ -246,14 +246,14 @@
       {
         "@id": "urn:makedire-hAAbGVmy",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:cp-YrEeSz3m",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/bin/cp /Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/word_generation.txt custom_timing_files/ev1.txt",
         "Used": [
           "bids::/Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/word_generation.txt"
@@ -262,14 +262,14 @@
       {
         "@id": "urn:makedire-zbwFEzNw",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:cp-EEjL6yrM",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/bin/cp /Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/word_shadowing.txt custom_timing_files/ev2.txt",
         "Used": [
           "bids::/Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/word_shadowing.txt"
@@ -278,14 +278,14 @@
       {
         "@id": "urn:filmgls-tfojDd6j",
         "Label": "film_gls",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/film_gls -rn stats -sa -ms 5 filtered_func_data design.mat 1000.0",
         "Used": []
       },
       {
         "@id": "urn:smoothes-RtoGXcPI",
         "Label": "smoothest",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
         "Used": [
           "bids::mask",
@@ -295,14 +295,14 @@
       {
         "@id": "urn:contrast-C2PVyL9l",
         "Label": "contrast_mgr",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/contrast_mgr stats design.con",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-76xeGCWn",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
         "Used": [
           "bids::mask",
@@ -312,14 +312,14 @@
       {
         "@id": "urn:echo-zam482ZY",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "echo 45203 > thresh_zstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:cluster-tD3guFw2",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -p 0.05 -d 0.384676 --volume=45203 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z > cluster_zstat1.txt",
         "Used": [
           "bids::stats/cope1",
@@ -329,7 +329,7 @@
       {
         "@id": "urn:cluster2-EiOgSBEx",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/cluster2html . cluster_zstat1",
         "Used": [
           "bids::cluster_zstat1"
@@ -338,7 +338,7 @@
       {
         "@id": "urn:fslstats-eJ5UST56",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat1"
@@ -347,14 +347,14 @@
       {
         "@id": "urn:overlay-mw6P2Yl8",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/overlay 1 0 example_func -a thresh_zstat1 2.300331 5.793015 rendered_thresh_zstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-tqi5V4Rr",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
         "Used": [
           "bids::rendered_thresh_zstat1"
@@ -363,7 +363,7 @@
       {
         "@id": "urn:cp-85L9VfbN",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/bin/cp /usr/local/fsl/etc/luts/ramp.gif .ramp.gif",
         "Used": [
           "bids::/usr/local/fsl/etc/luts/ramp.gif"
@@ -372,21 +372,21 @@
       {
         "@id": "urn:makedire-gCH0e57C",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "mkdir -p tsplot",
         "Used": []
       },
       {
         "@id": "urn:tsplot-sQPvUfWS",
         "Label": "tsplot",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/tsplot . -f filtered_func_data -o tsplot",
         "Used": []
       },
       {
         "@id": "urn:cluster-812ayXhq",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -p 0.05 -d 0.384676 --volume=45203 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat1_std.txt --scalarname=Z > cluster_zstat1_std.txt",
         "Used": [
           "bids::stats/cope1",
@@ -396,7 +396,7 @@
       {
         "@id": "urn:cluster2-bkJu8wYb",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/cluster2html . cluster_zstat1 -std",
         "Used": [
           "bids::cluster_zstat1"
@@ -405,14 +405,14 @@
       {
         "@id": "urn:makedire-pxx5hor8",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/bin/mkdir -p /Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/fmri+.feat/reg",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-CcrXUhxy",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslmaths /Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/structural_brain highres",
         "Used": [
           "bids::/Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/structural_brain"
@@ -421,7 +421,7 @@
       {
         "@id": "urn:fslmaths-R10gGsdr",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain standard",
         "Used": [
           "bids::/usr/local/fsl/data/standard/MNI152_T1_2mm_brain"
@@ -430,7 +430,7 @@
       {
         "@id": "urn:flirt-fvVRPRT5",
         "Label": "flirt",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/flirt -in example_func -ref highres -out example_func2highres -omat example_func2highres.mat -cost corratio -dof 7 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear",
         "Used": [
           "bids::example_func",
@@ -440,7 +440,7 @@
       {
         "@id": "urn:convertx-PQf5CMyQ",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
         "Used": [
           "bids::example_func2highres.mat"
@@ -449,7 +449,7 @@
       {
         "@id": "urn:slicer-7RnnONJA",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -459,7 +459,7 @@
       {
         "@id": "urn:pngappen-VAGzUgxU",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
         "Used": [
           "bids::sla.png",
@@ -479,7 +479,7 @@
       {
         "@id": "urn:slicer-5UQf4loB",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -489,7 +489,7 @@
       {
         "@id": "urn:pngappen-EAzSEN9O",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
         "Used": [
           "bids::sla.png",
@@ -509,7 +509,7 @@
       {
         "@id": "urn:pngappen-MLrzExnj",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
         "Used": [
           "bids::example_func2highres1.png",
@@ -519,7 +519,7 @@
       {
         "@id": "urn:rm-6WBPdNij",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/bin/rm -f sl?.png example_func2highres2.png",
         "Used": [
           "bids::example_func2highres2.png",
@@ -529,7 +529,7 @@
       {
         "@id": "urn:rm-I9krhlSI",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/bin/rm example_func2highres1.png",
         "Used": [
           "bids::example_func2highres1.png"
@@ -538,7 +538,7 @@
       {
         "@id": "urn:flirt-neRhcE4N",
         "Label": "flirt",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/flirt -in highres -ref standard -out highres2standard -omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear",
         "Used": [
           "bids::highres",
@@ -548,7 +548,7 @@
       {
         "@id": "urn:convertx-8teOYoH5",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat",
         "Used": [
           "bids::highres2standard.mat"
@@ -557,7 +557,7 @@
       {
         "@id": "urn:slicer-M7ZeWOyi",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/slicer highres2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::highres2standard",
@@ -567,7 +567,7 @@
       {
         "@id": "urn:pngappen-1m297Xyj",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png highres2standard1.png",
         "Used": [
           "bids::sla.png",
@@ -587,7 +587,7 @@
       {
         "@id": "urn:slicer-m8Q5vCPD",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/slicer standard highres2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::highres2standard",
@@ -597,7 +597,7 @@
       {
         "@id": "urn:pngappen-4NNLd5ew",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png highres2standard2.png",
         "Used": [
           "bids::sla.png",
@@ -617,7 +617,7 @@
       {
         "@id": "urn:pngappen-7rOC9QLu",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/pngappend highres2standard1.png highres2standard2.png highres2standard.png",
         "Used": [
           "bids::highres2standard1.png",
@@ -627,7 +627,7 @@
       {
         "@id": "urn:rm-p2L9F5qN",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/bin/rm -f sl?.png highres2standard2.png",
         "Used": [
           "bids::highres2standard2.png",
@@ -637,7 +637,7 @@
       {
         "@id": "urn:rm-8gdMveqq",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/bin/rm highres2standard1.png",
         "Used": [
           "bids::highres2standard1.png"
@@ -646,7 +646,7 @@
       {
         "@id": "urn:convertx-zzaEDYj0",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat",
         "Used": [
           "bids::example_func2highres.mat"
@@ -655,7 +655,7 @@
       {
         "@id": "urn:flirt-IzGlSqIc",
         "Label": "flirt",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear",
         "Used": [
           "bids::example_func",
@@ -666,7 +666,7 @@
       {
         "@id": "urn:convertx-NaXYQzXW",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat",
         "Used": [
           "bids::example_func2standard.mat"
@@ -675,7 +675,7 @@
       {
         "@id": "urn:slicer-UQXUwp1F",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/slicer example_func2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2standard",
@@ -685,7 +685,7 @@
       {
         "@id": "urn:pngappen-XWpLEvlM",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2standard1.png",
         "Used": [
           "bids::sla.png",
@@ -705,7 +705,7 @@
       {
         "@id": "urn:slicer-gieR3uyT",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/slicer standard example_func2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2standard",
@@ -715,7 +715,7 @@
       {
         "@id": "urn:pngappen-Q3DzJumP",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2standard2.png",
         "Used": [
           "bids::sla.png",
@@ -735,7 +735,7 @@
       {
         "@id": "urn:pngappen-SxqkKzF3",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/usr/local/fsl/bin/pngappend example_func2standard1.png example_func2standard2.png example_func2standard.png",
         "Used": [
           "bids::example_func2standard1.png",
@@ -745,7 +745,7 @@
       {
         "@id": "urn:rm-7fETH355",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-KLLV16PQ",
+        "AssociatedWith": "urn:fsl-KLLV16PQ",
         "Command": "/bin/rm -f sl?.png example_func2standard2.png",
         "Used": [
           "bids::example_func2standard2.png",
diff --git a/examples/from_parsers/fsl/fsl_full_examples001_report_log.png b/examples/from_parsers/fsl/fsl_full_examples001_report_log.png
index 869871fb..9cc9cf21 100644
Binary files a/examples/from_parsers/fsl/fsl_full_examples001_report_log.png and b/examples/from_parsers/fsl/fsl_full_examples001_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_gamma_basis_report_log.html b/examples/from_parsers/fsl/fsl_gamma_basis_report_log.html
index 504c2dae..e940a226 100644
--- a/examples/from_parsers/fsl/fsl_gamma_basis_report_log.html
+++ b/examples/from_parsers/fsl/fsl_gamma_basis_report_log.html
@@ -35,20 +35,20 @@ 
Progress Report / Log

 326910
Initialisation
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
 Total original volumes = 104
 
 /usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
 
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/example_func.nii.gz  -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/example_func.nii.gz  -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
 Option -F ( FEAT version parameter ) selected with  argument "6.00"
 Option -d ( output directory ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat"
 Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/logs/feat2_pre"
 Option -R ( html unwarping report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_unwarp.html"
 Option -r ( html registration report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_reg.html"
 Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with  argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
 Option -w ( highres dof ) selected with  argument "BBR"
 Option -x ( highres search ) selected with  argument "90"
 Option -s ( standard image ) selected with  argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ 
Progress Report / Log

 /bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/reg
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
 
 did not find file: example_func2highres.mat. Generating transform.
 
@@ -128,9 +128,9 @@ 
Progress Report / Log

 /bin/rm -rf prefiltered_func_data*
Stats
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
 
 /usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts  
 Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_gamma_basis_report_log.jsonld b/examples/from_parsers/fsl/fsl_gamma_basis_report_log.jsonld
index c0224870..52eaa90b 100644
--- a/examples/from_parsers/fsl/fsl_gamma_basis_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_gamma_basis_report_log.jsonld
@@ -15,16 +15,16 @@
       {
         "@id": "urn:fslmaths-qeUb1qc5",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold"
+          "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
         ]
       },
       {
         "@id": "urn:fslroi-VBxwwZY6",
         "Label": "fslroi",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
         "Used": [
           "bids::prefiltered_func_data"
@@ -33,43 +33,43 @@
       {
         "@id": "urn:mainfeat-7FPDQFA3",
         "Label": "mainfeatreg",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
           "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/example_func.nii.gz",
-          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
+          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:makedire-lVc4z7Bv",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/reg",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-DHqHCVuk",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:fslmaths-hSsHK6sO",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
         ]
       },
       {
         "@id": "urn:epireg-PfcVzMiS",
         "Label": "epi_reg",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
         "Used": [
           "bids::example_func",
@@ -80,7 +80,7 @@
       {
         "@id": "urn:convertx-WJotBeOj",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
         "Used": [
           "bids::example_func2highres.mat"
@@ -89,7 +89,7 @@
       {
         "@id": "urn:slicer-IvnNaijU",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -99,7 +99,7 @@
       {
         "@id": "urn:pngappen-Hjp62Yc9",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
         "Used": [
           "bids::sla.png",
@@ -119,7 +119,7 @@
       {
         "@id": "urn:slicer-4HjW8Tda",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -129,7 +129,7 @@
       {
         "@id": "urn:pngappen-FqJ58gVR",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
         "Used": [
           "bids::sla.png",
@@ -149,7 +149,7 @@
       {
         "@id": "urn:pngappen-OAGXpflt",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
         "Used": [
           "bids::example_func2highres1.png",
@@ -159,7 +159,7 @@
       {
         "@id": "urn:rm-ugjHnpxW",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/bin/rm -f sl?.png example_func2highres2.png",
         "Used": [
           "bids::example_func2highres2.png",
@@ -169,7 +169,7 @@
       {
         "@id": "urn:rm-SZJB2wRs",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/bin/rm example_func2highres1.png",
         "Used": [
           "bids::example_func2highres1.png"
@@ -178,7 +178,7 @@
       {
         "@id": "urn:mcflirt-fSkOmPFv",
         "Label": "mcflirt",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
         "Used": [
           "bids::prefiltered_func_data"
@@ -187,14 +187,14 @@
       {
         "@id": "urn:makedire-ykL6bIwa",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/bin/mkdir -p mc",
         "Used": []
       },
       {
         "@id": "urn:mv-r5PjOrob",
         "Label": "mv",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
         "Used": [
           "bids::prefiltered_func_data_mcf.mat",
@@ -208,7 +208,7 @@
       {
         "@id": "urn:fsltsplo-V40wbRN0",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -217,7 +217,7 @@
       {
         "@id": "urn:fsltsplo-S5OsKnAK",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -226,7 +226,7 @@
       {
         "@id": "urn:fsltsplo-SEpWzzeB",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
         "Used": [
           "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
@@ -235,7 +235,7 @@
       {
         "@id": "urn:fslmaths-4R2qoFkh",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -244,7 +244,7 @@
       {
         "@id": "urn:bet2-Y3qoaHaK",
         "Label": "bet2",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
         "Used": [
           "bids::mean_func"
@@ -253,7 +253,7 @@
       {
         "@id": "urn:immv-4kgkNuZh",
         "Label": "immv",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
         "Used": [
           "bids::mask_mask"
@@ -262,7 +262,7 @@
       {
         "@id": "urn:fslmaths-96ZZNvFa",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
         "Used": [
           "bids::mask",
@@ -272,7 +272,7 @@
       {
         "@id": "urn:fslstats-GBOY6eMl",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -281,7 +281,7 @@
       {
         "@id": "urn:fslmaths-UGKt7EeQ",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -290,7 +290,7 @@
       {
         "@id": "urn:fslstats-q94UYRly",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -299,7 +299,7 @@
       {
         "@id": "urn:fslmaths-xR0Ys5gM",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
         "Used": [
           "bids::mask"
@@ -308,7 +308,7 @@
       {
         "@id": "urn:fslmaths-1w02UWwW",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
         "Used": [
           "bids::mask",
@@ -318,7 +318,7 @@
       {
         "@id": "urn:fslmaths-0JxcZLu8",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -327,7 +327,7 @@
       {
         "@id": "urn:susan-TDeycXdk",
         "Label": "susan",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -336,7 +336,7 @@
       {
         "@id": "urn:fslmaths-d80aVlfN",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
         "Used": [
           "bids::mask",
@@ -346,7 +346,7 @@
       {
         "@id": "urn:fslmaths-s0Y29iqz",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
         "Used": [
           "bids::prefiltered_func_data_smooth"
@@ -355,7 +355,7 @@
       {
         "@id": "urn:fslmaths-JKhI0mGJ",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
         "Used": [
           "bids::prefiltered_func_data_intnorm"
@@ -364,7 +364,7 @@
       {
         "@id": "urn:fslmaths-TC3trTEP",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
         "Used": [
           "bids::prefiltered_func_data_intnorm",
@@ -374,7 +374,7 @@
       {
         "@id": "urn:imrm-HwmXAUaU",
         "Label": "imrm",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
         "Used": [
           "bids::tempMean"
@@ -383,7 +383,7 @@
       {
         "@id": "urn:fslmaths-tSgS8G2R",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
         "Used": [
           "bids::prefiltered_func_data_tempfilt"
@@ -392,7 +392,7 @@
       {
         "@id": "urn:fslmaths-AhdmqdXD",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
         "Used": [
           "bids::filtered_func_data"
@@ -401,7 +401,7 @@
       {
         "@id": "urn:rm-iMWORXue",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/bin/rm -rf prefiltered_func_data*",
         "Used": [
           "bids::prefiltered_func_data*"
@@ -410,39 +410,39 @@
       {
         "@id": "urn:makedire-u1ksLVof",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-o8YA0I8P",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
         ]
       },
       {
         "@id": "urn:makedire-Xs7pKLaA",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-ZTS63XMD",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
         ]
       },
       {
         "@id": "urn:filmgls-jaruefJt",
         "Label": "film_gls",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts",
         "Used": [
           "bids::design.con",
@@ -455,7 +455,7 @@
       {
         "@id": "urn:smoothes-s3pTDfVa",
         "Label": "smoothest",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 98 -m mask -r stats/res4d > stats/smoothness",
         "Used": [
           "bids::mask",
@@ -465,7 +465,7 @@
       {
         "@id": "urn:fslmaths-n2qLbaoB",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
         "Used": [
           "bids::mask",
@@ -475,14 +475,14 @@
       {
         "@id": "urn:echo-C1H4DAmG",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "echo 38352 > thresh_zstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-YBlEOore",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2",
         "Used": [
           "bids::mask",
@@ -492,14 +492,14 @@
       {
         "@id": "urn:echo-Y0j456v8",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "echo 38352 > thresh_zstat2.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-KJE4C0bu",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat3 -mas mask thresh_zstat3",
         "Used": [
           "bids::mask",
@@ -509,14 +509,14 @@
       {
         "@id": "urn:echo-qOxwR8Mo",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "echo 38352 > thresh_zstat3.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-E4jilCxt",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat4 -mas mask thresh_zstat4",
         "Used": [
           "bids::mask",
@@ -526,14 +526,14 @@
       {
         "@id": "urn:echo-3MOLIsgl",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "echo 38352 > thresh_zstat4.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-jPO5lIpX",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat5 -mas mask thresh_zstat5",
         "Used": [
           "bids::mask",
@@ -543,14 +543,14 @@
       {
         "@id": "urn:echo-dT2QGlOX",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "echo 38352 > thresh_zstat5.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-na7pDpFB",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat6 -mas mask thresh_zstat6",
         "Used": [
           "bids::mask",
@@ -560,14 +560,14 @@
       {
         "@id": "urn:echo-4PcOAySz",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "echo 38352 > thresh_zstat6.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-clta5DMl",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zfstat1 -mas mask thresh_zfstat1",
         "Used": [
           "bids::mask",
@@ -577,14 +577,14 @@
       {
         "@id": "urn:echo-qn9VFNxL",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "echo 38352 > thresh_zfstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-IhJIjkWO",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zfstat2 -mas mask thresh_zfstat2",
         "Used": [
           "bids::mask",
@@ -594,21 +594,21 @@
       {
         "@id": "urn:echo-6pG3ZhNt",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "echo 38352 > thresh_zfstat2.vol",
         "Used": []
       },
       {
         "@id": "urn:ptoz-oLMyRlmj",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-JM4FT4fe",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
         "Used": [
           "bids::stats/cope1",
@@ -618,7 +618,7 @@
       {
         "@id": "urn:cluster2-4gy3b7Dv",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
         "Used": [
           "bids::cluster_zstat1"
@@ -627,14 +627,14 @@
       {
         "@id": "urn:ptoz-93BR4ond",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-eZtqBxsh",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
         "Used": [
           "bids::stats/cope2",
@@ -644,7 +644,7 @@
       {
         "@id": "urn:cluster2-i3XEGcsV",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat2",
         "Used": [
           "bids::cluster_zstat2"
@@ -653,14 +653,14 @@
       {
         "@id": "urn:ptoz-O2QqU30d",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-f2RhlnID",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat3 -t 3.090232 --othresh=thresh_zstat3 -o cluster_mask_zstat3 --connectivity=26 --olmax=lmax_zstat3.txt --scalarname=Z --voxuncthresh -c stats/cope3 > cluster_zstat3.txt",
         "Used": [
           "bids::stats/cope3",
@@ -670,7 +670,7 @@
       {
         "@id": "urn:cluster2-eDt3axD4",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat3",
         "Used": [
           "bids::cluster_zstat3"
@@ -679,14 +679,14 @@
       {
         "@id": "urn:ptoz-dcSWGmgc",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-HDbgeLZt",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat4 -t 3.090232 --othresh=thresh_zstat4 -o cluster_mask_zstat4 --connectivity=26 --olmax=lmax_zstat4.txt --scalarname=Z --voxuncthresh -c stats/cope4 > cluster_zstat4.txt",
         "Used": [
           "bids::stats/cope4",
@@ -696,7 +696,7 @@
       {
         "@id": "urn:cluster2-FJInHTu7",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat4",
         "Used": [
           "bids::cluster_zstat4"
@@ -705,14 +705,14 @@
       {
         "@id": "urn:ptoz-PLRJwxPm",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-RlEhegMp",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat5 -t 3.090232 --othresh=thresh_zstat5 -o cluster_mask_zstat5 --connectivity=26 --olmax=lmax_zstat5.txt --scalarname=Z --voxuncthresh -c stats/cope5 > cluster_zstat5.txt",
         "Used": [
           "bids::stats/cope5",
@@ -722,7 +722,7 @@
       {
         "@id": "urn:cluster2-TS1gkeXO",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat5",
         "Used": [
           "bids::cluster_zstat5"
@@ -731,14 +731,14 @@
       {
         "@id": "urn:ptoz-jBncOG5N",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-ef7ehgcK",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat6 -t 3.090232 --othresh=thresh_zstat6 -o cluster_mask_zstat6 --connectivity=26 --olmax=lmax_zstat6.txt --scalarname=Z --voxuncthresh -c stats/cope6 > cluster_zstat6.txt",
         "Used": [
           "bids::stats/cope6",
@@ -748,7 +748,7 @@
       {
         "@id": "urn:cluster2-y8dpnA3u",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat6",
         "Used": [
           "bids::cluster_zstat6"
@@ -757,14 +757,14 @@
       {
         "@id": "urn:ptoz-ARjYR1mH",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-l1k6btTJ",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zfstat1 -t 3.090232 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z --voxuncthresh > cluster_zfstat1.txt",
         "Used": [
           "bids::thresh_zfstat1"
@@ -773,7 +773,7 @@
       {
         "@id": "urn:cluster2-LnaUBQbQ",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zfstat1",
         "Used": [
           "bids::cluster_zfstat1"
@@ -782,14 +782,14 @@
       {
         "@id": "urn:ptoz-FsDdgUhs",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-24hfHD40",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zfstat2 -t 3.090232 --othresh=thresh_zfstat2 -o cluster_mask_zfstat2 --connectivity=26 --olmax=lmax_zfstat2.txt --scalarname=Z --voxuncthresh > cluster_zfstat2.txt",
         "Used": [
           "bids::thresh_zfstat2"
@@ -798,7 +798,7 @@
       {
         "@id": "urn:cluster2-ZjVOQLu5",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zfstat2",
         "Used": [
           "bids::cluster_zfstat2"
@@ -807,7 +807,7 @@
       {
         "@id": "urn:fslstats-cKbjagRJ",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat1"
@@ -816,7 +816,7 @@
       {
         "@id": "urn:fslstats-4PLXFkqr",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat2 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat2"
@@ -825,7 +825,7 @@
       {
         "@id": "urn:fslstats-ix2R7uZH",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat3 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat3"
@@ -834,7 +834,7 @@
       {
         "@id": "urn:fslstats-okXD7eIF",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat4 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat4"
@@ -843,7 +843,7 @@
       {
         "@id": "urn:fslstats-zrf3wrdd",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat5 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat5"
@@ -852,7 +852,7 @@
       {
         "@id": "urn:fslstats-avQocUer",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat6 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat6"
@@ -861,7 +861,7 @@
       {
         "@id": "urn:fslstats-uRABuqdu",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zfstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zfstat1"
@@ -870,7 +870,7 @@
       {
         "@id": "urn:fslstats-JrUc32yN",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zfstat2 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zfstat2"
@@ -879,14 +879,14 @@
       {
         "@id": "urn:overlay-X86Egc5m",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090239 7.525257 rendered_thresh_zstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-TrwKgGLm",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
         "Used": [
           "bids::rendered_thresh_zstat1"
@@ -895,7 +895,7 @@
       {
         "@id": "urn:cp-qc6GeWl1",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
         "Used": [
           "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
@@ -904,14 +904,14 @@
       {
         "@id": "urn:overlay-D6oIJzxo",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat2 3.090239 7.525257 rendered_thresh_zstat2",
         "Used": []
       },
       {
         "@id": "urn:slicer-nhLfQ7et",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat2 -A 750 rendered_thresh_zstat2.png",
         "Used": [
           "bids::rendered_thresh_zstat2"
@@ -920,14 +920,14 @@
       {
         "@id": "urn:overlay-HlWyBj4y",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat3 3.090239 7.525257 rendered_thresh_zstat3",
         "Used": []
       },
       {
         "@id": "urn:slicer-kMPYw070",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat3 -A 750 rendered_thresh_zstat3.png",
         "Used": [
           "bids::rendered_thresh_zstat3"
@@ -936,14 +936,14 @@
       {
         "@id": "urn:overlay-OJxhPeRc",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat4 3.090239 7.525257 rendered_thresh_zstat4",
         "Used": []
       },
       {
         "@id": "urn:slicer-bbTTWKvI",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat4 -A 750 rendered_thresh_zstat4.png",
         "Used": [
           "bids::rendered_thresh_zstat4"
@@ -952,14 +952,14 @@
       {
         "@id": "urn:overlay-IzdEsoLz",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat5 3.090239 7.525257 rendered_thresh_zstat5",
         "Used": []
       },
       {
         "@id": "urn:slicer-2HP5rM9A",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat5 -A 750 rendered_thresh_zstat5.png",
         "Used": [
           "bids::rendered_thresh_zstat5"
@@ -968,14 +968,14 @@
       {
         "@id": "urn:overlay-LtsDrMgV",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat6 3.090239 7.525257 rendered_thresh_zstat6",
         "Used": []
       },
       {
         "@id": "urn:slicer-zRB9nLoG",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat6 -A 750 rendered_thresh_zstat6.png",
         "Used": [
           "bids::rendered_thresh_zstat6"
@@ -984,14 +984,14 @@
       {
         "@id": "urn:overlay-q6aDo9iF",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zfstat1 3.090239 7.525257 rendered_thresh_zfstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-nXkgAbpB",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zfstat1 -A 750 rendered_thresh_zfstat1.png",
         "Used": [
           "bids::rendered_thresh_zfstat1"
@@ -1000,14 +1000,14 @@
       {
         "@id": "urn:overlay-0BQ508sk",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zfstat2 3.090239 7.525257 rendered_thresh_zfstat2",
         "Used": []
       },
       {
         "@id": "urn:slicer-L7n6t8V4",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zfstat2 -A 750 rendered_thresh_zfstat2.png",
         "Used": [
           "bids::rendered_thresh_zfstat2"
@@ -1016,25 +1016,25 @@
       {
         "@id": "urn:makedire-aJnJKcVD",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "mkdir -p tsplot",
         "Used": []
       },
       {
         "@id": "urn:tsplot-omt5Es95",
         "Label": "tsplot",
-        "AssociatedWith": "urn:urn:fsl-Ld1arblU",
+        "AssociatedWith": "urn:fsl-Ld1arblU",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
         "Used": []
       }
     ],
     "Entities": [
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "Label": "sub-01_task-tonecounting_bold",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "digest": {
-          "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
+          "sha256": "33501604ae140e58832facff473a9578d5a549403bdbec53107d2b3eaab898ee"
         }
       },
       {
@@ -1064,11 +1064,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "Label": "sub-01_T1w_brain",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "digest": {
-          "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
+          "sha256": "8f1ae7ba69869c79b2cc5a83ce4ca24a7d666187256c2aa4d61a952b903b05b0"
         }
       },
       {
@@ -1104,11 +1104,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "Label": "sub-01_T1w",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "digest": {
-          "sha256": "3be6c69338e200d2a286a56cd9a0030539cf50201f412c910ade833e18354d27"
+          "sha256": "8dd4893a9c9500ce8c516f1a9845abf887087d00c2c47fc3524a17d924e78acf"
         }
       },
       {
@@ -1668,11 +1668,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "Label": "sub-01_tone_counting.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "digest": {
-          "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+          "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
         }
       },
       {
@@ -1691,11 +1691,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "Label": "sub-01_tone_counting_probe.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "digest": {
-          "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+          "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
         }
       },
       {
diff --git a/examples/from_parsers/fsl/fsl_gamma_basis_report_log.png b/examples/from_parsers/fsl/fsl_gamma_basis_report_log.png
index 32d8fe1f..45542a08 100644
Binary files a/examples/from_parsers/fsl/fsl_gamma_basis_report_log.png and b/examples/from_parsers/fsl/fsl_gamma_basis_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_gaussian_report_log.html b/examples/from_parsers/fsl/fsl_gaussian_report_log.html
index 614e75ee..18b4e270 100644
--- a/examples/from_parsers/fsl/fsl_gaussian_report_log.html
+++ b/examples/from_parsers/fsl/fsl_gaussian_report_log.html
@@ -35,20 +35,20 @@ 
Progress Report / Log

 326915
Initialisation
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
 Total original volumes = 104
 
 /usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
 
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/example_func.nii.gz  -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/example_func.nii.gz  -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
 Option -F ( FEAT version parameter ) selected with  argument "6.00"
 Option -d ( output directory ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat"
 Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/logs/feat2_pre"
 Option -R ( html unwarping report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_unwarp.html"
 Option -r ( html registration report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_reg.html"
 Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with  argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
 Option -w ( highres dof ) selected with  argument "BBR"
 Option -x ( highres search ) selected with  argument "90"
 Option -s ( standard image ) selected with  argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ 
Progress Report / Log

 /bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/reg
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
 
 did not find file: example_func2highres.mat. Generating transform.
 
@@ -128,9 +128,9 @@ 
Progress Report / Log

 /bin/rm -rf prefiltered_func_data*
Stats
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
 
 /usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con  
 Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_gaussian_report_log.jsonld b/examples/from_parsers/fsl/fsl_gaussian_report_log.jsonld
index 980579ac..272584db 100644
--- a/examples/from_parsers/fsl/fsl_gaussian_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_gaussian_report_log.jsonld
@@ -15,16 +15,16 @@
       {
         "@id": "urn:fslmaths-c40EgfsR",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold"
+          "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
         ]
       },
       {
         "@id": "urn:fslroi-BT8jJF5g",
         "Label": "fslroi",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
         "Used": [
           "bids::prefiltered_func_data"
@@ -33,43 +33,43 @@
       {
         "@id": "urn:mainfeat-tikUw4Yc",
         "Label": "mainfeatreg",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
           "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/example_func.nii.gz",
-          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
+          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:makedire-4q5WpPKB",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/reg",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-aZ0oYGeF",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:fslmaths-sOsEVkdS",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
         ]
       },
       {
         "@id": "urn:epireg-NXkPO3x2",
         "Label": "epi_reg",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
         "Used": [
           "bids::example_func",
@@ -80,7 +80,7 @@
       {
         "@id": "urn:convertx-a0Vf86Tw",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
         "Used": [
           "bids::example_func2highres.mat"
@@ -89,7 +89,7 @@
       {
         "@id": "urn:slicer-wUSva9lv",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -99,7 +99,7 @@
       {
         "@id": "urn:pngappen-fbEh7nJR",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
         "Used": [
           "bids::sla.png",
@@ -119,7 +119,7 @@
       {
         "@id": "urn:slicer-xGVl3dhc",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -129,7 +129,7 @@
       {
         "@id": "urn:pngappen-C0NWHKHZ",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
         "Used": [
           "bids::sla.png",
@@ -149,7 +149,7 @@
       {
         "@id": "urn:pngappen-JPfO5AdL",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
         "Used": [
           "bids::example_func2highres1.png",
@@ -159,7 +159,7 @@
       {
         "@id": "urn:rm-rHzvu8Pm",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/bin/rm -f sl?.png example_func2highres2.png",
         "Used": [
           "bids::example_func2highres2.png",
@@ -169,7 +169,7 @@
       {
         "@id": "urn:rm-oZgZdvYj",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/bin/rm example_func2highres1.png",
         "Used": [
           "bids::example_func2highres1.png"
@@ -178,7 +178,7 @@
       {
         "@id": "urn:mcflirt-9iSyFXGh",
         "Label": "mcflirt",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
         "Used": [
           "bids::prefiltered_func_data"
@@ -187,14 +187,14 @@
       {
         "@id": "urn:makedire-VSGQwlhb",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/bin/mkdir -p mc",
         "Used": []
       },
       {
         "@id": "urn:mv-a1clMa7z",
         "Label": "mv",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
         "Used": [
           "bids::prefiltered_func_data_mcf.mat",
@@ -208,7 +208,7 @@
       {
         "@id": "urn:fsltsplo-0AK42d62",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -217,7 +217,7 @@
       {
         "@id": "urn:fsltsplo-D2384XzX",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -226,7 +226,7 @@
       {
         "@id": "urn:fsltsplo-oFlR7AKx",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
         "Used": [
           "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
@@ -235,7 +235,7 @@
       {
         "@id": "urn:fslmaths-t17JOD8i",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -244,7 +244,7 @@
       {
         "@id": "urn:bet2-RLQM3p76",
         "Label": "bet2",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
         "Used": [
           "bids::mean_func"
@@ -253,7 +253,7 @@
       {
         "@id": "urn:immv-gwbMDqAA",
         "Label": "immv",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
         "Used": [
           "bids::mask_mask"
@@ -262,7 +262,7 @@
       {
         "@id": "urn:fslmaths-t2aHVzoS",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
         "Used": [
           "bids::mask",
@@ -272,7 +272,7 @@
       {
         "@id": "urn:fslstats-iN2bHXNs",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -281,7 +281,7 @@
       {
         "@id": "urn:fslmaths-8BSfMD2j",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -290,7 +290,7 @@
       {
         "@id": "urn:fslstats-24U2euPv",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -299,7 +299,7 @@
       {
         "@id": "urn:fslmaths-9SKMjmJH",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
         "Used": [
           "bids::mask"
@@ -308,7 +308,7 @@
       {
         "@id": "urn:fslmaths-LT5qFn1b",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
         "Used": [
           "bids::mask",
@@ -318,7 +318,7 @@
       {
         "@id": "urn:fslmaths-w1OidnBM",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -327,7 +327,7 @@
       {
         "@id": "urn:susan-6PHMBnDq",
         "Label": "susan",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -336,7 +336,7 @@
       {
         "@id": "urn:fslmaths-AtC5PthI",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
         "Used": [
           "bids::mask",
@@ -346,7 +346,7 @@
       {
         "@id": "urn:fslmaths-2DRcnfmM",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
         "Used": [
           "bids::prefiltered_func_data_smooth"
@@ -355,7 +355,7 @@
       {
         "@id": "urn:fslmaths-6z0BIKxs",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
         "Used": [
           "bids::prefiltered_func_data_intnorm"
@@ -364,7 +364,7 @@
       {
         "@id": "urn:fslmaths-mTFxCyoQ",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
         "Used": [
           "bids::prefiltered_func_data_intnorm",
@@ -374,7 +374,7 @@
       {
         "@id": "urn:imrm-OTEd4jdX",
         "Label": "imrm",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
         "Used": [
           "bids::tempMean"
@@ -383,7 +383,7 @@
       {
         "@id": "urn:fslmaths-vC7x32pX",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
         "Used": [
           "bids::prefiltered_func_data_tempfilt"
@@ -392,7 +392,7 @@
       {
         "@id": "urn:fslmaths-htzC3QnL",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
         "Used": [
           "bids::filtered_func_data"
@@ -401,7 +401,7 @@
       {
         "@id": "urn:rm-6K7QbTxg",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/bin/rm -rf prefiltered_func_data*",
         "Used": [
           "bids::prefiltered_func_data*"
@@ -410,39 +410,39 @@
       {
         "@id": "urn:makedire-ddWcoA2E",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-pdQxZQAo",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
         ]
       },
       {
         "@id": "urn:makedire-MvIqyL0b",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-8AM2FS0p",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
         ]
       },
       {
         "@id": "urn:filmgls-J1GidVef",
         "Label": "film_gls",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
         "Used": [
           "bids::design.con",
@@ -454,7 +454,7 @@
       {
         "@id": "urn:smoothes-VGJzmzTv",
         "Label": "smoothest",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
         "Used": [
           "bids::mask",
@@ -464,7 +464,7 @@
       {
         "@id": "urn:fslmaths-K3fmTMnl",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
         "Used": [
           "bids::mask",
@@ -474,14 +474,14 @@
       {
         "@id": "urn:echo-jVwSVYtg",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "echo 38352 > thresh_zstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-u2VVZ7tv",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2",
         "Used": [
           "bids::mask",
@@ -491,21 +491,21 @@
       {
         "@id": "urn:echo-HA8f2GFE",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "echo 38352 > thresh_zstat2.vol",
         "Used": []
       },
       {
         "@id": "urn:ptoz-bRHfLZiR",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-1qGG2rFS",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
         "Used": [
           "bids::stats/cope1",
@@ -515,7 +515,7 @@
       {
         "@id": "urn:cluster2-AbLpC1LT",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
         "Used": [
           "bids::cluster_zstat1"
@@ -524,14 +524,14 @@
       {
         "@id": "urn:ptoz-oUD5u0y9",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-pIRYl9sN",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
         "Used": [
           "bids::stats/cope2",
@@ -541,7 +541,7 @@
       {
         "@id": "urn:cluster2-iHy49U0U",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat2",
         "Used": [
           "bids::cluster_zstat2"
@@ -550,7 +550,7 @@
       {
         "@id": "urn:fslstats-68QurBZC",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat1"
@@ -559,7 +559,7 @@
       {
         "@id": "urn:fslstats-KGQicDB8",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat2 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat2"
@@ -568,14 +568,14 @@
       {
         "@id": "urn:overlay-K259t49U",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090259 7.129133 rendered_thresh_zstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-4gEMZuYv",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
         "Used": [
           "bids::rendered_thresh_zstat1"
@@ -584,7 +584,7 @@
       {
         "@id": "urn:cp-klo2wOQo",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
         "Used": [
           "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
@@ -593,14 +593,14 @@
       {
         "@id": "urn:overlay-HXXKsGWM",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat2 3.090259 7.129133 rendered_thresh_zstat2",
         "Used": []
       },
       {
         "@id": "urn:slicer-lHD16dgj",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat2 -A 750 rendered_thresh_zstat2.png",
         "Used": [
           "bids::rendered_thresh_zstat2"
@@ -609,25 +609,25 @@
       {
         "@id": "urn:makedire-wmAJGONO",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "mkdir -p tsplot",
         "Used": []
       },
       {
         "@id": "urn:tsplot-a71eZBwo",
         "Label": "tsplot",
-        "AssociatedWith": "urn:urn:fsl-LlDJMBmv",
+        "AssociatedWith": "urn:fsl-LlDJMBmv",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
         "Used": []
       }
     ],
     "Entities": [
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "Label": "sub-01_task-tonecounting_bold",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "digest": {
-          "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
+          "sha256": "33501604ae140e58832facff473a9578d5a549403bdbec53107d2b3eaab898ee"
         }
       },
       {
@@ -657,11 +657,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "Label": "sub-01_T1w_brain",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "digest": {
-          "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
+          "sha256": "8f1ae7ba69869c79b2cc5a83ce4ca24a7d666187256c2aa4d61a952b903b05b0"
         }
       },
       {
@@ -697,11 +697,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "Label": "sub-01_T1w",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "digest": {
-          "sha256": "3be6c69338e200d2a286a56cd9a0030539cf50201f412c910ade833e18354d27"
+          "sha256": "8dd4893a9c9500ce8c516f1a9845abf887087d00c2c47fc3524a17d924e78acf"
         }
       },
       {
@@ -1261,11 +1261,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "Label": "sub-01_tone_counting.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "digest": {
-          "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+          "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
         }
       },
       {
@@ -1284,11 +1284,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "Label": "sub-01_tone_counting_probe.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "digest": {
-          "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+          "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
         }
       },
       {
diff --git a/examples/from_parsers/fsl/fsl_gaussian_report_log.png b/examples/from_parsers/fsl/fsl_gaussian_report_log.png
index b07fdcda..485bb37e 100644
Binary files a/examples/from_parsers/fsl/fsl_gaussian_report_log.png and b/examples/from_parsers/fsl/fsl_gaussian_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_group_btw_report_log.jsonld b/examples/from_parsers/fsl/fsl_group_btw_report_log.jsonld
index 3649bdeb..0c1695fb 100644
--- a/examples/from_parsers/fsl/fsl_group_btw_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_group_btw_report_log.jsonld
@@ -15,112 +15,112 @@
       {
         "@id": "urn:featrega-taLbN7kR",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-Ld42ZjUi",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-ctJNOxTa",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-zLqqWQIB",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-ZhTHHow9",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-IFdSMxbu",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-GFZvesWK",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-nTql8x5v",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-DSQXA5UI",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-Dv6nh1jv",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-8OHPWu0G",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-M6g9zubD",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-c4xyEscj",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-bhf1mi9x",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat",
         "Used": []
       },
       {
         "@id": "urn:fslmerge-EKkeXMxH",
         "Label": "fslmerge",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t bg_image /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/reg/highres",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-xAVI0ILB",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths bg_image -inm 1000 -Tmean bg_image -odt float",
         "Used": [
           "bids::bg_image"
@@ -129,21 +129,21 @@
       {
         "@id": "urn:fslmerge-2F6G7rII",
         "Label": "fslmerge",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask",
         "Used": []
       },
       {
         "@id": "urn:makedire-74G7oRAv",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "mkdir -p inputreg",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-GzWzykG0",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ../mask -mul 14 -Tmean masksum -odt short",
         "Used": [
           "bids::mask"
@@ -152,7 +152,7 @@
       {
         "@id": "urn:fslmaths-8xYEeypD",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -thr 14 -add masksum masksum",
         "Used": [
           "bids::masksum"
@@ -161,14 +161,14 @@
       {
         "@id": "urn:overlay-ncDkuQ1G",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 0 0 -c ../bg_image -a masksum 0.9 28 masksum_overlay",
         "Used": []
       },
       {
         "@id": "urn:slicer-uWTpbMIs",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer masksum_overlay -S 2 750 masksum_overlay.png",
         "Used": [
           "bids::masksum_overlay"
@@ -177,7 +177,7 @@
       {
         "@id": "urn:fslmaths-MqM50oOn",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -mul 0 maskunique",
         "Used": [
           "bids::masksum"
@@ -186,7 +186,7 @@
       {
         "@id": "urn:fslmaths-ttzGVzPh",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask -mul -1 -add 1 -mul 1 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask",
@@ -196,7 +196,7 @@
       {
         "@id": "urn:fslmaths-ZzO3yLZn",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask -mul -1 -add 1 -mul 2 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask",
@@ -206,7 +206,7 @@
       {
         "@id": "urn:fslmaths-rgVzb0P7",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask -mul -1 -add 1 -mul 3 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask",
@@ -216,7 +216,7 @@
       {
         "@id": "urn:fslmaths-jjTUJlby",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask -mul -1 -add 1 -mul 4 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask",
@@ -226,7 +226,7 @@
       {
         "@id": "urn:fslmaths-CICGEO6f",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask -mul -1 -add 1 -mul 5 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask",
@@ -236,7 +236,7 @@
       {
         "@id": "urn:fslmaths-03CGMMoO",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask -mul -1 -add 1 -mul 6 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask",
@@ -246,7 +246,7 @@
       {
         "@id": "urn:fslmaths-UHAOAQx9",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask -mul -1 -add 1 -mul 7 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask",
@@ -256,7 +256,7 @@
       {
         "@id": "urn:fslmaths-z870NCtH",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask -mul -1 -add 1 -mul 8 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask",
@@ -266,7 +266,7 @@
       {
         "@id": "urn:fslmaths-1RPdsfVd",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask -mul -1 -add 1 -mul 9 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask",
@@ -276,7 +276,7 @@
       {
         "@id": "urn:fslmaths-F4G8zuWD",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask -mul -1 -add 1 -mul 10 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask",
@@ -286,7 +286,7 @@
       {
         "@id": "urn:fslmaths-LXmFBqUt",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask -mul -1 -add 1 -mul 11 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask",
@@ -296,7 +296,7 @@
       {
         "@id": "urn:fslmaths-9a4825SK",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask -mul -1 -add 1 -mul 12 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask",
@@ -306,7 +306,7 @@
       {
         "@id": "urn:fslmaths-lhUJMGSX",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask -mul -1 -add 1 -mul 13 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask",
@@ -316,7 +316,7 @@
       {
         "@id": "urn:fslmaths-8d7sRdMJ",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask -mul -1 -add 1 -mul 14 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask",
@@ -326,7 +326,7 @@
       {
         "@id": "urn:fslmaths-PbaO1I2Q",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -thr 13 -uthr 13 -bin -mul maskunique maskunique",
         "Used": [
           "bids::masksum",
@@ -336,14 +336,14 @@
       {
         "@id": "urn:overlay-54oJrhOb",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 0 0 ../bg_image -a maskunique 0.9 14 maskunique_overlay",
         "Used": []
       },
       {
         "@id": "urn:slicer-NsXw0tcg",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer maskunique_overlay -S 2 750 maskunique_overlay.png",
         "Used": [
           "bids::maskunique_overlay"
@@ -352,7 +352,7 @@
       {
         "@id": "urn:cp-ncFsCIyB",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
         "Used": [
           "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
@@ -361,7 +361,7 @@
       {
         "@id": "urn:fslmaths-gHoNgo4e",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -Tmin mask",
         "Used": [
           "bids::mask"
@@ -370,14 +370,14 @@
       {
         "@id": "urn:fslmerge-bsJhhObl",
         "Label": "fslmerge",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mean_func",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-hDOBFMeB",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mean_func -Tmean mean_func",
         "Used": [
           "bids::mean_func"
@@ -386,14 +386,14 @@
       {
         "@id": "urn:fslmerge-MN6jqooj",
         "Label": "fslmerge",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/cope1",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-htbOK1TX",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths cope1 -mas mask cope1",
         "Used": [
           "bids::cope1",
@@ -403,21 +403,21 @@
       {
         "@id": "urn:printf-D4bWARwN",
         "Label": "printf",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "printf '1.01544485714 ' >> design.lcon",
         "Used": []
       },
       {
         "@id": "urn:fslmerge-gRKzzuEF",
         "Label": "fslmerge",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/varcope1",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-FBNBf98S",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths varcope1 -mas mask varcope1",
         "Used": [
           "bids::mask",
@@ -427,7 +427,7 @@
       {
         "@id": "urn:printf-Q7ZYIaMG",
         "Label": "printf",
-        "AssociatedWith": "urn:urn:fsl-AZ1kWvHX",
+        "AssociatedWith": "urn:fsl-AZ1kWvHX",
         "Command": "printf '1 ' >> design.lcon",
         "Used": []
       }
diff --git a/examples/from_parsers/fsl/fsl_group_btw_report_log.png b/examples/from_parsers/fsl/fsl_group_btw_report_log.png
index cecb64f4..b1cce7c7 100644
Binary files a/examples/from_parsers/fsl/fsl_group_btw_report_log.png and b/examples/from_parsers/fsl/fsl_group_btw_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_group_ols_report_log.jsonld b/examples/from_parsers/fsl/fsl_group_ols_report_log.jsonld
index 209f0e7d..05237363 100644
--- a/examples/from_parsers/fsl/fsl_group_ols_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_group_ols_report_log.jsonld
@@ -15,112 +15,112 @@
       {
         "@id": "urn:featrega-kz9bS7ct",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-TnrpKqyu",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-vJGXiMfS",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-OZJIEtiK",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-6E1h8lsj",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-SnnIOQpI",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-Ir2BR6NO",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-wtZpV2I2",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-6Wd3Jl0c",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-0lNPdRUd",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-abHcHtuV",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-XEbqxtbN",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-pjZKLpPX",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-0G7B7ui3",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat",
         "Used": []
       },
       {
         "@id": "urn:fslmerge-76xgoM34",
         "Label": "fslmerge",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t bg_image /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/reg/highres",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-VWKPlcrS",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths bg_image -inm 1000 -Tmean bg_image -odt float",
         "Used": [
           "bids::bg_image"
@@ -129,21 +129,21 @@
       {
         "@id": "urn:fslmerge-a32yvqXQ",
         "Label": "fslmerge",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask",
         "Used": []
       },
       {
         "@id": "urn:makedire-k9baSZKA",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "mkdir -p inputreg",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-JgSWxigJ",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ../mask -mul 14 -Tmean masksum -odt short",
         "Used": [
           "bids::mask"
@@ -152,7 +152,7 @@
       {
         "@id": "urn:fslmaths-7T5AFccE",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -thr 14 -add masksum masksum",
         "Used": [
           "bids::masksum"
@@ -161,14 +161,14 @@
       {
         "@id": "urn:overlay-tYpJlwJl",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 0 0 -c ../bg_image -a masksum 0.9 28 masksum_overlay",
         "Used": []
       },
       {
         "@id": "urn:slicer-tJz5uoAI",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer masksum_overlay -S 2 750 masksum_overlay.png",
         "Used": [
           "bids::masksum_overlay"
@@ -177,7 +177,7 @@
       {
         "@id": "urn:fslmaths-nMJdYgWk",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -mul 0 maskunique",
         "Used": [
           "bids::masksum"
@@ -186,7 +186,7 @@
       {
         "@id": "urn:fslmaths-kWswirfI",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask -mul -1 -add 1 -mul 1 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask",
@@ -196,7 +196,7 @@
       {
         "@id": "urn:fslmaths-ROT1Bibi",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask -mul -1 -add 1 -mul 2 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask",
@@ -206,7 +206,7 @@
       {
         "@id": "urn:fslmaths-wFlYFWp9",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask -mul -1 -add 1 -mul 3 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask",
@@ -216,7 +216,7 @@
       {
         "@id": "urn:fslmaths-d498SwbU",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask -mul -1 -add 1 -mul 4 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask",
@@ -226,7 +226,7 @@
       {
         "@id": "urn:fslmaths-4fXwGyda",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask -mul -1 -add 1 -mul 5 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask",
@@ -236,7 +236,7 @@
       {
         "@id": "urn:fslmaths-1UZofUSb",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask -mul -1 -add 1 -mul 6 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask",
@@ -246,7 +246,7 @@
       {
         "@id": "urn:fslmaths-BIKlZwNp",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask -mul -1 -add 1 -mul 7 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask",
@@ -256,7 +256,7 @@
       {
         "@id": "urn:fslmaths-hiKmAIJI",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask -mul -1 -add 1 -mul 8 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask",
@@ -266,7 +266,7 @@
       {
         "@id": "urn:fslmaths-eywe19Yu",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask -mul -1 -add 1 -mul 9 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask",
@@ -276,7 +276,7 @@
       {
         "@id": "urn:fslmaths-OlQZMlYG",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask -mul -1 -add 1 -mul 10 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask",
@@ -286,7 +286,7 @@
       {
         "@id": "urn:fslmaths-YRZxT8UX",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask -mul -1 -add 1 -mul 11 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask",
@@ -296,7 +296,7 @@
       {
         "@id": "urn:fslmaths-7JPxpAVs",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask -mul -1 -add 1 -mul 12 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask",
@@ -306,7 +306,7 @@
       {
         "@id": "urn:fslmaths-w8m3u8MZ",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask -mul -1 -add 1 -mul 13 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask",
@@ -316,7 +316,7 @@
       {
         "@id": "urn:fslmaths-tMxDAUl5",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask -mul -1 -add 1 -mul 14 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask",
@@ -326,7 +326,7 @@
       {
         "@id": "urn:fslmaths-QmSHD91y",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -thr 13 -uthr 13 -bin -mul maskunique maskunique",
         "Used": [
           "bids::masksum",
@@ -336,14 +336,14 @@
       {
         "@id": "urn:overlay-4KfLztQ2",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 0 0 ../bg_image -a maskunique 0.9 14 maskunique_overlay",
         "Used": []
       },
       {
         "@id": "urn:slicer-kx0rowJX",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer maskunique_overlay -S 2 750 maskunique_overlay.png",
         "Used": [
           "bids::maskunique_overlay"
@@ -352,7 +352,7 @@
       {
         "@id": "urn:cp-YYsBl9eP",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
         "Used": [
           "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
@@ -361,7 +361,7 @@
       {
         "@id": "urn:fslmaths-3nby5gEF",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -Tmin mask",
         "Used": [
           "bids::mask"
@@ -370,14 +370,14 @@
       {
         "@id": "urn:fslmerge-w5YB5TQG",
         "Label": "fslmerge",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mean_func",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-OflGMfQe",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mean_func -Tmean mean_func",
         "Used": [
           "bids::mean_func"
@@ -386,14 +386,14 @@
       {
         "@id": "urn:fslmerge-JPXcP2c9",
         "Label": "fslmerge",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/cope1",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-xJH7mFXk",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths cope1 -mas mask cope1",
         "Used": [
           "bids::cope1",
@@ -403,21 +403,21 @@
       {
         "@id": "urn:printf-pPXCjAD7",
         "Label": "printf",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "printf '1.01544485714 ' >> design.lcon",
         "Used": []
       },
       {
         "@id": "urn:fslmerge-Cn8eCaMa",
         "Label": "fslmerge",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/varcope1",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-5HCQtQpR",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths varcope1 -mas mask varcope1",
         "Used": [
           "bids::mask",
@@ -427,7 +427,7 @@
       {
         "@id": "urn:printf-eE9dcaBI",
         "Label": "printf",
-        "AssociatedWith": "urn:urn:fsl-pruTgA5U",
+        "AssociatedWith": "urn:fsl-pruTgA5U",
         "Command": "printf '1 ' >> design.lcon",
         "Used": []
       }
diff --git a/examples/from_parsers/fsl/fsl_group_ols_report_log.png b/examples/from_parsers/fsl/fsl_group_ols_report_log.png
index 7a09ff25..9925d3fe 100644
Binary files a/examples/from_parsers/fsl/fsl_group_ols_report_log.png and b/examples/from_parsers/fsl/fsl_group_ols_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_group_wls_report_log.jsonld b/examples/from_parsers/fsl/fsl_group_wls_report_log.jsonld
index 786fc810..eac776c1 100644
--- a/examples/from_parsers/fsl/fsl_group_wls_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_group_wls_report_log.jsonld
@@ -15,112 +15,112 @@
       {
         "@id": "urn:featrega-1VWFcHZJ",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-l2PZn3tx",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-68UxMqVW",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-TJgn2wiK",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-U8wPwuXh",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-QmOTvPx0",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-giWl9DQL",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-EjbAIU63",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-7OqeynKv",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-3bZUXKTc",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-V6R1y3TZ",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-WUOZmSnB",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-MBjTRT8e",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat",
         "Used": []
       },
       {
         "@id": "urn:featrega-MdQ3FwfD",
         "Label": "featregapply",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/featregapply /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat",
         "Used": []
       },
       {
         "@id": "urn:fslmerge-9tudhZgO",
         "Label": "fslmerge",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t bg_image /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/reg/highres /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/reg/highres",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-EfydSzFo",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths bg_image -inm 1000 -Tmean bg_image -odt float",
         "Used": [
           "bids::bg_image"
@@ -129,21 +129,21 @@
       {
         "@id": "urn:fslmerge-h4I2cGx2",
         "Label": "fslmerge",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask",
         "Used": []
       },
       {
         "@id": "urn:makedire-VqwgIjpp",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "mkdir -p inputreg",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-o6nIOt9I",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ../mask -mul 14 -Tmean masksum -odt short",
         "Used": [
           "bids::mask"
@@ -152,7 +152,7 @@
       {
         "@id": "urn:fslmaths-25TZgJ2Z",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -thr 14 -add masksum masksum",
         "Used": [
           "bids::masksum"
@@ -161,14 +161,14 @@
       {
         "@id": "urn:overlay-5da3Upvh",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 0 0 -c ../bg_image -a masksum 0.9 28 masksum_overlay",
         "Used": []
       },
       {
         "@id": "urn:slicer-KcGy37CS",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer masksum_overlay -S 2 750 masksum_overlay.png",
         "Used": [
           "bids::masksum_overlay"
@@ -177,7 +177,7 @@
       {
         "@id": "urn:fslmaths-WYRQH8E1",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -mul 0 maskunique",
         "Used": [
           "bids::masksum"
@@ -186,7 +186,7 @@
       {
         "@id": "urn:fslmaths-PshObKmH",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask -mul -1 -add 1 -mul 1 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask",
@@ -196,7 +196,7 @@
       {
         "@id": "urn:fslmaths-JtVZ3Vhe",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask -mul -1 -add 1 -mul 2 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask",
@@ -206,7 +206,7 @@
       {
         "@id": "urn:fslmaths-P5Zg83HH",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask -mul -1 -add 1 -mul 3 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask",
@@ -216,7 +216,7 @@
       {
         "@id": "urn:fslmaths-6PpzikfW",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask -mul -1 -add 1 -mul 4 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask",
@@ -226,7 +226,7 @@
       {
         "@id": "urn:fslmaths-EbbCciPS",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask -mul -1 -add 1 -mul 5 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask",
@@ -236,7 +236,7 @@
       {
         "@id": "urn:fslmaths-Rd0FlVhM",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask -mul -1 -add 1 -mul 6 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask",
@@ -246,7 +246,7 @@
       {
         "@id": "urn:fslmaths-3QP8o8aF",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask -mul -1 -add 1 -mul 7 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask",
@@ -256,7 +256,7 @@
       {
         "@id": "urn:fslmaths-7UM4M7c6",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask -mul -1 -add 1 -mul 8 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask",
@@ -266,7 +266,7 @@
       {
         "@id": "urn:fslmaths-eDg3oFMF",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask -mul -1 -add 1 -mul 9 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask",
@@ -276,7 +276,7 @@
       {
         "@id": "urn:fslmaths-YvJZwpMz",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask -mul -1 -add 1 -mul 10 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask",
@@ -286,7 +286,7 @@
       {
         "@id": "urn:fslmaths-JTvgDKAY",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask -mul -1 -add 1 -mul 11 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask",
@@ -296,7 +296,7 @@
       {
         "@id": "urn:fslmaths-5B96iEFY",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask -mul -1 -add 1 -mul 12 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask",
@@ -306,7 +306,7 @@
       {
         "@id": "urn:fslmaths-NfGTyrav",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask -mul -1 -add 1 -mul 13 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask",
@@ -316,7 +316,7 @@
       {
         "@id": "urn:fslmaths-RnWwY7GC",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask -mul -1 -add 1 -mul 14 -add maskunique maskunique",
         "Used": [
           "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask",
@@ -326,7 +326,7 @@
       {
         "@id": "urn:fslmaths-o40Hcz8k",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -thr 13 -uthr 13 -bin -mul maskunique maskunique",
         "Used": [
           "bids::masksum",
@@ -336,14 +336,14 @@
       {
         "@id": "urn:overlay-f62oQ1Jq",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 0 0 ../bg_image -a maskunique 0.9 14 maskunique_overlay",
         "Used": []
       },
       {
         "@id": "urn:slicer-E5l7qDA8",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer maskunique_overlay -S 2 750 maskunique_overlay.png",
         "Used": [
           "bids::maskunique_overlay"
@@ -352,7 +352,7 @@
       {
         "@id": "urn:cp-tcMlGCoq",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
         "Used": [
           "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
@@ -361,7 +361,7 @@
       {
         "@id": "urn:fslmaths-x0pisi83",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -Tmin mask",
         "Used": [
           "bids::mask"
@@ -370,14 +370,14 @@
       {
         "@id": "urn:fslmerge-HWC7MrJw",
         "Label": "fslmerge",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mean_func",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-HK0LP66D",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mean_func -Tmean mean_func",
         "Used": [
           "bids::mean_func"
@@ -386,14 +386,14 @@
       {
         "@id": "urn:fslmerge-nVaqQIOY",
         "Label": "fslmerge",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/cope1",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-IXvSjYAX",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths cope1 -mas mask cope1",
         "Used": [
           "bids::cope1",
@@ -403,21 +403,21 @@
       {
         "@id": "urn:printf-lMEA45Fd",
         "Label": "printf",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "printf '1.01544485714 ' >> design.lcon",
         "Used": []
       },
       {
         "@id": "urn:fslmerge-LaUwdWrw",
         "Label": "fslmerge",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/varcope1",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-OPfMFJsc",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths varcope1 -mas mask varcope1",
         "Used": [
           "bids::mask",
@@ -427,7 +427,7 @@
       {
         "@id": "urn:printf-eQIlmExq",
         "Label": "printf",
-        "AssociatedWith": "urn:urn:fsl-Qv0D3pNB",
+        "AssociatedWith": "urn:fsl-Qv0D3pNB",
         "Command": "printf '1 ' >> design.lcon",
         "Used": []
       }
diff --git a/examples/from_parsers/fsl/fsl_group_wls_report_log.png b/examples/from_parsers/fsl/fsl_group_wls_report_log.png
index ac3f184e..906d630b 100644
Binary files a/examples/from_parsers/fsl/fsl_group_wls_report_log.png and b/examples/from_parsers/fsl/fsl_group_wls_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_hrf_fir_report_log.html b/examples/from_parsers/fsl/fsl_hrf_fir_report_log.html
index 94be2093..cdf382b1 100644
--- a/examples/from_parsers/fsl/fsl_hrf_fir_report_log.html
+++ b/examples/from_parsers/fsl/fsl_hrf_fir_report_log.html
@@ -35,20 +35,20 @@ 
Progress Report / Log

 326941
Initialisation
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
 Total original volumes = 104
 
 /usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
 
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/example_func.nii.gz  -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/example_func.nii.gz  -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
 Option -F ( FEAT version parameter ) selected with  argument "6.00"
 Option -d ( output directory ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat"
 Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/logs/feat2_pre"
 Option -R ( html unwarping report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_unwarp.html"
 Option -r ( html registration report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_reg.html"
 Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with  argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
 Option -w ( highres dof ) selected with  argument "BBR"
 Option -x ( highres search ) selected with  argument "90"
 Option -s ( standard image ) selected with  argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ 
Progress Report / Log

 /bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/reg
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
 
 did not find file: example_func2highres.mat. Generating transform.
 
@@ -128,9 +128,9 @@ 
Progress Report / Log

 /bin/rm -rf prefiltered_func_data*
Stats
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
 
 /usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts  
 Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_hrf_fir_report_log.jsonld b/examples/from_parsers/fsl/fsl_hrf_fir_report_log.jsonld
index aa4b7fee..a724a835 100644
--- a/examples/from_parsers/fsl/fsl_hrf_fir_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_hrf_fir_report_log.jsonld
@@ -15,16 +15,16 @@
       {
         "@id": "urn:fslmaths-nq5UWEBB",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold"
+          "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
         ]
       },
       {
         "@id": "urn:fslroi-N7dzlV3p",
         "Label": "fslroi",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
         "Used": [
           "bids::prefiltered_func_data"
@@ -33,43 +33,43 @@
       {
         "@id": "urn:mainfeat-aWd37ogx",
         "Label": "mainfeatreg",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
           "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/example_func.nii.gz",
-          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
+          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:makedire-o9d1hW2G",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/reg",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-pWofaAJa",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:fslmaths-STPjLbgH",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
         ]
       },
       {
         "@id": "urn:epireg-vYrJyf18",
         "Label": "epi_reg",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
         "Used": [
           "bids::example_func",
@@ -80,7 +80,7 @@
       {
         "@id": "urn:convertx-Ol04i8gE",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
         "Used": [
           "bids::example_func2highres.mat"
@@ -89,7 +89,7 @@
       {
         "@id": "urn:slicer-9sLi9qYh",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -99,7 +99,7 @@
       {
         "@id": "urn:pngappen-y4HSKVDo",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
         "Used": [
           "bids::sla.png",
@@ -119,7 +119,7 @@
       {
         "@id": "urn:slicer-nCd4Ud2V",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -129,7 +129,7 @@
       {
         "@id": "urn:pngappen-laujh6mc",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
         "Used": [
           "bids::sla.png",
@@ -149,7 +149,7 @@
       {
         "@id": "urn:pngappen-JPkZrHqL",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
         "Used": [
           "bids::example_func2highres1.png",
@@ -159,7 +159,7 @@
       {
         "@id": "urn:rm-N4UzNrDt",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/bin/rm -f sl?.png example_func2highres2.png",
         "Used": [
           "bids::example_func2highres2.png",
@@ -169,7 +169,7 @@
       {
         "@id": "urn:rm-BbCHnJGZ",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/bin/rm example_func2highres1.png",
         "Used": [
           "bids::example_func2highres1.png"
@@ -178,7 +178,7 @@
       {
         "@id": "urn:mcflirt-mBlw9T2X",
         "Label": "mcflirt",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
         "Used": [
           "bids::prefiltered_func_data"
@@ -187,14 +187,14 @@
       {
         "@id": "urn:makedire-tvzu7YZ9",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/bin/mkdir -p mc",
         "Used": []
       },
       {
         "@id": "urn:mv-tbG1qvio",
         "Label": "mv",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
         "Used": [
           "bids::prefiltered_func_data_mcf.mat",
@@ -208,7 +208,7 @@
       {
         "@id": "urn:fsltsplo-3Ygm84p1",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -217,7 +217,7 @@
       {
         "@id": "urn:fsltsplo-PqpsKom3",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -226,7 +226,7 @@
       {
         "@id": "urn:fsltsplo-ZNjGlTsw",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
         "Used": [
           "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
@@ -235,7 +235,7 @@
       {
         "@id": "urn:fslmaths-iQkoj0fa",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -244,7 +244,7 @@
       {
         "@id": "urn:bet2-sApm487o",
         "Label": "bet2",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
         "Used": [
           "bids::mean_func"
@@ -253,7 +253,7 @@
       {
         "@id": "urn:immv-WadYRMrM",
         "Label": "immv",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
         "Used": [
           "bids::mask_mask"
@@ -262,7 +262,7 @@
       {
         "@id": "urn:fslmaths-yGAwZhHM",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
         "Used": [
           "bids::mask",
@@ -272,7 +272,7 @@
       {
         "@id": "urn:fslstats-wY1o42Vq",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -281,7 +281,7 @@
       {
         "@id": "urn:fslmaths-U5aSpbjx",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -290,7 +290,7 @@
       {
         "@id": "urn:fslstats-lSDl1VcC",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -299,7 +299,7 @@
       {
         "@id": "urn:fslmaths-DdyB8Wig",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
         "Used": [
           "bids::mask"
@@ -308,7 +308,7 @@
       {
         "@id": "urn:fslmaths-IlGuzwXE",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
         "Used": [
           "bids::mask",
@@ -318,7 +318,7 @@
       {
         "@id": "urn:fslmaths-LGHPc31P",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -327,7 +327,7 @@
       {
         "@id": "urn:susan-8xf1ZGqg",
         "Label": "susan",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -336,7 +336,7 @@
       {
         "@id": "urn:fslmaths-ua6SnjTz",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
         "Used": [
           "bids::mask",
@@ -346,7 +346,7 @@
       {
         "@id": "urn:fslmaths-Nr58QEDF",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
         "Used": [
           "bids::prefiltered_func_data_smooth"
@@ -355,7 +355,7 @@
       {
         "@id": "urn:fslmaths-xGtZmbWb",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
         "Used": [
           "bids::prefiltered_func_data_intnorm"
@@ -364,7 +364,7 @@
       {
         "@id": "urn:fslmaths-tqFMMwBS",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
         "Used": [
           "bids::prefiltered_func_data_intnorm",
@@ -374,7 +374,7 @@
       {
         "@id": "urn:imrm-zBTUmmH3",
         "Label": "imrm",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
         "Used": [
           "bids::tempMean"
@@ -383,7 +383,7 @@
       {
         "@id": "urn:fslmaths-YMNePTWJ",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
         "Used": [
           "bids::prefiltered_func_data_tempfilt"
@@ -392,7 +392,7 @@
       {
         "@id": "urn:fslmaths-pP7eBc42",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
         "Used": [
           "bids::filtered_func_data"
@@ -401,7 +401,7 @@
       {
         "@id": "urn:rm-yBce1Xtf",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/bin/rm -rf prefiltered_func_data*",
         "Used": [
           "bids::prefiltered_func_data*"
@@ -410,39 +410,39 @@
       {
         "@id": "urn:makedire-GybSm7me",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-8D0gqBwQ",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
         ]
       },
       {
         "@id": "urn:makedire-LaEdoKMK",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-Agxavi0H",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
         ]
       },
       {
         "@id": "urn:filmgls-P4ifUteV",
         "Label": "film_gls",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts",
         "Used": [
           "bids::design.con",
@@ -455,7 +455,7 @@
       {
         "@id": "urn:smoothes-J4xR0VAI",
         "Label": "smoothest",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 98 -m mask -r stats/res4d > stats/smoothness",
         "Used": [
           "bids::mask",
@@ -465,7 +465,7 @@
       {
         "@id": "urn:fslmaths-QEY7hfH5",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
         "Used": [
           "bids::mask",
@@ -475,14 +475,14 @@
       {
         "@id": "urn:echo-acNmJmPz",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "echo 38352 > thresh_zstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-IQ18U7E5",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2",
         "Used": [
           "bids::mask",
@@ -492,14 +492,14 @@
       {
         "@id": "urn:echo-o4K0SINT",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "echo 38352 > thresh_zstat2.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-NGxIT52n",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat3 -mas mask thresh_zstat3",
         "Used": [
           "bids::mask",
@@ -509,14 +509,14 @@
       {
         "@id": "urn:echo-pkNaI7Dl",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "echo 38352 > thresh_zstat3.vol",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-1y2B6YqW",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zfstat1 -mas mask thresh_zfstat1",
         "Used": [
           "bids::mask",
@@ -526,21 +526,21 @@
       {
         "@id": "urn:echo-VBNs5nvy",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "echo 38352 > thresh_zfstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:ptoz-2V4cSwE4",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-MgJEe6d4",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
         "Used": [
           "bids::stats/cope1",
@@ -550,7 +550,7 @@
       {
         "@id": "urn:cluster2-aRueCeCD",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
         "Used": [
           "bids::cluster_zstat1"
@@ -559,14 +559,14 @@
       {
         "@id": "urn:ptoz-nfO1AgxR",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-Xfz11U8L",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
         "Used": [
           "bids::stats/cope2",
@@ -576,7 +576,7 @@
       {
         "@id": "urn:cluster2-Vw7VdGpH",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat2",
         "Used": [
           "bids::cluster_zstat2"
@@ -585,14 +585,14 @@
       {
         "@id": "urn:ptoz-qoMZL7p1",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-YJuz1prR",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat3 -t 3.090232 --othresh=thresh_zstat3 -o cluster_mask_zstat3 --connectivity=26 --olmax=lmax_zstat3.txt --scalarname=Z --voxuncthresh -c stats/cope3 > cluster_zstat3.txt",
         "Used": [
           "bids::stats/cope3",
@@ -602,7 +602,7 @@
       {
         "@id": "urn:cluster2-as1TvHvJ",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat3",
         "Used": [
           "bids::cluster_zstat3"
@@ -611,14 +611,14 @@
       {
         "@id": "urn:ptoz-1CLrMKJG",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-cFqbWSOQ",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zfstat1 -t 3.090232 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z --voxuncthresh > cluster_zfstat1.txt",
         "Used": [
           "bids::thresh_zfstat1"
@@ -627,7 +627,7 @@
       {
         "@id": "urn:cluster2-3aP1Q5qZ",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zfstat1",
         "Used": [
           "bids::cluster_zfstat1"
@@ -636,7 +636,7 @@
       {
         "@id": "urn:fslstats-rhTZM5Ju",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat1"
@@ -645,7 +645,7 @@
       {
         "@id": "urn:fslstats-BjgxFcRA",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat2 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat2"
@@ -654,7 +654,7 @@
       {
         "@id": "urn:fslstats-TSEDOSLQ",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat3 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat3"
@@ -663,7 +663,7 @@
       {
         "@id": "urn:fslstats-BP3sHODs",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zfstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zfstat1"
@@ -672,14 +672,14 @@
       {
         "@id": "urn:overlay-J0LVToUU",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090292 7.429559 rendered_thresh_zstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-WIJeQdex",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
         "Used": [
           "bids::rendered_thresh_zstat1"
@@ -688,7 +688,7 @@
       {
         "@id": "urn:cp-ZB6SRpaR",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
         "Used": [
           "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
@@ -697,14 +697,14 @@
       {
         "@id": "urn:overlay-ezv2kA1Z",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat2 3.090292 7.429559 rendered_thresh_zstat2",
         "Used": []
       },
       {
         "@id": "urn:slicer-d8V0x0iz",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat2 -A 750 rendered_thresh_zstat2.png",
         "Used": [
           "bids::rendered_thresh_zstat2"
@@ -713,14 +713,14 @@
       {
         "@id": "urn:overlay-N8TFYaTb",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat3 3.090292 7.429559 rendered_thresh_zstat3",
         "Used": []
       },
       {
         "@id": "urn:slicer-ziPQUrhv",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat3 -A 750 rendered_thresh_zstat3.png",
         "Used": [
           "bids::rendered_thresh_zstat3"
@@ -729,14 +729,14 @@
       {
         "@id": "urn:overlay-SHScIMUN",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zfstat1 3.090292 7.429559 rendered_thresh_zfstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-fXpdJStv",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zfstat1 -A 750 rendered_thresh_zfstat1.png",
         "Used": [
           "bids::rendered_thresh_zfstat1"
@@ -745,25 +745,25 @@
       {
         "@id": "urn:makedire-vSBvvW3S",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "mkdir -p tsplot",
         "Used": []
       },
       {
         "@id": "urn:tsplot-C8ocrLYQ",
         "Label": "tsplot",
-        "AssociatedWith": "urn:urn:fsl-ZtRHP0hk",
+        "AssociatedWith": "urn:fsl-ZtRHP0hk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
         "Used": []
       }
     ],
     "Entities": [
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "Label": "sub-01_task-tonecounting_bold",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "digest": {
-          "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
+          "sha256": "33501604ae140e58832facff473a9578d5a549403bdbec53107d2b3eaab898ee"
         }
       },
       {
@@ -793,11 +793,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "Label": "sub-01_T1w_brain",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "digest": {
-          "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
+          "sha256": "8f1ae7ba69869c79b2cc5a83ce4ca24a7d666187256c2aa4d61a952b903b05b0"
         }
       },
       {
@@ -833,11 +833,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "Label": "sub-01_T1w",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "digest": {
-          "sha256": "3be6c69338e200d2a286a56cd9a0030539cf50201f412c910ade833e18354d27"
+          "sha256": "8dd4893a9c9500ce8c516f1a9845abf887087d00c2c47fc3524a17d924e78acf"
         }
       },
       {
@@ -1397,11 +1397,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "Label": "sub-01_tone_counting.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "digest": {
-          "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+          "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
         }
       },
       {
@@ -1420,11 +1420,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "Label": "sub-01_tone_counting_probe.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "digest": {
-          "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+          "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
         }
       },
       {
diff --git a/examples/from_parsers/fsl/fsl_hrf_fir_report_log.png b/examples/from_parsers/fsl/fsl_hrf_fir_report_log.png
index a75c984e..83862052 100644
Binary files a/examples/from_parsers/fsl/fsl_hrf_fir_report_log.png and b/examples/from_parsers/fsl/fsl_hrf_fir_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.html b/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.html
index 842258e0..a722a6f3 100644
--- a/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.html
+++ b/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.html
@@ -35,20 +35,20 @@ 
Progress Report / Log

 326946
Initialisation
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
 Total original volumes = 104
 
 /usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
 
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/example_func.nii.gz  -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/example_func.nii.gz  -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
 Option -F ( FEAT version parameter ) selected with  argument "6.00"
 Option -d ( output directory ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat"
 Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/logs/feat2_pre"
 Option -R ( html unwarping report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_unwarp.html"
 Option -r ( html registration report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_reg.html"
 Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with  argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
 Option -w ( highres dof ) selected with  argument "BBR"
 Option -x ( highres search ) selected with  argument "90"
 Option -s ( standard image ) selected with  argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ 
Progress Report / Log

 /bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/reg
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
 
 did not find file: example_func2highres.mat. Generating transform.
 
@@ -128,9 +128,9 @@ 
Progress Report / Log

 /bin/rm -rf prefiltered_func_data*
Stats
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
 
 /usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con  
 Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.jsonld b/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.jsonld
index 883c4684..9b94b027 100644
--- a/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.jsonld
@@ -15,16 +15,16 @@
       {
         "@id": "urn:fslmaths-rEBajozz",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold"
+          "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
         ]
       },
       {
         "@id": "urn:fslroi-UkZikbZ1",
         "Label": "fslroi",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
         "Used": [
           "bids::prefiltered_func_data"
@@ -33,43 +33,43 @@
       {
         "@id": "urn:mainfeat-xtuN7r3U",
         "Label": "mainfeatreg",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
           "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/example_func.nii.gz",
-          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
+          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:makedire-f8e3PQFv",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/reg",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-XsmDlg5h",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:fslmaths-UULvGrJ8",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
         ]
       },
       {
         "@id": "urn:epireg-SVZAbVXX",
         "Label": "epi_reg",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
         "Used": [
           "bids::example_func",
@@ -80,7 +80,7 @@
       {
         "@id": "urn:convertx-9dX90OeD",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
         "Used": [
           "bids::example_func2highres.mat"
@@ -89,7 +89,7 @@
       {
         "@id": "urn:slicer-Rxdnb6PS",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -99,7 +99,7 @@
       {
         "@id": "urn:pngappen-Lbj7szgB",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
         "Used": [
           "bids::sla.png",
@@ -119,7 +119,7 @@
       {
         "@id": "urn:slicer-Z3jvXsRD",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -129,7 +129,7 @@
       {
         "@id": "urn:pngappen-51oaKZzY",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
         "Used": [
           "bids::sla.png",
@@ -149,7 +149,7 @@
       {
         "@id": "urn:pngappen-lbmNy7oN",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
         "Used": [
           "bids::example_func2highres1.png",
@@ -159,7 +159,7 @@
       {
         "@id": "urn:rm-5vefOeJG",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/bin/rm -f sl?.png example_func2highres2.png",
         "Used": [
           "bids::example_func2highres2.png",
@@ -169,7 +169,7 @@
       {
         "@id": "urn:rm-vE1cgYfE",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/bin/rm example_func2highres1.png",
         "Used": [
           "bids::example_func2highres1.png"
@@ -178,7 +178,7 @@
       {
         "@id": "urn:mcflirt-mpdbH7Bm",
         "Label": "mcflirt",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
         "Used": [
           "bids::prefiltered_func_data"
@@ -187,14 +187,14 @@
       {
         "@id": "urn:makedire-J2lSormN",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/bin/mkdir -p mc",
         "Used": []
       },
       {
         "@id": "urn:mv-xhrmBOA4",
         "Label": "mv",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
         "Used": [
           "bids::prefiltered_func_data_mcf.mat",
@@ -208,7 +208,7 @@
       {
         "@id": "urn:fsltsplo-BXivmu30",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -217,7 +217,7 @@
       {
         "@id": "urn:fsltsplo-Wjiiv0E3",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -226,7 +226,7 @@
       {
         "@id": "urn:fsltsplo-Fzexq6k9",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
         "Used": [
           "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
@@ -235,7 +235,7 @@
       {
         "@id": "urn:fslmaths-a5rzZke7",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -244,7 +244,7 @@
       {
         "@id": "urn:bet2-udXsp4cv",
         "Label": "bet2",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
         "Used": [
           "bids::mean_func"
@@ -253,7 +253,7 @@
       {
         "@id": "urn:immv-ZYFWZ1Gn",
         "Label": "immv",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
         "Used": [
           "bids::mask_mask"
@@ -262,7 +262,7 @@
       {
         "@id": "urn:fslmaths-I1OS1SJP",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
         "Used": [
           "bids::mask",
@@ -272,7 +272,7 @@
       {
         "@id": "urn:fslstats-wezyh368",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -281,7 +281,7 @@
       {
         "@id": "urn:fslmaths-7snwdwRw",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -290,7 +290,7 @@
       {
         "@id": "urn:fslstats-4Qi1I0em",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -299,7 +299,7 @@
       {
         "@id": "urn:fslmaths-8b8qCEmy",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
         "Used": [
           "bids::mask"
@@ -308,7 +308,7 @@
       {
         "@id": "urn:fslmaths-exNmgmHg",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
         "Used": [
           "bids::mask",
@@ -318,7 +318,7 @@
       {
         "@id": "urn:fslmaths-9zvUeSVt",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -327,7 +327,7 @@
       {
         "@id": "urn:susan-hUivqJAf",
         "Label": "susan",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -336,7 +336,7 @@
       {
         "@id": "urn:fslmaths-GuMPegWU",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
         "Used": [
           "bids::mask",
@@ -346,7 +346,7 @@
       {
         "@id": "urn:fslmaths-Uywrv3qZ",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
         "Used": [
           "bids::prefiltered_func_data_smooth"
@@ -355,7 +355,7 @@
       {
         "@id": "urn:fslmaths-UCRih4mS",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
         "Used": [
           "bids::prefiltered_func_data_intnorm"
@@ -364,7 +364,7 @@
       {
         "@id": "urn:fslmaths-S1K6eyBe",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
         "Used": [
           "bids::prefiltered_func_data_intnorm",
@@ -374,7 +374,7 @@
       {
         "@id": "urn:imrm-P5LbywF2",
         "Label": "imrm",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
         "Used": [
           "bids::tempMean"
@@ -383,7 +383,7 @@
       {
         "@id": "urn:fslmaths-iqrY5SnA",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
         "Used": [
           "bids::prefiltered_func_data_tempfilt"
@@ -392,7 +392,7 @@
       {
         "@id": "urn:fslmaths-dabqvNXy",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
         "Used": [
           "bids::filtered_func_data"
@@ -401,7 +401,7 @@
       {
         "@id": "urn:rm-Q738Srjt",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/bin/rm -rf prefiltered_func_data*",
         "Used": [
           "bids::prefiltered_func_data*"
@@ -410,39 +410,39 @@
       {
         "@id": "urn:makedire-np0NfI2n",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-9tAyRn9N",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
         ]
       },
       {
         "@id": "urn:makedire-mO0uYErJ",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-xwMlvwHA",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
         ]
       },
       {
         "@id": "urn:filmgls-bPmqxXVL",
         "Label": "film_gls",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
         "Used": [
           "bids::design.con",
@@ -454,7 +454,7 @@
       {
         "@id": "urn:smoothes-liqoxwMg",
         "Label": "smoothest",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
         "Used": [
           "bids::mask",
@@ -464,7 +464,7 @@
       {
         "@id": "urn:fslmaths-9UeSkXvv",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
         "Used": [
           "bids::mask",
@@ -474,21 +474,21 @@
       {
         "@id": "urn:echo-8T6HuBkS",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "echo 38352 > thresh_zstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:ptoz-7lMYOpQk",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-xTOqvqc1",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
         "Used": [
           "bids::stats/cope1",
@@ -498,7 +498,7 @@
       {
         "@id": "urn:cluster2-4aUMZyUO",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
         "Used": [
           "bids::cluster_zstat1"
@@ -507,7 +507,7 @@
       {
         "@id": "urn:fslstats-pInnygxp",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat1"
@@ -516,14 +516,14 @@
       {
         "@id": "urn:overlay-iRpUE43m",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090718 7.041752 rendered_thresh_zstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-dPyNd78C",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
         "Used": [
           "bids::rendered_thresh_zstat1"
@@ -532,7 +532,7 @@
       {
         "@id": "urn:cp-yLQL77nx",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
         "Used": [
           "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
@@ -541,25 +541,25 @@
       {
         "@id": "urn:makedire-mY11e8bD",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "mkdir -p tsplot",
         "Used": []
       },
       {
         "@id": "urn:tsplot-ms47hBRT",
         "Label": "tsplot",
-        "AssociatedWith": "urn:urn:fsl-rMiU3aNs",
+        "AssociatedWith": "urn:fsl-rMiU3aNs",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
         "Used": []
       }
     ],
     "Entities": [
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "Label": "sub-01_task-tonecounting_bold",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "digest": {
-          "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
+          "sha256": "33501604ae140e58832facff473a9578d5a549403bdbec53107d2b3eaab898ee"
         }
       },
       {
@@ -589,11 +589,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "Label": "sub-01_T1w_brain",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "digest": {
-          "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
+          "sha256": "8f1ae7ba69869c79b2cc5a83ce4ca24a7d666187256c2aa4d61a952b903b05b0"
         }
       },
       {
@@ -629,11 +629,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "Label": "sub-01_T1w",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "digest": {
-          "sha256": "3be6c69338e200d2a286a56cd9a0030539cf50201f412c910ade833e18354d27"
+          "sha256": "8dd4893a9c9500ce8c516f1a9845abf887087d00c2c47fc3524a17d924e78acf"
         }
       },
       {
@@ -1193,11 +1193,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "Label": "sub-01_tone_counting.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "digest": {
-          "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+          "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
         }
       },
       {
@@ -1216,11 +1216,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "Label": "sub-01_tone_counting_probe.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "digest": {
-          "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+          "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
         }
       },
       {
diff --git a/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.png b/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.png
index c6918dad..a0c211c8 100644
Binary files a/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.png and b/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.html b/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.html
index 4be811d2..a7d230d3 100644
--- a/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.html
+++ b/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.html
@@ -35,20 +35,20 @@ 
Progress Report / Log

 326885
Initialisation
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
 Total original volumes = 104
 
 /usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
 
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/example_func.nii.gz  -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/example_func.nii.gz  -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
 Option -F ( FEAT version parameter ) selected with  argument "6.00"
 Option -d ( output directory ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat"
 Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/logs/feat2_pre"
 Option -R ( html unwarping report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_unwarp.html"
 Option -r ( html registration report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_reg.html"
 Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with  argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
 Option -w ( highres dof ) selected with  argument "BBR"
 Option -x ( highres search ) selected with  argument "90"
 Option -s ( standard image ) selected with  argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ 
Progress Report / Log

 /bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/reg
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
 
 did not find file: example_func2highres.mat. Generating transform.
 
@@ -128,9 +128,9 @@ 
Progress Report / Log

 /bin/rm -rf prefiltered_func_data*
Stats
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
 
 /usr/local/packages/fsl-5.0.10/bin/mp_diffpow.sh mc/prefiltered_func_data_mcf.par mc/prefiltered_func_data_mcf_diff
 
diff --git a/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.jsonld b/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.jsonld
index e54c9f6a..5e8e40d5 100644
--- a/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.jsonld
@@ -15,16 +15,16 @@
       {
         "@id": "urn:fslmaths-dC2a0X3Y",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold"
+          "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
         ]
       },
       {
         "@id": "urn:fslroi-P33frSjV",
         "Label": "fslroi",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
         "Used": [
           "bids::prefiltered_func_data"
@@ -33,43 +33,43 @@
       {
         "@id": "urn:mainfeat-pePifb0g",
         "Label": "mainfeatreg",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
           "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/example_func.nii.gz",
-          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
+          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:makedire-GvuKuCNk",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/reg",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-suuOqrDC",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:fslmaths-q8MSO5Am",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
         ]
       },
       {
         "@id": "urn:epireg-5k2Yi4nS",
         "Label": "epi_reg",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
         "Used": [
           "bids::example_func",
@@ -80,7 +80,7 @@
       {
         "@id": "urn:convertx-n5s09vhW",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
         "Used": [
           "bids::example_func2highres.mat"
@@ -89,7 +89,7 @@
       {
         "@id": "urn:slicer-dKDUNHY2",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -99,7 +99,7 @@
       {
         "@id": "urn:pngappen-wVG3Hr3e",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
         "Used": [
           "bids::sla.png",
@@ -119,7 +119,7 @@
       {
         "@id": "urn:slicer-Taflf26K",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -129,7 +129,7 @@
       {
         "@id": "urn:pngappen-lfBGx27W",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
         "Used": [
           "bids::sla.png",
@@ -149,7 +149,7 @@
       {
         "@id": "urn:pngappen-CNwT0NHH",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
         "Used": [
           "bids::example_func2highres1.png",
@@ -159,7 +159,7 @@
       {
         "@id": "urn:rm-BtXDPS1B",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/bin/rm -f sl?.png example_func2highres2.png",
         "Used": [
           "bids::example_func2highres2.png",
@@ -169,7 +169,7 @@
       {
         "@id": "urn:rm-fyjZBW6p",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/bin/rm example_func2highres1.png",
         "Used": [
           "bids::example_func2highres1.png"
@@ -178,7 +178,7 @@
       {
         "@id": "urn:mcflirt-odII8geb",
         "Label": "mcflirt",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
         "Used": [
           "bids::prefiltered_func_data"
@@ -187,14 +187,14 @@
       {
         "@id": "urn:makedire-UK92L4x7",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/bin/mkdir -p mc",
         "Used": []
       },
       {
         "@id": "urn:mv-I5FDYgY1",
         "Label": "mv",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
         "Used": [
           "bids::prefiltered_func_data_mcf.mat",
@@ -208,7 +208,7 @@
       {
         "@id": "urn:fsltsplo-OyOBbM9y",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -217,7 +217,7 @@
       {
         "@id": "urn:fsltsplo-Oe0ij16S",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -226,7 +226,7 @@
       {
         "@id": "urn:fsltsplo-MM1luFDP",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
         "Used": [
           "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
@@ -235,7 +235,7 @@
       {
         "@id": "urn:fslmaths-EYKSK00I",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -244,7 +244,7 @@
       {
         "@id": "urn:bet2-PQSk41oe",
         "Label": "bet2",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
         "Used": [
           "bids::mean_func"
@@ -253,7 +253,7 @@
       {
         "@id": "urn:immv-IjjkMRPp",
         "Label": "immv",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
         "Used": [
           "bids::mask_mask"
@@ -262,7 +262,7 @@
       {
         "@id": "urn:fslmaths-XqLE8pkt",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
         "Used": [
           "bids::mask",
@@ -272,7 +272,7 @@
       {
         "@id": "urn:fslstats-Jr6RWDPe",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -281,7 +281,7 @@
       {
         "@id": "urn:fslmaths-VL4VqblJ",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -290,7 +290,7 @@
       {
         "@id": "urn:fslstats-7umKtLfk",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -299,7 +299,7 @@
       {
         "@id": "urn:fslmaths-ut9tGWVe",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
         "Used": [
           "bids::mask"
@@ -308,7 +308,7 @@
       {
         "@id": "urn:fslmaths-nOE8yxx7",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
         "Used": [
           "bids::mask",
@@ -318,7 +318,7 @@
       {
         "@id": "urn:fslmaths-OjIaOvPw",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -327,7 +327,7 @@
       {
         "@id": "urn:susan-SmymgzPJ",
         "Label": "susan",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -336,7 +336,7 @@
       {
         "@id": "urn:fslmaths-O8pCVrLL",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
         "Used": [
           "bids::mask",
@@ -346,7 +346,7 @@
       {
         "@id": "urn:fslmaths-MZCCcDOx",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
         "Used": [
           "bids::prefiltered_func_data_smooth"
@@ -355,7 +355,7 @@
       {
         "@id": "urn:fslmaths-As3g3UB7",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
         "Used": [
           "bids::prefiltered_func_data_intnorm"
@@ -364,7 +364,7 @@
       {
         "@id": "urn:fslmaths-I24yLD9V",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
         "Used": [
           "bids::prefiltered_func_data_intnorm",
@@ -374,7 +374,7 @@
       {
         "@id": "urn:imrm-JrZFnovL",
         "Label": "imrm",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
         "Used": [
           "bids::tempMean"
@@ -383,7 +383,7 @@
       {
         "@id": "urn:fslmaths-P4mbrSSu",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
         "Used": [
           "bids::prefiltered_func_data_tempfilt"
@@ -392,7 +392,7 @@
       {
         "@id": "urn:fslmaths-ZreUCdz4",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
         "Used": [
           "bids::filtered_func_data"
@@ -401,7 +401,7 @@
       {
         "@id": "urn:rm-hm0Sr96f",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/bin/rm -rf prefiltered_func_data*",
         "Used": [
           "bids::prefiltered_func_data*"
@@ -410,39 +410,39 @@
       {
         "@id": "urn:makedire-GemLkPxp",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-iX0H2Ui2",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
         ]
       },
       {
         "@id": "urn:makedire-6kNWcrAo",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-bY3ov1IQ",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
         ]
       },
       {
         "@id": "urn:mpdiffpo-ymFrapRB",
         "Label": "mp_diffpow.sh",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/mp_diffpow.sh mc/prefiltered_func_data_mcf.par mc/prefiltered_func_data_mcf_diff",
         "Used": [
           "bids::mc/prefiltered_func_data_mcf.par"
@@ -451,21 +451,21 @@
       {
         "@id": "urn:paste-ASrDOVxs",
         "Label": "paste",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "paste -d ' ' mc/prefiltered_func_data_mcf.par mc/prefiltered_func_data_mcf_diff.dat > mc/prefiltered_func_data_mcf_final.par",
         "Used": []
       },
       {
         "@id": "urn:paste-KbppIr8M",
         "Label": "paste",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "paste -d ' ' mc/prefiltered_func_data_mcf_final.par > confoundevs.txt",
         "Used": []
       },
       {
         "@id": "urn:featmode-dY5I3r5p",
         "Label": "feat_model",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/feat_model design confoundevs.txt",
         "Used": [
           "bids::design"
@@ -474,7 +474,7 @@
       {
         "@id": "urn:filmgls-3IoqFYtu",
         "Label": "film_gls",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
         "Used": [
           "bids::design.con",
@@ -486,7 +486,7 @@
       {
         "@id": "urn:smoothes-paAW6C17",
         "Label": "smoothest",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 78 -m mask -r stats/res4d > stats/smoothness",
         "Used": [
           "bids::mask",
@@ -496,7 +496,7 @@
       {
         "@id": "urn:fslmaths-H8tXahSy",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
         "Used": [
           "bids::mask",
@@ -506,21 +506,21 @@
       {
         "@id": "urn:echo-JYr0kACn",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "echo 38352 > thresh_zstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:ptoz-In84LLOp",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-E7oup06U",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
         "Used": [
           "bids::stats/cope1",
@@ -530,7 +530,7 @@
       {
         "@id": "urn:cluster2-ymvd5MhO",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
         "Used": [
           "bids::cluster_zstat1"
@@ -539,7 +539,7 @@
       {
         "@id": "urn:fslstats-c927620Q",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat1"
@@ -548,14 +548,14 @@
       {
         "@id": "urn:overlay-9EILhFVq",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.093412 5.467648 rendered_thresh_zstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-lKcrJvxP",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
         "Used": [
           "bids::rendered_thresh_zstat1"
@@ -564,7 +564,7 @@
       {
         "@id": "urn:cp-pEZlO6Nc",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
         "Used": [
           "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
@@ -573,25 +573,25 @@
       {
         "@id": "urn:makedire-M3VVjUGh",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "mkdir -p tsplot",
         "Used": []
       },
       {
         "@id": "urn:tsplot-DUfA2b5q",
         "Label": "tsplot",
-        "AssociatedWith": "urn:urn:fsl-O45Gx0i4",
+        "AssociatedWith": "urn:fsl-O45Gx0i4",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
         "Used": []
       }
     ],
     "Entities": [
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "Label": "sub-01_task-tonecounting_bold",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "digest": {
-          "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
+          "sha256": "33501604ae140e58832facff473a9578d5a549403bdbec53107d2b3eaab898ee"
         }
       },
       {
@@ -621,11 +621,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "Label": "sub-01_T1w_brain",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "digest": {
-          "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
+          "sha256": "8f1ae7ba69869c79b2cc5a83ce4ca24a7d666187256c2aa4d61a952b903b05b0"
         }
       },
       {
@@ -661,11 +661,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "Label": "sub-01_T1w",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "digest": {
-          "sha256": "3be6c69338e200d2a286a56cd9a0030539cf50201f412c910ade833e18354d27"
+          "sha256": "8dd4893a9c9500ce8c516f1a9845abf887087d00c2c47fc3524a17d924e78acf"
         }
       },
       {
@@ -1225,11 +1225,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "Label": "sub-01_tone_counting.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "digest": {
-          "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+          "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
         }
       },
       {
@@ -1248,11 +1248,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "Label": "sub-01_tone_counting_probe.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "digest": {
-          "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+          "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
         }
       },
       {
diff --git a/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.png b/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.png
index 7c519e1a..20b304b5 100644
Binary files a/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.png and b/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_motion_reg_report_log.html b/examples/from_parsers/fsl/fsl_motion_reg_report_log.html
index 0fce4c35..bf9a3111 100644
--- a/examples/from_parsers/fsl/fsl_motion_reg_report_log.html
+++ b/examples/from_parsers/fsl/fsl_motion_reg_report_log.html
@@ -35,20 +35,20 @@ 
Progress Report / Log

 326890
Initialisation
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
 Total original volumes = 104
 
 /usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
 
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/example_func.nii.gz  -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/example_func.nii.gz  -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
 Option -F ( FEAT version parameter ) selected with  argument "6.00"
 Option -d ( output directory ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat"
 Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/logs/feat2_pre"
 Option -R ( html unwarping report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_unwarp.html"
 Option -r ( html registration report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_reg.html"
 Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with  argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
 Option -w ( highres dof ) selected with  argument "BBR"
 Option -x ( highres search ) selected with  argument "90"
 Option -s ( standard image ) selected with  argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ 
Progress Report / Log

 /bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/reg
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
 
 did not find file: example_func2highres.mat. Generating transform.
 
@@ -128,9 +128,9 @@ 
Progress Report / Log

 /bin/rm -rf prefiltered_func_data*
Stats
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
 
 cp mc/prefiltered_func_data_mcf.par mc/prefiltered_func_data_mcf_final.par
 
diff --git a/examples/from_parsers/fsl/fsl_motion_reg_report_log.jsonld b/examples/from_parsers/fsl/fsl_motion_reg_report_log.jsonld
index e00912c6..bf4ca927 100644
--- a/examples/from_parsers/fsl/fsl_motion_reg_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_motion_reg_report_log.jsonld
@@ -15,16 +15,16 @@
       {
         "@id": "urn:fslmaths-3e1BW8zk",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold"
+          "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
         ]
       },
       {
         "@id": "urn:fslroi-P8KgYNMI",
         "Label": "fslroi",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
         "Used": [
           "bids::prefiltered_func_data"
@@ -33,43 +33,43 @@
       {
         "@id": "urn:mainfeat-L2O1FWWa",
         "Label": "mainfeatreg",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
           "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/example_func.nii.gz",
-          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
+          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:makedire-081RCxsU",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/reg",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-oZkoFxMk",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:fslmaths-Di35akWj",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
         ]
       },
       {
         "@id": "urn:epireg-g2VLNGNl",
         "Label": "epi_reg",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
         "Used": [
           "bids::example_func",
@@ -80,7 +80,7 @@
       {
         "@id": "urn:convertx-OwOGE44S",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
         "Used": [
           "bids::example_func2highres.mat"
@@ -89,7 +89,7 @@
       {
         "@id": "urn:slicer-WDHg7RO5",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -99,7 +99,7 @@
       {
         "@id": "urn:pngappen-gg2Ssdze",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
         "Used": [
           "bids::sla.png",
@@ -119,7 +119,7 @@
       {
         "@id": "urn:slicer-xfVLnC1i",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -129,7 +129,7 @@
       {
         "@id": "urn:pngappen-DdSGKIgw",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
         "Used": [
           "bids::sla.png",
@@ -149,7 +149,7 @@
       {
         "@id": "urn:pngappen-AABwFbAU",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
         "Used": [
           "bids::example_func2highres1.png",
@@ -159,7 +159,7 @@
       {
         "@id": "urn:rm-9FeJXu6N",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/bin/rm -f sl?.png example_func2highres2.png",
         "Used": [
           "bids::example_func2highres2.png",
@@ -169,7 +169,7 @@
       {
         "@id": "urn:rm-QeRTve2R",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/bin/rm example_func2highres1.png",
         "Used": [
           "bids::example_func2highres1.png"
@@ -178,7 +178,7 @@
       {
         "@id": "urn:mcflirt-mRIur6l3",
         "Label": "mcflirt",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
         "Used": [
           "bids::prefiltered_func_data"
@@ -187,14 +187,14 @@
       {
         "@id": "urn:makedire-AoaD1CwM",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/bin/mkdir -p mc",
         "Used": []
       },
       {
         "@id": "urn:mv-2yFPQBIr",
         "Label": "mv",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
         "Used": [
           "bids::prefiltered_func_data_mcf.mat",
@@ -208,7 +208,7 @@
       {
         "@id": "urn:fsltsplo-J0iwwUfZ",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -217,7 +217,7 @@
       {
         "@id": "urn:fsltsplo-D7UjyFRB",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -226,7 +226,7 @@
       {
         "@id": "urn:fsltsplo-InC74Sut",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
         "Used": [
           "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
@@ -235,7 +235,7 @@
       {
         "@id": "urn:fslmaths-R434LBry",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -244,7 +244,7 @@
       {
         "@id": "urn:bet2-WJQyP3oC",
         "Label": "bet2",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
         "Used": [
           "bids::mean_func"
@@ -253,7 +253,7 @@
       {
         "@id": "urn:immv-4v7jamiF",
         "Label": "immv",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
         "Used": [
           "bids::mask_mask"
@@ -262,7 +262,7 @@
       {
         "@id": "urn:fslmaths-qYlHII1V",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
         "Used": [
           "bids::mask",
@@ -272,7 +272,7 @@
       {
         "@id": "urn:fslstats-4JFp7lV9",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -281,7 +281,7 @@
       {
         "@id": "urn:fslmaths-YUTXrUXd",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -290,7 +290,7 @@
       {
         "@id": "urn:fslstats-MyWqhTsi",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -299,7 +299,7 @@
       {
         "@id": "urn:fslmaths-wwPgPnYX",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
         "Used": [
           "bids::mask"
@@ -308,7 +308,7 @@
       {
         "@id": "urn:fslmaths-C3yoMH6k",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
         "Used": [
           "bids::mask",
@@ -318,7 +318,7 @@
       {
         "@id": "urn:fslmaths-Cx8FTnEr",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -327,7 +327,7 @@
       {
         "@id": "urn:susan-2AISnNgW",
         "Label": "susan",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -336,7 +336,7 @@
       {
         "@id": "urn:fslmaths-uhxHBqAa",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
         "Used": [
           "bids::mask",
@@ -346,7 +346,7 @@
       {
         "@id": "urn:fslmaths-OGv4Qr30",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
         "Used": [
           "bids::prefiltered_func_data_smooth"
@@ -355,7 +355,7 @@
       {
         "@id": "urn:fslmaths-kI7gzSJZ",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
         "Used": [
           "bids::prefiltered_func_data_intnorm"
@@ -364,7 +364,7 @@
       {
         "@id": "urn:fslmaths-tmHau3zK",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
         "Used": [
           "bids::prefiltered_func_data_intnorm",
@@ -374,7 +374,7 @@
       {
         "@id": "urn:imrm-NX9LduVv",
         "Label": "imrm",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
         "Used": [
           "bids::tempMean"
@@ -383,7 +383,7 @@
       {
         "@id": "urn:fslmaths-8mzN1fkC",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
         "Used": [
           "bids::prefiltered_func_data_tempfilt"
@@ -392,7 +392,7 @@
       {
         "@id": "urn:fslmaths-tvhntGIA",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
         "Used": [
           "bids::filtered_func_data"
@@ -401,7 +401,7 @@
       {
         "@id": "urn:rm-0HzAUihb",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/bin/rm -rf prefiltered_func_data*",
         "Used": [
           "bids::prefiltered_func_data*"
@@ -410,39 +410,39 @@
       {
         "@id": "urn:makedire-nVCXGaK7",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-Yaoid2yI",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
         ]
       },
       {
         "@id": "urn:makedire-Z7VhBRjC",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-BP3JdcoO",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
         ]
       },
       {
         "@id": "urn:cp-QigRY0AI",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "cp mc/prefiltered_func_data_mcf.par mc/prefiltered_func_data_mcf_final.par",
         "Used": [
           "bids::mc/prefiltered_func_data_mcf.par"
@@ -451,14 +451,14 @@
       {
         "@id": "urn:paste-T2ti4avE",
         "Label": "paste",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "paste -d ' ' mc/prefiltered_func_data_mcf_final.par > confoundevs.txt",
         "Used": []
       },
       {
         "@id": "urn:featmode-QiHfDLNN",
         "Label": "feat_model",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/feat_model design confoundevs.txt",
         "Used": [
           "bids::design"
@@ -467,7 +467,7 @@
       {
         "@id": "urn:filmgls-AynXvtZy",
         "Label": "film_gls",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
         "Used": [
           "bids::design.con",
@@ -479,7 +479,7 @@
       {
         "@id": "urn:smoothes-zejB0NIO",
         "Label": "smoothest",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 96 -m mask -r stats/res4d > stats/smoothness",
         "Used": [
           "bids::mask",
@@ -489,7 +489,7 @@
       {
         "@id": "urn:fslmaths-Fs9p1PuI",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
         "Used": [
           "bids::mask",
@@ -499,21 +499,21 @@
       {
         "@id": "urn:echo-w4Z3IJwq",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "echo 38352 > thresh_zstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:ptoz-3z1yNibF",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
         "Used": []
       },
       {
         "@id": "urn:cluster-dQTSoZRU",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
         "Used": [
           "bids::stats/cope1",
@@ -523,7 +523,7 @@
       {
         "@id": "urn:cluster2-ojcUUeuy",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
         "Used": [
           "bids::cluster_zstat1"
@@ -532,7 +532,7 @@
       {
         "@id": "urn:fslstats-FhQi5D0S",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat1"
@@ -541,14 +541,14 @@
       {
         "@id": "urn:overlay-MQWSN0yZ",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.091832 5.263171 rendered_thresh_zstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-KQKRKhwm",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
         "Used": [
           "bids::rendered_thresh_zstat1"
@@ -557,7 +557,7 @@
       {
         "@id": "urn:cp-2T3xfElR",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
         "Used": [
           "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
@@ -566,25 +566,25 @@
       {
         "@id": "urn:makedire-Ybe9be1w",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "mkdir -p tsplot",
         "Used": []
       },
       {
         "@id": "urn:tsplot-b6M9Wmgz",
         "Label": "tsplot",
-        "AssociatedWith": "urn:urn:fsl-q1u8Lfn3",
+        "AssociatedWith": "urn:fsl-q1u8Lfn3",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
         "Used": []
       }
     ],
     "Entities": [
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "Label": "sub-01_task-tonecounting_bold",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "digest": {
-          "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
+          "sha256": "33501604ae140e58832facff473a9578d5a549403bdbec53107d2b3eaab898ee"
         }
       },
       {
@@ -614,11 +614,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "Label": "sub-01_T1w_brain",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "digest": {
-          "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
+          "sha256": "8f1ae7ba69869c79b2cc5a83ce4ca24a7d666187256c2aa4d61a952b903b05b0"
         }
       },
       {
@@ -654,11 +654,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "Label": "sub-01_T1w",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "digest": {
-          "sha256": "3be6c69338e200d2a286a56cd9a0030539cf50201f412c910ade833e18354d27"
+          "sha256": "8dd4893a9c9500ce8c516f1a9845abf887087d00c2c47fc3524a17d924e78acf"
         }
       },
       {
@@ -1218,11 +1218,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "Label": "sub-01_tone_counting.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "digest": {
-          "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+          "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
         }
       },
       {
@@ -1241,11 +1241,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "Label": "sub-01_tone_counting_probe.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "digest": {
-          "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+          "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
         }
       },
       {
diff --git a/examples/from_parsers/fsl/fsl_motion_reg_report_log.png b/examples/from_parsers/fsl/fsl_motion_reg_report_log.png
index abdee953..642ab7f7 100644
Binary files a/examples/from_parsers/fsl/fsl_motion_reg_report_log.png and b/examples/from_parsers/fsl/fsl_motion_reg_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.html b/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.html
index 4324db37..35beaa16 100644
--- a/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.html
+++ b/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.html
@@ -35,20 +35,20 @@ 
Progress Report / Log

 326951
Initialisation
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
 Total original volumes = 104
 
 /usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
 
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/example_func.nii.gz  -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/example_func.nii.gz  -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
 Option -F ( FEAT version parameter ) selected with  argument "6.00"
 Option -d ( output directory ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat"
 Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/logs/feat2_pre"
 Option -R ( html unwarping report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_unwarp.html"
 Option -r ( html registration report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_reg.html"
 Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with  argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
 Option -w ( highres dof ) selected with  argument "BBR"
 Option -x ( highres search ) selected with  argument "90"
 Option -s ( standard image ) selected with  argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ 
Progress Report / Log

 /bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/reg
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
 
 did not find file: example_func2highres.mat. Generating transform.
 
@@ -128,9 +128,9 @@ 
Progress Report / Log

 /bin/rm -rf prefiltered_func_data*
Stats
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
 
 /usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con  
 Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.jsonld b/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.jsonld
index f3782021..181ffab6 100644
--- a/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.jsonld
@@ -15,16 +15,16 @@
       {
         "@id": "urn:fslmaths-CQbxzFTw",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold"
+          "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
         ]
       },
       {
         "@id": "urn:fslroi-wGZBqcbE",
         "Label": "fslroi",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
         "Used": [
           "bids::prefiltered_func_data"
@@ -33,43 +33,43 @@
       {
         "@id": "urn:mainfeat-Z5CbKU9F",
         "Label": "mainfeatreg",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
           "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/example_func.nii.gz",
-          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
+          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:makedire-NOEtFviS",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/reg",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-T1fVWMQu",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:fslmaths-2vYi9QDl",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
         ]
       },
       {
         "@id": "urn:epireg-B1VKnLMt",
         "Label": "epi_reg",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
         "Used": [
           "bids::example_func",
@@ -80,7 +80,7 @@
       {
         "@id": "urn:convertx-gcVgFYO6",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
         "Used": [
           "bids::example_func2highres.mat"
@@ -89,7 +89,7 @@
       {
         "@id": "urn:slicer-9NGIvNbx",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -99,7 +99,7 @@
       {
         "@id": "urn:pngappen-SVwn1wOf",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
         "Used": [
           "bids::sla.png",
@@ -119,7 +119,7 @@
       {
         "@id": "urn:slicer-aUDIirTp",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -129,7 +129,7 @@
       {
         "@id": "urn:pngappen-HDABNtYq",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
         "Used": [
           "bids::sla.png",
@@ -149,7 +149,7 @@
       {
         "@id": "urn:pngappen-du46OFzf",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
         "Used": [
           "bids::example_func2highres1.png",
@@ -159,7 +159,7 @@
       {
         "@id": "urn:rm-iBAEppWw",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/bin/rm -f sl?.png example_func2highres2.png",
         "Used": [
           "bids::example_func2highres2.png",
@@ -169,7 +169,7 @@
       {
         "@id": "urn:rm-ULp49SaM",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/bin/rm example_func2highres1.png",
         "Used": [
           "bids::example_func2highres1.png"
@@ -178,7 +178,7 @@
       {
         "@id": "urn:mcflirt-VrAGRiNW",
         "Label": "mcflirt",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
         "Used": [
           "bids::prefiltered_func_data"
@@ -187,14 +187,14 @@
       {
         "@id": "urn:makedire-rsmkMsdJ",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/bin/mkdir -p mc",
         "Used": []
       },
       {
         "@id": "urn:mv-eJZYi4bU",
         "Label": "mv",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
         "Used": [
           "bids::prefiltered_func_data_mcf.mat",
@@ -208,7 +208,7 @@
       {
         "@id": "urn:fsltsplo-jfXPMkZi",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -217,7 +217,7 @@
       {
         "@id": "urn:fsltsplo-tVA4OWyL",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -226,7 +226,7 @@
       {
         "@id": "urn:fsltsplo-CVpNhDKM",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
         "Used": [
           "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
@@ -235,7 +235,7 @@
       {
         "@id": "urn:fslmaths-PCDp4ETS",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -244,7 +244,7 @@
       {
         "@id": "urn:bet2-zwxs3XiV",
         "Label": "bet2",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
         "Used": [
           "bids::mean_func"
@@ -253,7 +253,7 @@
       {
         "@id": "urn:immv-aNaAxFct",
         "Label": "immv",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
         "Used": [
           "bids::mask_mask"
@@ -262,7 +262,7 @@
       {
         "@id": "urn:fslmaths-mR5ox17n",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
         "Used": [
           "bids::mask",
@@ -272,7 +272,7 @@
       {
         "@id": "urn:fslstats-DM7S9Mpc",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -281,7 +281,7 @@
       {
         "@id": "urn:fslmaths-WkfiIcbD",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -290,7 +290,7 @@
       {
         "@id": "urn:fslstats-aG1XtjHz",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -299,7 +299,7 @@
       {
         "@id": "urn:fslmaths-CtpyYKuB",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
         "Used": [
           "bids::mask"
@@ -308,7 +308,7 @@
       {
         "@id": "urn:fslmaths-2WC0lJN1",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
         "Used": [
           "bids::mask",
@@ -318,7 +318,7 @@
       {
         "@id": "urn:fslmaths-khNo5iOT",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -327,7 +327,7 @@
       {
         "@id": "urn:susan-HnfKAKRm",
         "Label": "susan",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -336,7 +336,7 @@
       {
         "@id": "urn:fslmaths-bhbGoy1D",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
         "Used": [
           "bids::mask",
@@ -346,7 +346,7 @@
       {
         "@id": "urn:fslmaths-v1t2Tib0",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
         "Used": [
           "bids::prefiltered_func_data_smooth"
@@ -355,7 +355,7 @@
       {
         "@id": "urn:fslmaths-f5vk8v8D",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
         "Used": [
           "bids::prefiltered_func_data_intnorm"
@@ -364,7 +364,7 @@
       {
         "@id": "urn:fslmaths-syGOJJLj",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
         "Used": [
           "bids::prefiltered_func_data_intnorm",
@@ -374,7 +374,7 @@
       {
         "@id": "urn:imrm-hHibgoES",
         "Label": "imrm",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
         "Used": [
           "bids::tempMean"
@@ -383,7 +383,7 @@
       {
         "@id": "urn:fslmaths-e9nQDxGR",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
         "Used": [
           "bids::prefiltered_func_data_tempfilt"
@@ -392,7 +392,7 @@
       {
         "@id": "urn:fslmaths-oR3LoS44",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
         "Used": [
           "bids::filtered_func_data"
@@ -401,7 +401,7 @@
       {
         "@id": "urn:rm-UBJlqLmj",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/bin/rm -rf prefiltered_func_data*",
         "Used": [
           "bids::prefiltered_func_data*"
@@ -410,39 +410,39 @@
       {
         "@id": "urn:makedire-GyMaT50A",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-EtMronL8",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
         ]
       },
       {
         "@id": "urn:makedire-5sWMxcHV",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-IQqtsVCJ",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
         ]
       },
       {
         "@id": "urn:filmgls-Ynnm5y4b",
         "Label": "film_gls",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
         "Used": [
           "bids::design.con",
@@ -454,7 +454,7 @@
       {
         "@id": "urn:smoothes-M85mOmBI",
         "Label": "smoothest",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
         "Used": [
           "bids::mask",
@@ -464,7 +464,7 @@
       {
         "@id": "urn:fslmaths-u2OKI4tM",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
         "Used": [
           "bids::mask",
@@ -474,14 +474,14 @@
       {
         "@id": "urn:echo-O7bBldSG",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "echo 38352 > thresh_zstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:cluster-arWUdanS",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 2.3 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z -p 0.05 -d 0.70114 --volume=38352 -c stats/cope1 > cluster_zstat1.txt",
         "Used": [
           "bids::stats/cope1",
@@ -491,7 +491,7 @@
       {
         "@id": "urn:cluster2-SSw3QWij",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
         "Used": [
           "bids::cluster_zstat1"
@@ -500,7 +500,7 @@
       {
         "@id": "urn:fslstats-vYUU0538",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat1"
@@ -509,14 +509,14 @@
       {
         "@id": "urn:overlay-ingy4BcX",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 2.300208 7.488793 rendered_thresh_zstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-mTcDkz7J",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
         "Used": [
           "bids::rendered_thresh_zstat1"
@@ -525,7 +525,7 @@
       {
         "@id": "urn:cp-PR5EAyjU",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
         "Used": [
           "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
@@ -534,25 +534,25 @@
       {
         "@id": "urn:makedire-ZUoir1kH",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "mkdir -p tsplot",
         "Used": []
       },
       {
         "@id": "urn:tsplot-3cwiWj6a",
         "Label": "tsplot",
-        "AssociatedWith": "urn:urn:fsl-z2mBRkGk",
+        "AssociatedWith": "urn:fsl-z2mBRkGk",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
         "Used": []
       }
     ],
     "Entities": [
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "Label": "sub-01_task-tonecounting_bold",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "digest": {
-          "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
+          "sha256": "33501604ae140e58832facff473a9578d5a549403bdbec53107d2b3eaab898ee"
         }
       },
       {
@@ -582,11 +582,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "Label": "sub-01_T1w_brain",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "digest": {
-          "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
+          "sha256": "8f1ae7ba69869c79b2cc5a83ce4ca24a7d666187256c2aa4d61a952b903b05b0"
         }
       },
       {
@@ -622,11 +622,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "Label": "sub-01_T1w",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "digest": {
-          "sha256": "3be6c69338e200d2a286a56cd9a0030539cf50201f412c910ade833e18354d27"
+          "sha256": "8dd4893a9c9500ce8c516f1a9845abf887087d00c2c47fc3524a17d924e78acf"
         }
       },
       {
@@ -1186,11 +1186,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "Label": "sub-01_tone_counting.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "digest": {
-          "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+          "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
         }
       },
       {
@@ -1209,11 +1209,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "Label": "sub-01_tone_counting_probe.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "digest": {
-          "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+          "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
         }
       },
       {
diff --git a/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.png b/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.png
index 0d146534..14eee83b 100644
Binary files a/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.png and b/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.html b/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.html
index e902e09a..6103f229 100644
--- a/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.html
+++ b/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.html
@@ -35,20 +35,20 @@ 
Progress Report / Log

 326956
Initialisation
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
 Total original volumes = 104
 
 /usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
 
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/example_func.nii.gz  -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_reg.html  -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/example_func.nii.gz  -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w  BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 
 Option -F ( FEAT version parameter ) selected with  argument "6.00"
 Option -d ( output directory ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat"
 Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/logs/feat2_pre"
 Option -R ( html unwarping report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_unwarp.html"
 Option -r ( html registration report ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_reg.html"
 Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with  argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with  argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
 Option -w ( highres dof ) selected with  argument "BBR"
 Option -x ( highres search ) selected with  argument "90"
 Option -s ( standard image ) selected with  argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ 
Progress Report / Log

 /bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/reg
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
 
 
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
 
 did not find file: example_func2highres.mat. Generating transform.
 
@@ -128,9 +128,9 @@ 
Progress Report / Log

 /bin/rm -rf prefiltered_func_data*
Stats
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
 
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
 
 /usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con  
 Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.jsonld b/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.jsonld
index 6392e081..396c9382 100644
--- a/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.jsonld
@@ -15,16 +15,16 @@
       {
         "@id": "urn:fslmaths-0UEDBgwF",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold"
+          "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
         ]
       },
       {
         "@id": "urn:fslroi-BiurVc38",
         "Label": "fslroi",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
         "Used": [
           "bids::prefiltered_func_data"
@@ -33,43 +33,43 @@
       {
         "@id": "urn:mainfeat-MbvgcKNU",
         "Label": "mainfeatreg",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
           "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/example_func.nii.gz",
-          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
+          "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:makedire-XQJb6bN7",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/reg",
         "Used": []
       },
       {
         "@id": "urn:fslmaths-wVW9AYbV",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
         ]
       },
       {
         "@id": "urn:fslmaths-zVtrpznD",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
+          "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
         ]
       },
       {
         "@id": "urn:epireg-oMUx8O4H",
         "Label": "epi_reg",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
         "Used": [
           "bids::example_func",
@@ -80,7 +80,7 @@
       {
         "@id": "urn:convertx-CpKNgCUu",
         "Label": "convert_xfm",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
         "Used": [
           "bids::example_func2highres.mat"
@@ -89,7 +89,7 @@
       {
         "@id": "urn:slicer-kSvyNzUC",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -99,7 +99,7 @@
       {
         "@id": "urn:pngappen-YzcHp6V7",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
         "Used": [
           "bids::sla.png",
@@ -119,7 +119,7 @@
       {
         "@id": "urn:slicer-KvB5HBpn",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
         "Used": [
           "bids::example_func2highres",
@@ -129,7 +129,7 @@
       {
         "@id": "urn:pngappen-RZLqGcTy",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
         "Used": [
           "bids::sla.png",
@@ -149,7 +149,7 @@
       {
         "@id": "urn:pngappen-WgIoMyNq",
         "Label": "pngappend",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
         "Used": [
           "bids::example_func2highres1.png",
@@ -159,7 +159,7 @@
       {
         "@id": "urn:rm-CAgyyYms",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/bin/rm -f sl?.png example_func2highres2.png",
         "Used": [
           "bids::example_func2highres2.png",
@@ -169,7 +169,7 @@
       {
         "@id": "urn:rm-SlsnfD6L",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/bin/rm example_func2highres1.png",
         "Used": [
           "bids::example_func2highres1.png"
@@ -178,7 +178,7 @@
       {
         "@id": "urn:mcflirt-jKj3SG5l",
         "Label": "mcflirt",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
         "Used": [
           "bids::prefiltered_func_data"
@@ -187,14 +187,14 @@
       {
         "@id": "urn:makedire-tHA0cfqk",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/bin/mkdir -p mc",
         "Used": []
       },
       {
         "@id": "urn:mv-N7HIMtzW",
         "Label": "mv",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
         "Used": [
           "bids::prefiltered_func_data_mcf.mat",
@@ -208,7 +208,7 @@
       {
         "@id": "urn:fsltsplo-SmYBfYdR",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -217,7 +217,7 @@
       {
         "@id": "urn:fsltsplo-72Yhjlf3",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
         "Used": [
           "bids::prefiltered_func_data_mcf.par"
@@ -226,7 +226,7 @@
       {
         "@id": "urn:fsltsplo-ujOqVhKN",
         "Label": "fsl_tsplot",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
         "Used": [
           "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
@@ -235,7 +235,7 @@
       {
         "@id": "urn:fslmaths-mM2GOkAg",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -244,7 +244,7 @@
       {
         "@id": "urn:bet2-xTMutGSF",
         "Label": "bet2",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
         "Used": [
           "bids::mean_func"
@@ -253,7 +253,7 @@
       {
         "@id": "urn:immv-YxptIEZG",
         "Label": "immv",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
         "Used": [
           "bids::mask_mask"
@@ -262,7 +262,7 @@
       {
         "@id": "urn:fslmaths-s8nkMei9",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
         "Used": [
           "bids::mask",
@@ -272,7 +272,7 @@
       {
         "@id": "urn:fslstats-vXvx6lY9",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -281,7 +281,7 @@
       {
         "@id": "urn:fslmaths-H7MMEeHy",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
         "Used": [
           "bids::prefiltered_func_data_bet"
@@ -290,7 +290,7 @@
       {
         "@id": "urn:fslstats-FeBt6eRG",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
         "Used": [
           "bids::prefiltered_func_data_mcf"
@@ -299,7 +299,7 @@
       {
         "@id": "urn:fslmaths-NIhmMG59",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
         "Used": [
           "bids::mask"
@@ -308,7 +308,7 @@
       {
         "@id": "urn:fslmaths-p6fahobq",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
         "Used": [
           "bids::mask",
@@ -318,7 +318,7 @@
       {
         "@id": "urn:fslmaths-LQpiwNy6",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -327,7 +327,7 @@
       {
         "@id": "urn:susan-K3ufRWdA",
         "Label": "susan",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
         "Used": [
           "bids::prefiltered_func_data_thresh"
@@ -336,7 +336,7 @@
       {
         "@id": "urn:fslmaths-iraiJEXd",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
         "Used": [
           "bids::mask",
@@ -346,7 +346,7 @@
       {
         "@id": "urn:fslmaths-fjFdgb7Z",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
         "Used": [
           "bids::prefiltered_func_data_smooth"
@@ -355,7 +355,7 @@
       {
         "@id": "urn:fslmaths-Ug0ahjSo",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
         "Used": [
           "bids::prefiltered_func_data_intnorm"
@@ -364,7 +364,7 @@
       {
         "@id": "urn:fslmaths-f2LRAapL",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
         "Used": [
           "bids::prefiltered_func_data_intnorm",
@@ -374,7 +374,7 @@
       {
         "@id": "urn:imrm-QaqXCLYu",
         "Label": "imrm",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
         "Used": [
           "bids::tempMean"
@@ -383,7 +383,7 @@
       {
         "@id": "urn:fslmaths-O6KmaYGx",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
         "Used": [
           "bids::prefiltered_func_data_tempfilt"
@@ -392,7 +392,7 @@
       {
         "@id": "urn:fslmaths-gbe18HHZ",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
         "Used": [
           "bids::filtered_func_data"
@@ -401,7 +401,7 @@
       {
         "@id": "urn:rm-7ucPRlke",
         "Label": "rm",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/bin/rm -rf prefiltered_func_data*",
         "Used": [
           "bids::prefiltered_func_data*"
@@ -410,39 +410,39 @@
       {
         "@id": "urn:makedire-8EO8Aqpg",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-Jw0fO03v",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
         ]
       },
       {
         "@id": "urn:makedire-gXxLy0nh",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "mkdir -p custom_timing_files",
         "Used": []
       },
       {
         "@id": "urn:fslfixte-yrsiSJkG",
         "Label": "fslFixText",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
-        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
+        "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
         "Used": [
-          "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt"
+          "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
         ]
       },
       {
         "@id": "urn:filmgls-5qTK83BP",
         "Label": "film_gls",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
         "Used": [
           "bids::design.con",
@@ -454,7 +454,7 @@
       {
         "@id": "urn:smoothes-87cHdl82",
         "Label": "smoothest",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
         "Used": [
           "bids::mask",
@@ -464,7 +464,7 @@
       {
         "@id": "urn:fslmaths-ANaeZf8r",
         "Label": "fslmaths",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
         "Used": [
           "bids::mask",
@@ -474,21 +474,21 @@
       {
         "@id": "urn:echo-TuxoJVVO",
         "Label": "echo",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "echo 38352 > thresh_zstat1.vol",
         "Used": []
       },
       {
         "@id": "urn:ptoz-HpAgX3aE",
         "Label": "ptoz",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.05 -g 5805",
         "Used": []
       },
       {
         "@id": "urn:cluster-PZLrv8qv",
         "Label": "cluster",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 5.042313 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z -r 6.60665 --voxthresh -c stats/cope1 > cluster_zstat1.txt",
         "Used": [
           "bids::stats/cope1",
@@ -498,7 +498,7 @@
       {
         "@id": "urn:cluster2-jDBjYNPn",
         "Label": "cluster2html",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
         "Used": [
           "bids::cluster_zstat1"
@@ -507,7 +507,7 @@
       {
         "@id": "urn:fslstats-8hlZCrqU",
         "Label": "fslstats",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
         "Used": [
           "bids::thresh_zstat1"
@@ -516,14 +516,14 @@
       {
         "@id": "urn:overlay-Dpx5cD5B",
         "Label": "overlay",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 5.043745 7.488793 rendered_thresh_zstat1",
         "Used": []
       },
       {
         "@id": "urn:slicer-DY4kWvOe",
         "Label": "slicer",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
         "Used": [
           "bids::rendered_thresh_zstat1"
@@ -532,7 +532,7 @@
       {
         "@id": "urn:cp-2ftxTogj",
         "Label": "cp",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
         "Used": [
           "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
@@ -541,25 +541,25 @@
       {
         "@id": "urn:makedire-CA7AqUTd",
         "Label": "Make directory",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "mkdir -p tsplot",
         "Used": []
       },
       {
         "@id": "urn:tsplot-dRxmDBIq",
         "Label": "tsplot",
-        "AssociatedWith": "urn:urn:fsl-un0J9v6I",
+        "AssociatedWith": "urn:fsl-un0J9v6I",
         "Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
         "Used": []
       }
     ],
     "Entities": [
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "Label": "sub-01_task-tonecounting_bold",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
         "digest": {
-          "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
+          "sha256": "33501604ae140e58832facff473a9578d5a549403bdbec53107d2b3eaab898ee"
         }
       },
       {
@@ -589,11 +589,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "Label": "sub-01_T1w_brain",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
         "digest": {
-          "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
+          "sha256": "8f1ae7ba69869c79b2cc5a83ce4ca24a7d666187256c2aa4d61a952b903b05b0"
         }
       },
       {
@@ -629,11 +629,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "Label": "sub-01_T1w",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
         "digest": {
-          "sha256": "3be6c69338e200d2a286a56cd9a0030539cf50201f412c910ade833e18354d27"
+          "sha256": "8dd4893a9c9500ce8c516f1a9845abf887087d00c2c47fc3524a17d924e78acf"
         }
       },
       {
@@ -1193,11 +1193,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "Label": "sub-01_tone_counting.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
         "digest": {
-          "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+          "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
         }
       },
       {
@@ -1216,11 +1216,11 @@
         }
       },
       {
-        "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "Label": "sub-01_tone_counting_probe.txt",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+        "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
         "digest": {
-          "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+          "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
         }
       },
       {
diff --git a/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.png b/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.png
index 189370e9..03533b54 100644
Binary files a/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.png and b/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.png differ
diff --git a/examples/from_parsers/spm/spm_2_t_test_batch.jsonld b/examples/from_parsers/spm/spm_2_t_test_batch.jsonld
index 647f6e25..e2d064c3 100644
--- a/examples/from_parsers/spm/spm_2_t_test_batch.jsonld
+++ b/examples/from_parsers/spm/spm_2_t_test_batch.jsonld
@@ -16,24 +16,24 @@
         "@id": "urn:movefile-BRVbHU21",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
+          "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-Oku8US2z",
-        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+        "AssociatedWith": "urn:spm-Oku8US2z",
+        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
         }
       },
       {
         "@id": "urn:movefile-HaY5ANd7",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz"
+          "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-Oku8US2z",
-        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+        "AssociatedWith": "urn:spm-Oku8US2z",
+        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
         }
       },
       {
@@ -42,7 +42,7 @@
         "Used": [
           "urn:uuid:d899ee07-a7c3-4f6e-9e05-69ecc85c4e56"
         ],
-        "AssociatedWith": "urn:urn:spm-Oku8US2z",
+        "AssociatedWith": "urn:spm-Oku8US2z",
         "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -51,7 +51,7 @@
         "Used": [
           "urn:uuid:df7eff64-3f23-4fda-824e-e2dcafc46f75"
         ],
-        "AssociatedWith": "urn:urn:spm-Oku8US2z",
+        "AssociatedWith": "urn:spm-Oku8US2z",
         "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -60,7 +60,7 @@
         "Used": [
           "urn:uuid:397ff0ef-8a7f-4cb3-943f-2c5d419808cb"
         ],
-        "AssociatedWith": "urn:urn:spm-Oku8US2z",
+        "AssociatedWith": "urn:spm-Oku8US2z",
         "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
         "Parameters": {
           "eoptions.quality": "0.9",
@@ -84,7 +84,7 @@
           "urn:uuid:9daef47f-1c26-402a-8d50-e4c33b798080",
           "urn:uuid:b2b6b61f-325a-497d-99b3-d85a41230778"
         ],
-        "AssociatedWith": "urn:urn:spm-Oku8US2z",
+        "AssociatedWith": "urn:spm-Oku8US2z",
         "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
         "Parameters": {
           "other": "{''}",
@@ -100,7 +100,7 @@
         "Used": [
           "urn:uuid:b2b6b61f-325a-497d-99b3-d85a41230778"
         ],
-        "AssociatedWith": "urn:urn:spm-Oku8US2z",
+        "AssociatedWith": "urn:spm-Oku8US2z",
         "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
         "Parameters": {
           "channel.biasreg": "0.001",
@@ -143,10 +143,10 @@
         "@id": "urn:normaliz-533EtjkJ",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz",
+          "bids::c1anat_sub-01_T1w.nii",
           "urn:uuid:9daef47f-1c26-402a-8d50-e4c33b798080"
         ],
-        "AssociatedWith": "urn:urn:spm-Oku8US2z",
+        "AssociatedWith": "urn:spm-Oku8US2z",
         "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -159,9 +159,9 @@
         "@id": "urn:normaliz-pl28hrz0",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz"
+          "bids::c1anat_sub-01_T1w.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-Oku8US2z",
+        "AssociatedWith": "urn:spm-Oku8US2z",
         "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -176,7 +176,7 @@
         "Used": [
           "urn:uuid:558a08f8-cc0f-4f64-9587-c734cd72d4fe"
         ],
-        "AssociatedWith": "urn:urn:spm-Oku8US2z",
+        "AssociatedWith": "urn:spm-Oku8US2z",
         "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
         "Parameters": {
           "fwhm": "[6, 6, 6]",
@@ -190,10 +190,10 @@
         "Label": "Stat Design",
         "Used": [
           "urn:uuid:1c70ac4f-9d4a-4682-8331-00f1fe6826ab",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
+          "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
         ],
-        "AssociatedWith": "urn:urn:spm-Oku8US2z",
-        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_2_T_test'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+        "AssociatedWith": "urn:spm-Oku8US2z",
+        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_2_T_test'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_2_T_test'}",
           "timing.units": "'secs'",
@@ -219,7 +219,7 @@
         "Used": [
           "urn:uuid:22cb89fb-8b91-4b72-802a-a29236185147"
         ],
-        "AssociatedWith": "urn:urn:spm-Oku8US2z",
+        "AssociatedWith": "urn:spm-Oku8US2z",
         "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -232,7 +232,7 @@
         "Used": [
           "urn:uuid:283181d2-881e-4fb3-af47-1f44af243625"
         ],
-        "AssociatedWith": "urn:urn:spm-Oku8US2z",
+        "AssociatedWith": "urn:spm-Oku8US2z",
         "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.name = 'tone counting probe vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.weights = [0 1];\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -250,7 +250,7 @@
         "Used": [
           "urn:uuid:237a2ba0-568c-40f8-b707-c49ba5e24f4e"
         ],
-        "AssociatedWith": "urn:urn:spm-Oku8US2z",
+        "AssociatedWith": "urn:spm-Oku8US2z",
         "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -268,19 +268,19 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "digest": {
-          "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+          "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
         "Label": "anat_sub-01_T1w.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
         "digest": {
-          "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+          "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
         }
       },
       {
@@ -309,7 +309,7 @@
         "GeneratedBy": "urn:gunzip4-IZN4lsQP"
       },
       {
-        "@id": "bids::c1xxx.nii.gz",
+        "@id": "bids::c1anat_sub-01_T1w.nii",
         "Label": "segment1",
         "AtLocation": "c1anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-jPXOheEj",
@@ -318,7 +318,7 @@
         }
       },
       {
-        "@id": "bids::c2xxx.nii.gz",
+        "@id": "bids::c2anat_sub-01_T1w.nii",
         "Label": "segment2",
         "AtLocation": "c2anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-jPXOheEj",
@@ -332,11 +332,11 @@
         "GeneratedBy": "urn:normaliz-533EtjkJ"
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "Label": "ONSETS_sub-01-MultiCond.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "digest": {
-          "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+          "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_2_t_test_batch.png b/examples/from_parsers/spm/spm_2_t_test_batch.png
index e3a8c26a..63219948 100644
Binary files a/examples/from_parsers/spm/spm_2_t_test_batch.png and b/examples/from_parsers/spm/spm_2_t_test_batch.png differ
diff --git a/examples/from_parsers/spm/spm_HRF_informed_basis_batch.jsonld b/examples/from_parsers/spm/spm_HRF_informed_basis_batch.jsonld
index a10fb8c9..c8f25d9e 100644
--- a/examples/from_parsers/spm/spm_HRF_informed_basis_batch.jsonld
+++ b/examples/from_parsers/spm/spm_HRF_informed_basis_batch.jsonld
@@ -16,24 +16,24 @@
         "@id": "urn:movefile-gzlPmudm",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
+          "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-acOHF07M",
-        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+        "AssociatedWith": "urn:spm-acOHF07M",
+        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
         }
       },
       {
         "@id": "urn:movefile-ybi7EcAT",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz"
+          "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-acOHF07M",
-        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+        "AssociatedWith": "urn:spm-acOHF07M",
+        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
         }
       },
       {
@@ -42,7 +42,7 @@
         "Used": [
           "urn:uuid:747672f0-0684-4712-88d7-7caece60c42c"
         ],
-        "AssociatedWith": "urn:urn:spm-acOHF07M",
+        "AssociatedWith": "urn:spm-acOHF07M",
         "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -51,7 +51,7 @@
         "Used": [
           "urn:uuid:36203fcb-8c36-4398-8626-9fb725695b3a"
         ],
-        "AssociatedWith": "urn:urn:spm-acOHF07M",
+        "AssociatedWith": "urn:spm-acOHF07M",
         "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -60,7 +60,7 @@
         "Used": [
           "urn:uuid:dda513d4-ddb2-4de3-8f87-fb8621f2b48e"
         ],
-        "AssociatedWith": "urn:urn:spm-acOHF07M",
+        "AssociatedWith": "urn:spm-acOHF07M",
         "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
         "Parameters": {
           "eoptions.quality": "0.9",
@@ -84,7 +84,7 @@
           "urn:uuid:00b87638-397e-4a77-9523-896dc7559560",
           "urn:uuid:c410a960-d03c-4151-87b8-f58dab758b29"
         ],
-        "AssociatedWith": "urn:urn:spm-acOHF07M",
+        "AssociatedWith": "urn:spm-acOHF07M",
         "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
         "Parameters": {
           "other": "{''}",
@@ -100,7 +100,7 @@
         "Used": [
           "urn:uuid:00b87638-397e-4a77-9523-896dc7559560"
         ],
-        "AssociatedWith": "urn:urn:spm-acOHF07M",
+        "AssociatedWith": "urn:spm-acOHF07M",
         "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
         "Parameters": {
           "channel.biasreg": "0.001",
@@ -143,10 +143,10 @@
         "@id": "urn:normaliz-ZR78Z1Z8",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz",
+          "bids::c1anat_sub-01_T1w.nii",
           "urn:uuid:c410a960-d03c-4151-87b8-f58dab758b29"
         ],
-        "AssociatedWith": "urn:urn:spm-acOHF07M",
+        "AssociatedWith": "urn:spm-acOHF07M",
         "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -159,9 +159,9 @@
         "@id": "urn:normaliz-ZEdAv6uD",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz"
+          "bids::c1anat_sub-01_T1w.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-acOHF07M",
+        "AssociatedWith": "urn:spm-acOHF07M",
         "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -176,7 +176,7 @@
         "Used": [
           "urn:uuid:037e6a92-83f4-4faa-992b-6e18e31af216"
         ],
-        "AssociatedWith": "urn:urn:spm-acOHF07M",
+        "AssociatedWith": "urn:spm-acOHF07M",
         "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
         "Parameters": {
           "fwhm": "[6, 6, 6]",
@@ -190,10 +190,10 @@
         "Label": "Stat Design",
         "Used": [
           "urn:uuid:f8863426-2990-49f3-8228-7c70ae2e41fb",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
+          "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
         ],
-        "AssociatedWith": "urn:urn:spm-acOHF07M",
-        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_HRF_informed_basis'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [1 1];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+        "AssociatedWith": "urn:spm-acOHF07M",
+        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_HRF_informed_basis'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [1 1];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_HRF_informed_basis'}",
           "timing.units": "'secs'",
@@ -219,7 +219,7 @@
         "Used": [
           "urn:uuid:acced37c-e797-480a-bb60-90518dd89a5a"
         ],
-        "AssociatedWith": "urn:urn:spm-acOHF07M",
+        "AssociatedWith": "urn:spm-acOHF07M",
         "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -232,7 +232,7 @@
         "Used": [
           "urn:uuid:99fb6d5b-1d5e-4460-9a59-b669a7b1f326"
         ],
-        "AssociatedWith": "urn:urn:spm-acOHF07M",
+        "AssociatedWith": "urn:spm-acOHF07M",
         "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0 0 0 0 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -247,7 +247,7 @@
         "Used": [
           "urn:uuid:9585246b-56b1-478a-84ba-6cf5cb399a11"
         ],
-        "AssociatedWith": "urn:urn:spm-acOHF07M",
+        "AssociatedWith": "urn:spm-acOHF07M",
         "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -265,19 +265,19 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "digest": {
-          "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+          "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
         "Label": "anat_sub-01_T1w.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
         "digest": {
-          "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+          "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
         }
       },
       {
@@ -306,7 +306,7 @@
         "GeneratedBy": "urn:gunzip4-YMI34NTy"
       },
       {
-        "@id": "bids::c1xxx.nii.gz",
+        "@id": "bids::c1anat_sub-01_T1w.nii",
         "Label": "segment1",
         "AtLocation": "c1anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-cEoNDdlV",
@@ -315,7 +315,7 @@
         }
       },
       {
-        "@id": "bids::c2xxx.nii.gz",
+        "@id": "bids::c2anat_sub-01_T1w.nii",
         "Label": "segment2",
         "AtLocation": "c2anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-cEoNDdlV",
@@ -329,11 +329,11 @@
         "GeneratedBy": "urn:normaliz-ZR78Z1Z8"
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "Label": "ONSETS_sub-01-MultiCond.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "digest": {
-          "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+          "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_HRF_informed_basis_batch.png b/examples/from_parsers/spm/spm_HRF_informed_basis_batch.png
index 5562a361..04e45ab3 100644
Binary files a/examples/from_parsers/spm/spm_HRF_informed_basis_batch.png and b/examples/from_parsers/spm/spm_HRF_informed_basis_batch.png differ
diff --git a/examples/from_parsers/spm/spm_con_f_batch.jsonld b/examples/from_parsers/spm/spm_con_f_batch.jsonld
index 6dda7469..61a3f6b4 100644
--- a/examples/from_parsers/spm/spm_con_f_batch.jsonld
+++ b/examples/from_parsers/spm/spm_con_f_batch.jsonld
@@ -16,24 +16,24 @@
         "@id": "urn:movefile-l6on4kPt",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
+          "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-LIc1sKxA",
-        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+        "AssociatedWith": "urn:spm-LIc1sKxA",
+        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
         }
       },
       {
         "@id": "urn:movefile-gCawKlZC",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz"
+          "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-LIc1sKxA",
-        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+        "AssociatedWith": "urn:spm-LIc1sKxA",
+        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
         }
       },
       {
@@ -42,7 +42,7 @@
         "Used": [
           "urn:uuid:f924aef0-c377-4618-90cd-49b9737ac11b"
         ],
-        "AssociatedWith": "urn:urn:spm-LIc1sKxA",
+        "AssociatedWith": "urn:spm-LIc1sKxA",
         "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -51,7 +51,7 @@
         "Used": [
           "urn:uuid:dcbe17a9-4395-42db-81ad-f008aba1aa73"
         ],
-        "AssociatedWith": "urn:urn:spm-LIc1sKxA",
+        "AssociatedWith": "urn:spm-LIc1sKxA",
         "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -60,7 +60,7 @@
         "Used": [
           "urn:uuid:d7fe707e-3f18-495a-9770-0880b857106a"
         ],
-        "AssociatedWith": "urn:urn:spm-LIc1sKxA",
+        "AssociatedWith": "urn:spm-LIc1sKxA",
         "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
         "Parameters": {
           "eoptions.quality": "0.9",
@@ -84,7 +84,7 @@
           "urn:uuid:7dee6d95-ad21-48fd-82b3-94b72841daa9",
           "urn:uuid:f513ed91-4479-4983-a375-948d936720b2"
         ],
-        "AssociatedWith": "urn:urn:spm-LIc1sKxA",
+        "AssociatedWith": "urn:spm-LIc1sKxA",
         "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
         "Parameters": {
           "other": "{''}",
@@ -100,7 +100,7 @@
         "Used": [
           "urn:uuid:f513ed91-4479-4983-a375-948d936720b2"
         ],
-        "AssociatedWith": "urn:urn:spm-LIc1sKxA",
+        "AssociatedWith": "urn:spm-LIc1sKxA",
         "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
         "Parameters": {
           "channel.biasreg": "0.001",
@@ -143,10 +143,10 @@
         "@id": "urn:normaliz-sQlDnSmF",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz",
+          "bids::c1anat_sub-01_T1w.nii",
           "urn:uuid:7dee6d95-ad21-48fd-82b3-94b72841daa9"
         ],
-        "AssociatedWith": "urn:urn:spm-LIc1sKxA",
+        "AssociatedWith": "urn:spm-LIc1sKxA",
         "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -159,9 +159,9 @@
         "@id": "urn:normaliz-NtUekQwA",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz"
+          "bids::c1anat_sub-01_T1w.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-LIc1sKxA",
+        "AssociatedWith": "urn:spm-LIc1sKxA",
         "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -176,7 +176,7 @@
         "Used": [
           "urn:uuid:69bc2ab3-775e-48d7-adf5-f26c27756556"
         ],
-        "AssociatedWith": "urn:urn:spm-LIc1sKxA",
+        "AssociatedWith": "urn:spm-LIc1sKxA",
         "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
         "Parameters": {
           "fwhm": "[6, 6, 6]",
@@ -190,10 +190,10 @@
         "Label": "Stat Design",
         "Used": [
           "urn:uuid:6c3ee28c-e553-4883-87e8-be4bcf1ef14e",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
+          "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
         ],
-        "AssociatedWith": "urn:urn:spm-LIc1sKxA",
-        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_f_test'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+        "AssociatedWith": "urn:spm-LIc1sKxA",
+        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_f_test'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_f_test'}",
           "timing.units": "'secs'",
@@ -219,7 +219,7 @@
         "Used": [
           "urn:uuid:6d42344f-9f8a-49f4-9e32-812a3fa10f4f"
         ],
-        "AssociatedWith": "urn:urn:spm-LIc1sKxA",
+        "AssociatedWith": "urn:spm-LIc1sKxA",
         "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -232,7 +232,7 @@
         "Used": [
           "urn:uuid:d85f47b5-55f9-4f28-ba22-d59267366a84"
         ],
-        "AssociatedWith": "urn:urn:spm-LIc1sKxA",
+        "AssociatedWith": "urn:spm-LIc1sKxA",
         "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.fcon.name": "'tone counting vs baseline'",
@@ -247,7 +247,7 @@
         "Used": [
           "urn:uuid:c0af5110-55f0-4492-847d-c70be4c4b90b"
         ],
-        "AssociatedWith": "urn:urn:spm-LIc1sKxA",
+        "AssociatedWith": "urn:spm-LIc1sKxA",
         "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -265,19 +265,19 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "digest": {
-          "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+          "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
         "Label": "anat_sub-01_T1w.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
         "digest": {
-          "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+          "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
         }
       },
       {
@@ -306,7 +306,7 @@
         "GeneratedBy": "urn:gunzip4-c5kwgRLI"
       },
       {
-        "@id": "bids::c1xxx.nii.gz",
+        "@id": "bids::c1anat_sub-01_T1w.nii",
         "Label": "segment1",
         "AtLocation": "c1anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-1il83Pxd",
@@ -315,7 +315,7 @@
         }
       },
       {
-        "@id": "bids::c2xxx.nii.gz",
+        "@id": "bids::c2anat_sub-01_T1w.nii",
         "Label": "segment2",
         "AtLocation": "c2anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-1il83Pxd",
@@ -329,11 +329,11 @@
         "GeneratedBy": "urn:normaliz-sQlDnSmF"
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "Label": "ONSETS_sub-01-MultiCond.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "digest": {
-          "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+          "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_con_f_batch.png b/examples/from_parsers/spm/spm_con_f_batch.png
index 318c7fa3..1f04e078 100644
Binary files a/examples/from_parsers/spm/spm_con_f_batch.png and b/examples/from_parsers/spm/spm_con_f_batch.png differ
diff --git a/examples/from_parsers/spm/spm_conjunction_batch.jsonld b/examples/from_parsers/spm/spm_conjunction_batch.jsonld
index d51b84ff..eeb1d1cd 100644
--- a/examples/from_parsers/spm/spm_conjunction_batch.jsonld
+++ b/examples/from_parsers/spm/spm_conjunction_batch.jsonld
@@ -16,24 +16,24 @@
         "@id": "urn:movefile-tGqsV6q1",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
+          "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-VrPimuXr",
-        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+        "AssociatedWith": "urn:spm-VrPimuXr",
+        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
         }
       },
       {
         "@id": "urn:movefile-fPTQrpaA",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz"
+          "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-VrPimuXr",
-        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+        "AssociatedWith": "urn:spm-VrPimuXr",
+        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
         }
       },
       {
@@ -42,7 +42,7 @@
         "Used": [
           "urn:uuid:2c041aaf-c929-4e12-90b5-cdf5a6ade028"
         ],
-        "AssociatedWith": "urn:urn:spm-VrPimuXr",
+        "AssociatedWith": "urn:spm-VrPimuXr",
         "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -51,7 +51,7 @@
         "Used": [
           "urn:uuid:473debad-a73f-48c7-b52d-5fe5822d3c13"
         ],
-        "AssociatedWith": "urn:urn:spm-VrPimuXr",
+        "AssociatedWith": "urn:spm-VrPimuXr",
         "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -60,7 +60,7 @@
         "Used": [
           "urn:uuid:3a64eb02-6ded-4241-aff4-cd111dc36067"
         ],
-        "AssociatedWith": "urn:urn:spm-VrPimuXr",
+        "AssociatedWith": "urn:spm-VrPimuXr",
         "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
         "Parameters": {
           "eoptions.quality": "0.9",
@@ -84,7 +84,7 @@
           "urn:uuid:14f4afb9-bb97-4388-ab12-b659b98d6623",
           "urn:uuid:dbbfa8c4-6083-4348-b3ea-83228889aec2"
         ],
-        "AssociatedWith": "urn:urn:spm-VrPimuXr",
+        "AssociatedWith": "urn:spm-VrPimuXr",
         "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
         "Parameters": {
           "other": "{''}",
@@ -100,7 +100,7 @@
         "Used": [
           "urn:uuid:14f4afb9-bb97-4388-ab12-b659b98d6623"
         ],
-        "AssociatedWith": "urn:urn:spm-VrPimuXr",
+        "AssociatedWith": "urn:spm-VrPimuXr",
         "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
         "Parameters": {
           "channel.biasreg": "0.001",
@@ -143,10 +143,10 @@
         "@id": "urn:normaliz-DWfjdY79",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz",
+          "bids::c1anat_sub-01_T1w.nii",
           "urn:uuid:dbbfa8c4-6083-4348-b3ea-83228889aec2"
         ],
-        "AssociatedWith": "urn:urn:spm-VrPimuXr",
+        "AssociatedWith": "urn:spm-VrPimuXr",
         "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -159,9 +159,9 @@
         "@id": "urn:normaliz-R5mjdY3T",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz"
+          "bids::c1anat_sub-01_T1w.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-VrPimuXr",
+        "AssociatedWith": "urn:spm-VrPimuXr",
         "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -176,7 +176,7 @@
         "Used": [
           "urn:uuid:24e209e7-b6d1-4657-9d88-3a95ac5cbb5f"
         ],
-        "AssociatedWith": "urn:urn:spm-VrPimuXr",
+        "AssociatedWith": "urn:spm-VrPimuXr",
         "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
         "Parameters": {
           "fwhm": "[6, 6, 6]",
@@ -190,10 +190,10 @@
         "Label": "Stat Design",
         "Used": [
           "urn:uuid:aea8ebea-ec5f-4039-bd16-b99011d66766",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
+          "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
         ],
-        "AssociatedWith": "urn:urn:spm-VrPimuXr",
-        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_partial_conjunction'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+        "AssociatedWith": "urn:spm-VrPimuXr",
+        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_partial_conjunction'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_partial_conjunction'}",
           "timing.units": "'secs'",
@@ -219,7 +219,7 @@
         "Used": [
           "urn:uuid:1228ef88-6dd1-4270-866b-396a614e9ae5"
         ],
-        "AssociatedWith": "urn:urn:spm-VrPimuXr",
+        "AssociatedWith": "urn:spm-VrPimuXr",
         "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -232,7 +232,7 @@
         "Used": [
           "urn:uuid:b9686194-6f64-439f-90d7-badf8f509837"
         ],
-        "AssociatedWith": "urn:urn:spm-VrPimuXr",
+        "AssociatedWith": "urn:spm-VrPimuXr",
         "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.name = 'tone counting probe vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.weights = [0 1];\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -250,7 +250,7 @@
         "Used": [
           "urn:uuid:b84b03c2-3796-4f03-8a8a-0929d5dbf8bf"
         ],
-        "AssociatedWith": "urn:urn:spm-VrPimuXr",
+        "AssociatedWith": "urn:spm-VrPimuXr",
         "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = [1 2];\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -268,19 +268,19 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "digest": {
-          "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+          "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
         "Label": "anat_sub-01_T1w.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
         "digest": {
-          "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+          "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
         }
       },
       {
@@ -309,7 +309,7 @@
         "GeneratedBy": "urn:gunzip4-WwCnI7oL"
       },
       {
-        "@id": "bids::c1xxx.nii.gz",
+        "@id": "bids::c1anat_sub-01_T1w.nii",
         "Label": "segment1",
         "AtLocation": "c1anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-b7l5mBx1",
@@ -318,7 +318,7 @@
         }
       },
       {
-        "@id": "bids::c2xxx.nii.gz",
+        "@id": "bids::c2anat_sub-01_T1w.nii",
         "Label": "segment2",
         "AtLocation": "c2anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-b7l5mBx1",
@@ -332,11 +332,11 @@
         "GeneratedBy": "urn:normaliz-DWfjdY79"
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "Label": "ONSETS_sub-01-MultiCond.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "digest": {
-          "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+          "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_conjunction_batch.png b/examples/from_parsers/spm/spm_conjunction_batch.png
index 42732b52..d191651e 100644
Binary files a/examples/from_parsers/spm/spm_conjunction_batch.png and b/examples/from_parsers/spm/spm_conjunction_batch.png differ
diff --git a/examples/from_parsers/spm/spm_contrast_mask_batch.jsonld b/examples/from_parsers/spm/spm_contrast_mask_batch.jsonld
index 1655560e..9a85cb12 100644
--- a/examples/from_parsers/spm/spm_contrast_mask_batch.jsonld
+++ b/examples/from_parsers/spm/spm_contrast_mask_batch.jsonld
@@ -16,24 +16,24 @@
         "@id": "urn:movefile-yUJIwuSB",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
+          "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-9BNLPRS1",
-        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+        "AssociatedWith": "urn:spm-9BNLPRS1",
+        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
         }
       },
       {
         "@id": "urn:movefile-fRoKDI2e",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz"
+          "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-9BNLPRS1",
-        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+        "AssociatedWith": "urn:spm-9BNLPRS1",
+        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
         }
       },
       {
@@ -42,7 +42,7 @@
         "Used": [
           "urn:uuid:357f205f-1573-4bc1-8f0e-d94d48788a5d"
         ],
-        "AssociatedWith": "urn:urn:spm-9BNLPRS1",
+        "AssociatedWith": "urn:spm-9BNLPRS1",
         "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -51,7 +51,7 @@
         "Used": [
           "urn:uuid:6a87cd1a-ea9a-4d7d-b8d4-8dddc1bf2340"
         ],
-        "AssociatedWith": "urn:urn:spm-9BNLPRS1",
+        "AssociatedWith": "urn:spm-9BNLPRS1",
         "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -60,7 +60,7 @@
         "Used": [
           "urn:uuid:9941a786-0a67-439d-8bca-bafc3b34cbc2"
         ],
-        "AssociatedWith": "urn:urn:spm-9BNLPRS1",
+        "AssociatedWith": "urn:spm-9BNLPRS1",
         "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
         "Parameters": {
           "eoptions.quality": "0.9",
@@ -84,7 +84,7 @@
           "urn:uuid:07dfde62-9084-4f4d-b991-e3c8be405785",
           "urn:uuid:78b1081a-34a1-4dce-96f0-89a9f7c53801"
         ],
-        "AssociatedWith": "urn:urn:spm-9BNLPRS1",
+        "AssociatedWith": "urn:spm-9BNLPRS1",
         "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
         "Parameters": {
           "other": "{''}",
@@ -100,7 +100,7 @@
         "Used": [
           "urn:uuid:07dfde62-9084-4f4d-b991-e3c8be405785"
         ],
-        "AssociatedWith": "urn:urn:spm-9BNLPRS1",
+        "AssociatedWith": "urn:spm-9BNLPRS1",
         "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
         "Parameters": {
           "channel.biasreg": "0.001",
@@ -143,10 +143,10 @@
         "@id": "urn:normaliz-Rt8gp4xI",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz",
+          "bids::c1anat_sub-01_T1w.nii",
           "urn:uuid:78b1081a-34a1-4dce-96f0-89a9f7c53801"
         ],
-        "AssociatedWith": "urn:urn:spm-9BNLPRS1",
+        "AssociatedWith": "urn:spm-9BNLPRS1",
         "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -159,9 +159,9 @@
         "@id": "urn:normaliz-tmfheJ0r",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz"
+          "bids::c1anat_sub-01_T1w.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-9BNLPRS1",
+        "AssociatedWith": "urn:spm-9BNLPRS1",
         "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -176,7 +176,7 @@
         "Used": [
           "urn:uuid:5d723e97-e2b2-4a28-9d61-3d89050ad61f"
         ],
-        "AssociatedWith": "urn:urn:spm-9BNLPRS1",
+        "AssociatedWith": "urn:spm-9BNLPRS1",
         "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
         "Parameters": {
           "fwhm": "[6, 6, 6]",
@@ -190,10 +190,10 @@
         "Label": "Stat Design",
         "Used": [
           "urn:uuid:85cbe84d-fbf4-4366-825d-54931c139b4d",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
+          "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
         ],
-        "AssociatedWith": "urn:urn:spm-9BNLPRS1",
-        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+        "AssociatedWith": "urn:spm-9BNLPRS1",
+        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask'}",
           "timing.units": "'secs'",
@@ -219,7 +219,7 @@
         "Used": [
           "urn:uuid:abafb5fa-fa32-4591-9115-a717462f2ce5"
         ],
-        "AssociatedWith": "urn:urn:spm-9BNLPRS1",
+        "AssociatedWith": "urn:spm-9BNLPRS1",
         "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -232,7 +232,7 @@
         "Used": [
           "urn:uuid:ca9dcba3-debf-4891-b190-d312089278da"
         ],
-        "AssociatedWith": "urn:urn:spm-9BNLPRS1",
+        "AssociatedWith": "urn:spm-9BNLPRS1",
         "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.name = 'tone counting probe vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.weights = [0 1];\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -250,7 +250,7 @@
         "Used": [
           "urn:uuid:fd8fe8cb-966a-49ab-b146-36373fe5be5a"
         ],
-        "AssociatedWith": "urn:urn:spm-9BNLPRS1",
+        "AssociatedWith": "urn:spm-9BNLPRS1",
         "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = 1;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.contrast.contrasts = 2;\nmatlabbatch{14}.spm.stats.results.conspec.mask.contrast.thresh = 0.05;\nmatlabbatch{14}.spm.stats.results.conspec.mask.contrast.mtype = 0;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -270,19 +270,19 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "digest": {
-          "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+          "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
         "Label": "anat_sub-01_T1w.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
         "digest": {
-          "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+          "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
         }
       },
       {
@@ -311,7 +311,7 @@
         "GeneratedBy": "urn:gunzip4-7VNZFWp2"
       },
       {
-        "@id": "bids::c1xxx.nii.gz",
+        "@id": "bids::c1anat_sub-01_T1w.nii",
         "Label": "segment1",
         "AtLocation": "c1anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-8MUq9DK6",
@@ -320,7 +320,7 @@
         }
       },
       {
-        "@id": "bids::c2xxx.nii.gz",
+        "@id": "bids::c2anat_sub-01_T1w.nii",
         "Label": "segment2",
         "AtLocation": "c2anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-8MUq9DK6",
@@ -334,11 +334,11 @@
         "GeneratedBy": "urn:normaliz-Rt8gp4xI"
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "Label": "ONSETS_sub-01-MultiCond.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "digest": {
-          "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+          "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_contrast_mask_batch.png b/examples/from_parsers/spm/spm_contrast_mask_batch.png
index 8f3a48c2..0827c6b2 100644
Binary files a/examples/from_parsers/spm/spm_contrast_mask_batch.png and b/examples/from_parsers/spm/spm_contrast_mask_batch.png differ
diff --git a/examples/from_parsers/spm/spm_covariate_batch.jsonld b/examples/from_parsers/spm/spm_covariate_batch.jsonld
index 51ec9620..498a9d62 100644
--- a/examples/from_parsers/spm/spm_covariate_batch.jsonld
+++ b/examples/from_parsers/spm/spm_covariate_batch.jsonld
@@ -16,22 +16,22 @@
         "@id": "urn:statsfac-klpMDd74",
         "Label": "stats.factorial_design",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub01/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub02/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub03/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub04/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub05/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub06/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub07/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub08/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub09/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub10/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub11/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub12/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub13/con_0001.nii"
+          "bids:ds000052:/derivatives/RESULTS/Sub01/con_0001.nii",
+          "bids:ds000052:/derivatives/RESULTS/Sub02/con_0001.nii",
+          "bids:ds000052:/derivatives/RESULTS/Sub03/con_0001.nii",
+          "bids:ds000052:/derivatives/RESULTS/Sub04/con_0001.nii",
+          "bids:ds000052:/derivatives/RESULTS/Sub05/con_0001.nii",
+          "bids:ds000052:/derivatives/RESULTS/Sub06/con_0001.nii",
+          "bids:ds000052:/derivatives/RESULTS/Sub07/con_0001.nii",
+          "bids:ds000052:/derivatives/RESULTS/Sub08/con_0001.nii",
+          "bids:ds000052:/derivatives/RESULTS/Sub09/con_0001.nii",
+          "bids:ds000052:/derivatives/RESULTS/Sub10/con_0001.nii",
+          "bids:ds000052:/derivatives/RESULTS/Sub11/con_0001.nii",
+          "bids:ds000052:/derivatives/RESULTS/Sub12/con_0001.nii",
+          "bids:ds000052:/derivatives/RESULTS/Sub13/con_0001.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-ILFsPa9q",
-        "Command": "matlabbatch{1}.spm.stats.factorial_design.dir = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Group/Con1/Covariate'};\nmatlabbatch{1}.spm.stats.factorial_design.des.t1.scans = {'/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub01/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub02/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub03/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub04/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub05/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub06/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub07/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub08/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub09/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub10/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub11/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub12/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub13/con_0001.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.cov.c = [1 2 3 4 5 6 7 8 9 10 11 12 13];\nmatlabbatch{1}.spm.stats.factorial_design.cov.cname = 'Subject ID Covariate';\nmatlabbatch{1}.spm.stats.factorial_design.cov.iCFI = 1;\nmatlabbatch{1}.spm.stats.factorial_design.cov.iCC = 1;\nmatlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.im = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.em = {''};\nmatlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;",
+        "AssociatedWith": "urn:spm-ILFsPa9q",
+        "Command": "matlabbatch{1}.spm.stats.factorial_design.dir = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Group/Con1/Covariate'};\nmatlabbatch{1}.spm.stats.factorial_design.des.t1.scans = {'ds000052/derivatives/RESULTS/Sub01/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub02/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub03/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub04/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub05/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub06/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub07/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub08/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub09/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub10/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub11/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub12/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub13/con_0001.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.cov.c = [1 2 3 4 5 6 7 8 9 10 11 12 13];\nmatlabbatch{1}.spm.stats.factorial_design.cov.cname = 'Subject ID Covariate';\nmatlabbatch{1}.spm.stats.factorial_design.cov.iCFI = 1;\nmatlabbatch{1}.spm.stats.factorial_design.cov.iCC = 1;\nmatlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.im = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.em = {''};\nmatlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Group/Con1/Covariate'}",
           "cov.c": "[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13]",
@@ -53,7 +53,7 @@
         "Used": [
           "urn:uuid:cfc80838-d9ff-4793-ac2c-e0a0851ad593"
         ],
-        "AssociatedWith": "urn:urn:spm-ILFsPa9q",
+        "AssociatedWith": "urn:spm-ILFsPa9q",
         "Command": "matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('Factorial design specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -66,7 +66,7 @@
         "Used": [
           "urn:uuid:9e95a934-5b6d-4d9c-a449-95270860b977"
         ],
-        "AssociatedWith": "urn:urn:spm-ILFsPa9q",
+        "AssociatedWith": "urn:spm-ILFsPa9q",
         "Command": "matlabbatch{3}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.name = 'mr vs plain covariate';\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.weights = 1;\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{3}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'mr vs plain covariate'",
@@ -81,7 +81,7 @@
         "Used": [
           "urn:uuid:5e027a17-5b75-42a3-b146-0daadab5e6fe"
         ],
-        "AssociatedWith": "urn:urn:spm-ILFsPa9q",
+        "AssociatedWith": "urn:spm-ILFsPa9q",
         "Command": "matlabbatch{4}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{4}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{4}.spm.stats.results.conspec.contrasts = 1;\nmatlabbatch{4}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{4}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{4}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{4}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{4}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{4}.spm.stats.results.units = 1;\nmatlabbatch{4}.spm.stats.results.print = 'pdf';\nmatlabbatch{4}.spm.stats.results.write.none = 1;",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -99,107 +99,107 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub01/con_0001.nii",
+        "@id": "bids:ds000052:/derivatives/RESULTS/Sub01/con_0001.nii",
         "Label": "Sub01_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub01/con_0001.nii",
+        "AtLocation": "ds000052/derivatives/RESULTS/Sub01/con_0001.nii",
         "digest": {
-          "sha256": "704577900564ed2e3e736d470b01bad03b83022cf231d8378a167ec7348905f1"
+          "sha256": "c14419840edfdea555406b52849de36be2f7230b0877b056b9101011cbf1fd7d"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub02/con_0001.nii",
+        "@id": "bids:ds000052:/derivatives/RESULTS/Sub02/con_0001.nii",
         "Label": "Sub02_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub02/con_0001.nii",
+        "AtLocation": "ds000052/derivatives/RESULTS/Sub02/con_0001.nii",
         "digest": {
-          "sha256": "14babae7ee4ec3b0900aba762fbacb79528cfa00d1a7bcd26b71136e15ddbb61"
+          "sha256": "741bcd68a30e79ea65ea38035ab841c67bc108e65ffc4c3b93ac9d8d1363e8d3"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub03/con_0001.nii",
+        "@id": "bids:ds000052:/derivatives/RESULTS/Sub03/con_0001.nii",
         "Label": "Sub03_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub03/con_0001.nii",
+        "AtLocation": "ds000052/derivatives/RESULTS/Sub03/con_0001.nii",
         "digest": {
-          "sha256": "714d199baaa9dfa41cf5c4ca0f9a776f3267ae67035bb2ce47280233c4f27605"
+          "sha256": "25040c6d252b447614a368ac2af1ac90abd612f050039700d7aa9a7dff0794e3"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub04/con_0001.nii",
+        "@id": "bids:ds000052:/derivatives/RESULTS/Sub04/con_0001.nii",
         "Label": "Sub04_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub04/con_0001.nii",
+        "AtLocation": "ds000052/derivatives/RESULTS/Sub04/con_0001.nii",
         "digest": {
-          "sha256": "40d17679357316a794c6022e01bb3961d089c91ef7d3bc1758e36dad76d3d8ca"
+          "sha256": "21d270ed11f33895cc0aa0181f443872c11d8c2cc336386c6bcc35c6eadf3c21"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub05/con_0001.nii",
+        "@id": "bids:ds000052:/derivatives/RESULTS/Sub05/con_0001.nii",
         "Label": "Sub05_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub05/con_0001.nii",
+        "AtLocation": "ds000052/derivatives/RESULTS/Sub05/con_0001.nii",
         "digest": {
-          "sha256": "e19f465c6715be288733d5a058f5d77ddf860988c4ddc0fbe4ca8e1b998c367e"
+          "sha256": "95a6e92d930cd24b203e3923df7413f928bc6036d1c1ecffca52c879de159a65"
         }
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       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub06/con_0001.nii",
+        "@id": "bids:ds000052:/derivatives/RESULTS/Sub06/con_0001.nii",
         "Label": "Sub06_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub06/con_0001.nii",
+        "AtLocation": "ds000052/derivatives/RESULTS/Sub06/con_0001.nii",
         "digest": {
-          "sha256": "8871fd17416dd4fa6d4fc1eaec9f9de8ecc4881ab3a717248bdcbeab339f62ea"
+          "sha256": "d624963f2c71c041a275bc88536e89234ddbe0becba129fedc32e3256abab7bd"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub07/con_0001.nii",
+        "@id": "bids:ds000052:/derivatives/RESULTS/Sub07/con_0001.nii",
         "Label": "Sub07_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub07/con_0001.nii",
+        "AtLocation": "ds000052/derivatives/RESULTS/Sub07/con_0001.nii",
         "digest": {
-          "sha256": "26bea69994f70bb534f943c181a9e29285a4847588c3b37b078390c517148ce7"
+          "sha256": "369e1c91a65a2b54ed8bc6285d2473e56b490cb5595022ac9a221882b2167ee2"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub08/con_0001.nii",
+        "@id": "bids:ds000052:/derivatives/RESULTS/Sub08/con_0001.nii",
         "Label": "Sub08_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub08/con_0001.nii",
+        "AtLocation": "ds000052/derivatives/RESULTS/Sub08/con_0001.nii",
         "digest": {
-          "sha256": "607ec837ad2ac763888312643b9a26dac34935f3877640166953d1d39b11f7d4"
+          "sha256": "6c196ea2d482a350cb343d20e601fc50fb8d153e11d970bbb242aa13c39e7cce"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub09/con_0001.nii",
+        "@id": "bids:ds000052:/derivatives/RESULTS/Sub09/con_0001.nii",
         "Label": "Sub09_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub09/con_0001.nii",
+        "AtLocation": "ds000052/derivatives/RESULTS/Sub09/con_0001.nii",
         "digest": {
-          "sha256": "1dfee1d8dd34377d9c9647574c17ca67f958dab99ddbee7c2fda1ad8514f135f"
+          "sha256": "6a93a12c6d89080af5ea69ec7a3078e843def7269ed4d4cf776ccc7d080f8cfe"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub10/con_0001.nii",
+        "@id": "bids:ds000052:/derivatives/RESULTS/Sub10/con_0001.nii",
         "Label": "Sub10_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub10/con_0001.nii",
+        "AtLocation": "ds000052/derivatives/RESULTS/Sub10/con_0001.nii",
         "digest": {
-          "sha256": "93177653f7acb26a20a92f6df631b9ffdc119e8e40ecc9247e276439e27574b2"
+          "sha256": "f923f8151fdf7119e5cb426a935cae7f1aa1582822fb07a865364c3bba02e3c9"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub11/con_0001.nii",
+        "@id": "bids:ds000052:/derivatives/RESULTS/Sub11/con_0001.nii",
         "Label": "Sub11_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub11/con_0001.nii",
+        "AtLocation": "ds000052/derivatives/RESULTS/Sub11/con_0001.nii",
         "digest": {
-          "sha256": "e2431595e2d7c4cf169ad2f2c4af36e864cbf4ff096cea38de561563e18d54f6"
+          "sha256": "e076877ebd2146a298d0380ddbe45580171fc71cfa94eb8ac337118ccef3bbff"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub12/con_0001.nii",
+        "@id": "bids:ds000052:/derivatives/RESULTS/Sub12/con_0001.nii",
         "Label": "Sub12_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub12/con_0001.nii",
+        "AtLocation": "ds000052/derivatives/RESULTS/Sub12/con_0001.nii",
         "digest": {
-          "sha256": "fb18a6c85cf95c02a096c6c5f6d2711e9615b62f181ca3a8d166ccf2712a9d62"
+          "sha256": "cc40406387b7b11378733abac384fbfc2193ba48f8bab85290cc1cbb3aabfd27"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub13/con_0001.nii",
+        "@id": "bids:ds000052:/derivatives/RESULTS/Sub13/con_0001.nii",
         "Label": "Sub13_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub13/con_0001.nii",
+        "AtLocation": "ds000052/derivatives/RESULTS/Sub13/con_0001.nii",
         "digest": {
-          "sha256": "cc87406762aa344c9da8d218226464f61a05c1486aa7b9ad0708de27a8ee879d"
+          "sha256": "16c2d63a3e674532436f5e263ee7da006d79483fa114a4a6f1cfc31c56d8cda9"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_covariate_batch.m b/examples/from_parsers/spm/spm_covariate_batch.m
index 6e9afdf6..931871f9 100644
--- a/examples/from_parsers/spm/spm_covariate_batch.m
+++ b/examples/from_parsers/spm/spm_covariate_batch.m
@@ -6,19 +6,19 @@
 matlabbatch{1}.spm.stats.factorial_design.dir = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Group/Con1/Covariate'};
 %%
 matlabbatch{1}.spm.stats.factorial_design.des.t1.scans = {
-                                                          '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub01/con_0001.nii,1'
-                                                          '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub02/con_0001.nii,1'
-                                                          '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub03/con_0001.nii,1'
-                                                          '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub04/con_0001.nii,1'
-                                                          '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub05/con_0001.nii,1'
-                                                          '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub06/con_0001.nii,1'
-                                                          '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub07/con_0001.nii,1'
-                                                          '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub08/con_0001.nii,1'
-                                                          '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub09/con_0001.nii,1'
-                                                          '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub10/con_0001.nii,1'
-                                                          '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub11/con_0001.nii,1'
-                                                          '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub12/con_0001.nii,1'
-                                                          '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub13/con_0001.nii,1'
+                                                          'ds000052/derivatives/RESULTS/Sub01/con_0001.nii,1'
+                                                          'ds000052/derivatives/RESULTS/Sub02/con_0001.nii,1'
+                                                          'ds000052/derivatives/RESULTS/Sub03/con_0001.nii,1'
+                                                          'ds000052/derivatives/RESULTS/Sub04/con_0001.nii,1'
+                                                          'ds000052/derivatives/RESULTS/Sub05/con_0001.nii,1'
+                                                          'ds000052/derivatives/RESULTS/Sub06/con_0001.nii,1'
+                                                          'ds000052/derivatives/RESULTS/Sub07/con_0001.nii,1'
+                                                          'ds000052/derivatives/RESULTS/Sub08/con_0001.nii,1'
+                                                          'ds000052/derivatives/RESULTS/Sub09/con_0001.nii,1'
+                                                          'ds000052/derivatives/RESULTS/Sub10/con_0001.nii,1'
+                                                          'ds000052/derivatives/RESULTS/Sub11/con_0001.nii,1'
+                                                          'ds000052/derivatives/RESULTS/Sub12/con_0001.nii,1'
+                                                          'ds000052/derivatives/RESULTS/Sub13/con_0001.nii,1'
                                                           };
 %%
 %%
diff --git a/examples/from_parsers/spm/spm_covariate_batch.png b/examples/from_parsers/spm/spm_covariate_batch.png
index b9f8abc3..401717dc 100644
Binary files a/examples/from_parsers/spm/spm_covariate_batch.png and b/examples/from_parsers/spm/spm_covariate_batch.png differ
diff --git a/examples/from_parsers/spm/spm_default_batch.jsonld b/examples/from_parsers/spm/spm_default_batch.jsonld
index 1559845b..05ae3dd7 100644
--- a/examples/from_parsers/spm/spm_default_batch.jsonld
+++ b/examples/from_parsers/spm/spm_default_batch.jsonld
@@ -16,24 +16,24 @@
         "@id": "urn:movefile-R2ejLXJG",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
+          "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-gmrVZH0W",
-        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+        "AssociatedWith": "urn:spm-gmrVZH0W",
+        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
         }
       },
       {
         "@id": "urn:movefile-hivUZu8r",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz"
+          "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-gmrVZH0W",
-        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+        "AssociatedWith": "urn:spm-gmrVZH0W",
+        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
         }
       },
       {
@@ -42,7 +42,7 @@
         "Used": [
           "urn:uuid:8bc92dcc-ff1e-49c3-9d0f-0ca7a0978c4c"
         ],
-        "AssociatedWith": "urn:urn:spm-gmrVZH0W",
+        "AssociatedWith": "urn:spm-gmrVZH0W",
         "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -51,7 +51,7 @@
         "Used": [
           "urn:uuid:2022f810-7796-4926-b5ef-b6351613bf09"
         ],
-        "AssociatedWith": "urn:urn:spm-gmrVZH0W",
+        "AssociatedWith": "urn:spm-gmrVZH0W",
         "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -60,7 +60,7 @@
         "Used": [
           "urn:uuid:833d4a70-af77-4275-9995-28633331ce6f"
         ],
-        "AssociatedWith": "urn:urn:spm-gmrVZH0W",
+        "AssociatedWith": "urn:spm-gmrVZH0W",
         "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
         "Parameters": {
           "eoptions.quality": "0.9",
@@ -84,7 +84,7 @@
           "urn:uuid:98ed04e6-b64d-4072-ac94-72573b9239f7",
           "urn:uuid:ffaf2426-c9c9-461a-8c0b-e7090b56835b"
         ],
-        "AssociatedWith": "urn:urn:spm-gmrVZH0W",
+        "AssociatedWith": "urn:spm-gmrVZH0W",
         "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
         "Parameters": {
           "other": "{''}",
@@ -100,7 +100,7 @@
         "Used": [
           "urn:uuid:98ed04e6-b64d-4072-ac94-72573b9239f7"
         ],
-        "AssociatedWith": "urn:urn:spm-gmrVZH0W",
+        "AssociatedWith": "urn:spm-gmrVZH0W",
         "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
         "Parameters": {
           "channel.biasreg": "0.001",
@@ -143,10 +143,10 @@
         "@id": "urn:normaliz-UQldWGr6",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz",
+          "bids::c1anat_sub-01_T1w.nii",
           "urn:uuid:ffaf2426-c9c9-461a-8c0b-e7090b56835b"
         ],
-        "AssociatedWith": "urn:urn:spm-gmrVZH0W",
+        "AssociatedWith": "urn:spm-gmrVZH0W",
         "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -159,9 +159,9 @@
         "@id": "urn:normaliz-cSR3dWyW",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz"
+          "bids::c1anat_sub-01_T1w.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-gmrVZH0W",
+        "AssociatedWith": "urn:spm-gmrVZH0W",
         "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -176,7 +176,7 @@
         "Used": [
           "urn:uuid:c664b813-5420-42eb-a5a5-9c05ab5f4e95"
         ],
-        "AssociatedWith": "urn:urn:spm-gmrVZH0W",
+        "AssociatedWith": "urn:spm-gmrVZH0W",
         "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
         "Parameters": {
           "fwhm": "[6, 6, 6]",
@@ -190,10 +190,10 @@
         "Label": "Stat Design",
         "Used": [
           "urn:uuid:6749b2cb-16d7-4e8d-a0e9-5e7af5c41a66",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
+          "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
         ],
-        "AssociatedWith": "urn:urn:spm-gmrVZH0W",
-        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_p0001'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+        "AssociatedWith": "urn:spm-gmrVZH0W",
+        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_p0001'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_p0001'}",
           "timing.units": "'secs'",
@@ -219,7 +219,7 @@
         "Used": [
           "urn:uuid:8d6e09be-e06d-49d2-9490-3303a4ae36e9"
         ],
-        "AssociatedWith": "urn:urn:spm-gmrVZH0W",
+        "AssociatedWith": "urn:spm-gmrVZH0W",
         "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -232,7 +232,7 @@
         "Used": [
           "urn:uuid:2f3e3ace-ed36-41c6-98e3-ac229e6cece4"
         ],
-        "AssociatedWith": "urn:urn:spm-gmrVZH0W",
+        "AssociatedWith": "urn:spm-gmrVZH0W",
         "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -247,7 +247,7 @@
         "Used": [
           "urn:uuid:d3038c12-9d83-4af2-a740-7c83b7ec0161"
         ],
-        "AssociatedWith": "urn:urn:spm-gmrVZH0W",
+        "AssociatedWith": "urn:spm-gmrVZH0W",
         "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -265,19 +265,19 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "digest": {
-          "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+          "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
         "Label": "anat_sub-01_T1w.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
         "digest": {
-          "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+          "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
         }
       },
       {
@@ -306,7 +306,7 @@
         "GeneratedBy": "urn:gunzip4-CspxFW4L"
       },
       {
-        "@id": "bids::c1xxx.nii.gz",
+        "@id": "bids::c1anat_sub-01_T1w.nii",
         "Label": "segment1",
         "AtLocation": "c1anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-OSxYXQ3N",
@@ -315,7 +315,7 @@
         }
       },
       {
-        "@id": "bids::c2xxx.nii.gz",
+        "@id": "bids::c2anat_sub-01_T1w.nii",
         "Label": "segment2",
         "AtLocation": "c2anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-OSxYXQ3N",
@@ -329,11 +329,11 @@
         "GeneratedBy": "urn:normaliz-UQldWGr6"
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "Label": "ONSETS_sub-01-MultiCond.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "digest": {
-          "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+          "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_default_batch.png b/examples/from_parsers/spm/spm_default_batch.png
index 364ac121..89b3288d 100644
Binary files a/examples/from_parsers/spm/spm_default_batch.png and b/examples/from_parsers/spm/spm_default_batch.png differ
diff --git a/examples/from_parsers/spm/spm_explicit_mask_batch.jsonld b/examples/from_parsers/spm/spm_explicit_mask_batch.jsonld
index b196bdfc..2dea16b0 100644
--- a/examples/from_parsers/spm/spm_explicit_mask_batch.jsonld
+++ b/examples/from_parsers/spm/spm_explicit_mask_batch.jsonld
@@ -16,24 +16,24 @@
         "@id": "urn:movefile-jGxWpvIe",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
+          "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-BV9bpoY8",
-        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+        "AssociatedWith": "urn:spm-BV9bpoY8",
+        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
         }
       },
       {
         "@id": "urn:movefile-YafG4xzl",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz"
+          "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-BV9bpoY8",
-        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+        "AssociatedWith": "urn:spm-BV9bpoY8",
+        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
         }
       },
       {
@@ -42,7 +42,7 @@
         "Used": [
           "urn:uuid:8ba73954-26e1-4ff7-9d9b-66dfabc07097"
         ],
-        "AssociatedWith": "urn:urn:spm-BV9bpoY8",
+        "AssociatedWith": "urn:spm-BV9bpoY8",
         "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -51,7 +51,7 @@
         "Used": [
           "urn:uuid:e7f95829-5ab9-44a6-8ba3-f137c1611a61"
         ],
-        "AssociatedWith": "urn:urn:spm-BV9bpoY8",
+        "AssociatedWith": "urn:spm-BV9bpoY8",
         "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -60,7 +60,7 @@
         "Used": [
           "urn:uuid:c50bff1d-2d38-4a41-aa74-bfc2d7e430c7"
         ],
-        "AssociatedWith": "urn:urn:spm-BV9bpoY8",
+        "AssociatedWith": "urn:spm-BV9bpoY8",
         "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
         "Parameters": {
           "eoptions.quality": "0.9",
@@ -84,7 +84,7 @@
           "urn:uuid:52afae0b-ad7e-4658-b27c-4905e2de3984",
           "urn:uuid:f2617557-abba-4df6-874a-3c010e8fd72a"
         ],
-        "AssociatedWith": "urn:urn:spm-BV9bpoY8",
+        "AssociatedWith": "urn:spm-BV9bpoY8",
         "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
         "Parameters": {
           "other": "{''}",
@@ -100,7 +100,7 @@
         "Used": [
           "urn:uuid:52afae0b-ad7e-4658-b27c-4905e2de3984"
         ],
-        "AssociatedWith": "urn:urn:spm-BV9bpoY8",
+        "AssociatedWith": "urn:spm-BV9bpoY8",
         "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
         "Parameters": {
           "channel.biasreg": "0.001",
@@ -143,10 +143,10 @@
         "@id": "urn:normaliz-C3cRQGpI",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz",
+          "bids::c1anat_sub-01_T1w.nii",
           "urn:uuid:f2617557-abba-4df6-874a-3c010e8fd72a"
         ],
-        "AssociatedWith": "urn:urn:spm-BV9bpoY8",
+        "AssociatedWith": "urn:spm-BV9bpoY8",
         "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -159,9 +159,9 @@
         "@id": "urn:normaliz-PQInmCre",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz"
+          "bids::c1anat_sub-01_T1w.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-BV9bpoY8",
+        "AssociatedWith": "urn:spm-BV9bpoY8",
         "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -176,7 +176,7 @@
         "Used": [
           "urn:uuid:74b85b8d-dabe-461a-8437-f651eeb688f1"
         ],
-        "AssociatedWith": "urn:urn:spm-BV9bpoY8",
+        "AssociatedWith": "urn:spm-BV9bpoY8",
         "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
         "Parameters": {
           "fwhm": "[6, 6, 6]",
@@ -190,11 +190,11 @@
         "Label": "Stat Design",
         "Used": [
           "urn:uuid:bc9496f8-bcf3-4739-b090-4cdefbb34658",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+          "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
           "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask/mask.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-BV9bpoY8",
-        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_explicit_mask'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask/mask.nii,1'};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+        "AssociatedWith": "urn:spm-BV9bpoY8",
+        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_explicit_mask'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask/mask.nii,1'};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_explicit_mask'}",
           "timing.units": "'secs'",
@@ -219,7 +219,7 @@
         "Used": [
           "urn:uuid:722ca52b-0e63-4bf3-bf23-c30162249c80"
         ],
-        "AssociatedWith": "urn:urn:spm-BV9bpoY8",
+        "AssociatedWith": "urn:spm-BV9bpoY8",
         "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -232,7 +232,7 @@
         "Used": [
           "urn:uuid:254a2df1-3258-4823-9d72-9c544501cb45"
         ],
-        "AssociatedWith": "urn:urn:spm-BV9bpoY8",
+        "AssociatedWith": "urn:spm-BV9bpoY8",
         "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -247,7 +247,7 @@
         "Used": [
           "urn:uuid:a1ee1a5b-4890-4153-b8ca-892a637471e1"
         ],
-        "AssociatedWith": "urn:urn:spm-BV9bpoY8",
+        "AssociatedWith": "urn:spm-BV9bpoY8",
         "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -265,19 +265,19 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "digest": {
-          "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+          "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
         "Label": "anat_sub-01_T1w.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
         "digest": {
-          "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+          "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
         }
       },
       {
@@ -306,7 +306,7 @@
         "GeneratedBy": "urn:gunzip4-bRqp0Ozl"
       },
       {
-        "@id": "bids::c1xxx.nii.gz",
+        "@id": "bids::c1anat_sub-01_T1w.nii",
         "Label": "segment1",
         "AtLocation": "c1anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-ucSpHhHm",
@@ -315,7 +315,7 @@
         }
       },
       {
-        "@id": "bids::c2xxx.nii.gz",
+        "@id": "bids::c2anat_sub-01_T1w.nii",
         "Label": "segment2",
         "AtLocation": "c2anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-ucSpHhHm",
@@ -329,11 +329,11 @@
         "GeneratedBy": "urn:normaliz-C3cRQGpI"
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "Label": "ONSETS_sub-01-MultiCond.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "digest": {
-          "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+          "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_explicit_mask_batch.png b/examples/from_parsers/spm/spm_explicit_mask_batch.png
index 928cf8f6..26559d3e 100644
Binary files a/examples/from_parsers/spm/spm_explicit_mask_batch.png and b/examples/from_parsers/spm/spm_explicit_mask_batch.png differ
diff --git a/examples/from_parsers/spm/spm_group_ols_batch.jsonld b/examples/from_parsers/spm/spm_group_ols_batch.jsonld
index 8666d4a3..0ffa21d6 100644
--- a/examples/from_parsers/spm/spm_group_ols_batch.jsonld
+++ b/examples/from_parsers/spm/spm_group_ols_batch.jsonld
@@ -16,23 +16,23 @@
         "@id": "urn:statsfac-txmFBMTH",
         "Label": "stats.factorial_design",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/con_0001.nii",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/con_0001.nii"
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-01/con_0001.nii",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-02/con_0001.nii",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-03/con_0001.nii",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-04/con_0001.nii",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-05/con_0001.nii",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-06/con_0001.nii",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-07/con_0001.nii",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-08/con_0001.nii",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-09/con_0001.nii",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-10/con_0001.nii",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-11/con_0001.nii",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-12/con_0001.nii",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-13/con_0001.nii",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-14/con_0001.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-tmzVSYkl",
-        "Command": "matlabbatch{1}.spm.stats.factorial_design.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_t_test'};\nmatlabbatch{1}.spm.stats.factorial_design.des.t1.scans = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/con_0001.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.im = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.em = {''};\nmatlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;",
+        "AssociatedWith": "urn:spm-tmzVSYkl",
+        "Command": "matlabbatch{1}.spm.stats.factorial_design.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_t_test'};\nmatlabbatch{1}.spm.stats.factorial_design.des.t1.scans = {'ds011/derivatives/SPM/LEVEL1/sub-01/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-02/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-03/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-04/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-05/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-06/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-07/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-08/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-09/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-10/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-11/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-12/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-13/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-14/con_0001.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.im = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.em = {''};\nmatlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_t_test'}",
           "cov": "struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {})",
@@ -51,7 +51,7 @@
         "Used": [
           "urn:uuid:992d5295-4683-4a9d-adac-ba9e417e892d"
         ],
-        "AssociatedWith": "urn:urn:spm-tmzVSYkl",
+        "AssociatedWith": "urn:spm-tmzVSYkl",
         "Command": "matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('Factorial design specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -64,7 +64,7 @@
         "Used": [
           "urn:uuid:3f7c5997-5086-4784-8228-73b2631c18f5"
         ],
-        "AssociatedWith": "urn:urn:spm-tmzVSYkl",
+        "AssociatedWith": "urn:spm-tmzVSYkl",
         "Command": "matlabbatch{3}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.name = 'con-01';\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.weights = 1;\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{3}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'con-01'",
@@ -79,7 +79,7 @@
         "Used": [
           "urn:uuid:94a73b31-ec31-4e8a-bf32-3f67f1e4d027"
         ],
-        "AssociatedWith": "urn:urn:spm-tmzVSYkl",
+        "AssociatedWith": "urn:spm-tmzVSYkl",
         "Command": "matlabbatch{4}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{4}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{4}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{4}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{4}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{4}.spm.stats.results.conspec.extent = 120;\nmatlabbatch{4}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{4}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{4}.spm.stats.results.units = 1;\nmatlabbatch{4}.spm.stats.results.print = 'pdf';\nmatlabbatch{4}.spm.stats.results.write.tspm.basename = 'thresh';",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -97,115 +97,115 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/con_0001.nii",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-01/con_0001.nii",
         "Label": "sub-01_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/con_0001.nii",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-01/con_0001.nii",
         "digest": {
-          "sha256": "6ed900b612440819b1ee78120c31845727d5efd253ec5a4ecd854a089df24632"
+          "sha256": "ae87ebacacac9fa044115eb7f72f465ed7df0cd564afeea1b21c31a53eb5a5d9"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/con_0001.nii",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-02/con_0001.nii",
         "Label": "sub-02_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/con_0001.nii",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-02/con_0001.nii",
         "digest": {
-          "sha256": "29fa8570577a60a7e696ec351bd5691ac56363eead45a356c62955cde829bf2f"
+          "sha256": "7b39fed4ec7aa41bc936735eb90614f2999338b8ebc323d522ff78cae3e9f771"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/con_0001.nii",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-03/con_0001.nii",
         "Label": "sub-03_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/con_0001.nii",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-03/con_0001.nii",
         "digest": {
-          "sha256": "ef3b712491acc95eeb160602a3c00225d383fba86e6f9c10bb8c8d1f0e1856e0"
+          "sha256": "248d7d970e5382f37be821713be2a94b495c2a0cb374cd12843f7b11b7b15357"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/con_0001.nii",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-04/con_0001.nii",
         "Label": "sub-04_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/con_0001.nii",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-04/con_0001.nii",
         "digest": {
-          "sha256": "c7abe341e414634bb339e95b796e6852069d462b43d175926b35390b1dda3822"
+          "sha256": "26db772214370fd1b0d1593312940d717d1d013dc52b5645a2d3f3b93c606ab9"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/con_0001.nii",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-05/con_0001.nii",
         "Label": "sub-05_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/con_0001.nii",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-05/con_0001.nii",
         "digest": {
-          "sha256": "9fd384b58154c0d76897084a262de2a59850e86aebf25175d425cab5c64c0c8f"
+          "sha256": "5c2373d05b955686e92b1143f623fd2a203810da7f079f85ba60f0605925b6e3"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/con_0001.nii",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-06/con_0001.nii",
         "Label": "sub-06_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/con_0001.nii",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-06/con_0001.nii",
         "digest": {
-          "sha256": "7d4a384efbb99af0e4dbfa333193c6c47cf315ad112f7e13fa7c34a280708097"
+          "sha256": "39c6029429ff0b8b7739ba5cf49ec609d39b87ac1f4f6eb500d1537aefaec3df"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/con_0001.nii",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-07/con_0001.nii",
         "Label": "sub-07_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/con_0001.nii",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-07/con_0001.nii",
         "digest": {
-          "sha256": "695d8ce6fee350c4f1f75a38a1913959e363f3ae96c224e30703d564d6635fd0"
+          "sha256": "61b19b16193c7c29b36e99ed192fe08fdc465b887fe68d6f42a2c5856d48fce1"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/con_0001.nii",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-08/con_0001.nii",
         "Label": "sub-08_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/con_0001.nii",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-08/con_0001.nii",
         "digest": {
-          "sha256": "31118b396b250e757aa372893cdbce86ceab283c2e51dc21501c68b6c6048318"
+          "sha256": "74f3311a2884e50ebe2d8ac35d656f25e2e866674dcc82e39a7220a711138a7b"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/con_0001.nii",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-09/con_0001.nii",
         "Label": "sub-09_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/con_0001.nii",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-09/con_0001.nii",
         "digest": {
-          "sha256": "23caf9a8e4ce2a1dd1df54197790b512610381fd5ca30650e2c370bcc1446f50"
+          "sha256": "6488f9d23381e94eb7820fe3278be4cbace66cf4fdbcffc670fcce12fb2f7d4c"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/con_0001.nii",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-10/con_0001.nii",
         "Label": "sub-10_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/con_0001.nii",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-10/con_0001.nii",
         "digest": {
-          "sha256": "9e874e772e65c78cfa0b69591841cda01a3db0a953ccb345a4e2d22ecce0d783"
+          "sha256": "5b5de6f711454549d0856063de3516465e8006e8a7c2496e3e7f376f6e95003c"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/con_0001.nii",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-11/con_0001.nii",
         "Label": "sub-11_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/con_0001.nii",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-11/con_0001.nii",
         "digest": {
-          "sha256": "b76148bef6738f69125d542e630dd83c91e65e4bf2122d4e3b7eb4870c503647"
+          "sha256": "1e366bf13ff4d821d33d13776322c280b386ef362af73fa2c3e4379f8b093a46"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/con_0001.nii",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-12/con_0001.nii",
         "Label": "sub-12_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/con_0001.nii",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-12/con_0001.nii",
         "digest": {
-          "sha256": "efc402e0e889c64156eedefc45aa73baef871f491bb38087ed2ba88333a13c5d"
+          "sha256": "bfd0934a7da341836e1d45d2a1607bc25e3d1963d5f5fdbb3a1b089ac99cb683"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/con_0001.nii",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-13/con_0001.nii",
         "Label": "sub-13_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/con_0001.nii",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-13/con_0001.nii",
         "digest": {
-          "sha256": "30d7f60a178fcc805321140edc1223b452640468ce370c845eec552daec178f9"
+          "sha256": "e2ff39848ea765ac4077e8eb0bc9a8cbf68aaf25b03d0eb569294aa64c0a47b8"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/con_0001.nii",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-14/con_0001.nii",
         "Label": "sub-14_con_0001.nii",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/con_0001.nii",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-14/con_0001.nii",
         "digest": {
-          "sha256": "645ffc262eccd1ee6318d1b6f73294d9cedd4ea772ccbab0fdd9bc57c5f6e27c"
+          "sha256": "59b92ae61893090c2213e60524a7325bba900871c3b7cddd3ed2839aef67686d"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_group_ols_batch.png b/examples/from_parsers/spm/spm_group_ols_batch.png
index 43d3bde0..46a3168d 100644
Binary files a/examples/from_parsers/spm/spm_group_ols_batch.png and b/examples/from_parsers/spm/spm_group_ols_batch.png differ
diff --git a/examples/from_parsers/spm/spm_group_wls_batch.jsonld b/examples/from_parsers/spm/spm_group_wls_batch.jsonld
index 4af1ac0e..ed36754f 100644
--- a/examples/from_parsers/spm/spm_group_wls_batch.jsonld
+++ b/examples/from_parsers/spm/spm_group_wls_batch.jsonld
@@ -16,23 +16,23 @@
         "@id": "urn:statsmfx-6NcnuSxV",
         "Label": "stats.mfx.ffx",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/SPM.mat",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/SPM.mat",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/SPM.mat",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/SPM.mat",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/SPM.mat",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/SPM.mat",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/SPM.mat",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/SPM.mat",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/SPM.mat",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/SPM.mat",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/SPM.mat",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/SPM.mat",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/SPM.mat",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/SPM.mat"
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-01/SPM.mat",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-02/SPM.mat",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-03/SPM.mat",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-04/SPM.mat",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-06/SPM.mat",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-07/SPM.mat",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-08/SPM.mat",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-09/SPM.mat",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-10/SPM.mat",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-11/SPM.mat",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-12/SPM.mat",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-13/SPM.mat",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-14/SPM.mat",
+          "bids:ds011:/derivatives/SPM/LEVEL1/sub-05/SPM.mat"
         ],
-        "AssociatedWith": "urn:urn:spm-FjaG6SLD",
-        "Command": "matlabbatch{1}.spm.stats.mfx.ffx.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_WLS_t_test'};\nmatlabbatch{1}.spm.stats.mfx.ffx.spmmat = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/SPM.mat',};",
+        "AssociatedWith": "urn:spm-FjaG6SLD",
+        "Command": "matlabbatch{1}.spm.stats.mfx.ffx.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_WLS_t_test'};\nmatlabbatch{1}.spm.stats.mfx.ffx.spmmat = {'ds011/derivatives/SPM/LEVEL1/sub-01/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-02/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-03/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-04/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-06/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-07/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-08/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-09/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-10/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-11/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-12/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-13/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-14/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-05/SPM.mat',};",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_WLS_t_test'}"
         }
@@ -43,7 +43,7 @@
         "Used": [
           "urn:uuid:c9346e65-f190-4a60-9a5b-ad26f0c85da3"
         ],
-        "AssociatedWith": "urn:urn:spm-FjaG6SLD",
+        "AssociatedWith": "urn:spm-FjaG6SLD",
         "Command": "matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('FFX Specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -56,7 +56,7 @@
         "Used": [
           "urn:uuid:73c5f0c0-cfe5-4458-acfd-50c8bb5815d2"
         ],
-        "AssociatedWith": "urn:urn:spm-FjaG6SLD",
+        "AssociatedWith": "urn:spm-FjaG6SLD",
         "Command": "matlabbatch{3}.spm.stats.mfx.spec.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{3}.spm.stats.mfx.spec.contrast = [];",
         "Parameters": {
           "contrast": "[]"
@@ -68,7 +68,7 @@
         "Used": [
           "urn:uuid:73bd38cc-7a73-483f-9f5e-c83b7013635a"
         ],
-        "AssociatedWith": "urn:urn:spm-FjaG6SLD",
+        "AssociatedWith": "urn:spm-FjaG6SLD",
         "Command": "matlabbatch{4}.spm.stats.fmri_est.spmmat(1) = cfg_dep('MFX Specification: SPM.mat File', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{4}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{4}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -81,7 +81,7 @@
         "Used": [
           "urn:uuid:63220836-af6f-43c5-b08a-4f738039ab3a"
         ],
-        "AssociatedWith": "urn:urn:spm-FjaG6SLD",
+        "AssociatedWith": "urn:spm-FjaG6SLD",
         "Command": "matlabbatch{5}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{5}.spm.stats.con.consess{1}.tcon.name = 'con-01: Tone Counting vs Baseline';\nmatlabbatch{5}.spm.stats.con.consess{1}.tcon.weights = 1;\nmatlabbatch{5}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{5}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'con-01: Tone Counting vs Baseline'",
@@ -96,7 +96,7 @@
         "Used": [
           "urn:uuid:2502b6a5-f5c5-4310-845e-816607158694"
         ],
-        "AssociatedWith": "urn:urn:spm-FjaG6SLD",
+        "AssociatedWith": "urn:spm-FjaG6SLD",
         "Command": "matlabbatch{6}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{6}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{6}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{6}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{6}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{6}.spm.stats.results.conspec.extent = 2;\nmatlabbatch{6}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{6}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{6}.spm.stats.results.units = 1;\nmatlabbatch{6}.spm.stats.results.print = 'pdf';\nmatlabbatch{6}.spm.stats.results.write.tspm.basename = 'thresh';",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -114,115 +114,115 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/SPM.mat",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-01/SPM.mat",
         "Label": "sub-01_SPM.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/SPM.mat",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-01/SPM.mat",
         "digest": {
-          "sha256": "441618d2bff3613f944118e5942d8e66b6d9727e997267dcdbcedc9ca924ddcf"
+          "sha256": "7ee54cdfc3a3766d1cd9fc53eb3b080fb8eda5ce92a6be7abd226bb7482e3821"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/SPM.mat",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-02/SPM.mat",
         "Label": "sub-02_SPM.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/SPM.mat",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-02/SPM.mat",
         "digest": {
-          "sha256": "30fa910dd37ad302a1beef5f9f4a19b92c01222ecb99e685f3127588ce7bfafb"
+          "sha256": "08ac55808031570c33ef9f9348ad3a8bd8a88df6829933f41bda58cd328d20be"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/SPM.mat",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-03/SPM.mat",
         "Label": "sub-03_SPM.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/SPM.mat",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-03/SPM.mat",
         "digest": {
-          "sha256": "76053c189ea109e3c3bf6271ba440f8d2a234fd9f9dfb19f648624224ba3c67f"
+          "sha256": "48a60737f0c66071641ebbce1169788e79a684b40dedd9130bdf295a304949bf"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/SPM.mat",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-04/SPM.mat",
         "Label": "sub-04_SPM.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/SPM.mat",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-04/SPM.mat",
         "digest": {
-          "sha256": "4dc9d4316a1acd3e5b73a80d3d047c78736cdea4b6bbd231b35a863565a6deb0"
+          "sha256": "a4b7bc85e7fe3a8e8bf83a2cd6188ddbdf298b1827d754f6cb170cfb3d6bcdfc"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/SPM.mat",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-06/SPM.mat",
         "Label": "sub-06_SPM.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/SPM.mat",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-06/SPM.mat",
         "digest": {
-          "sha256": "ec9afe39bb1915d78d656bbf925c8bd91a58e95776e263bcf86aee3051210d3c"
+          "sha256": "fe65b7d9b8836ba80f8c86d90a255773fea0279d4f4546900354b38089a7109f"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/SPM.mat",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-07/SPM.mat",
         "Label": "sub-07_SPM.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/SPM.mat",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-07/SPM.mat",
         "digest": {
-          "sha256": "7025698ecf8d02b19ef4d94462beefc902ca603eed07023df5019cfe3e59cf53"
+          "sha256": "12ec99599b441a31ddaf8ec5cf8383ef3e4eb93be1237e0ef31dad36d8c933af"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/SPM.mat",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-08/SPM.mat",
         "Label": "sub-08_SPM.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/SPM.mat",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-08/SPM.mat",
         "digest": {
-          "sha256": "72a13f603f81068778e7112453946f9ea13e24771d9f061c0a5ddf0131805bb9"
+          "sha256": "cfc4a42edfa2ce9aaf5b5bbabea235dde525928ac8bb8789dae6000c73a62c00"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/SPM.mat",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-09/SPM.mat",
         "Label": "sub-09_SPM.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/SPM.mat",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-09/SPM.mat",
         "digest": {
-          "sha256": "6176e571e96deca6f880327802a63eb19dc038f1922701f4068eaf0ed6414257"
+          "sha256": "f82ba0e7b0812e1e4ca501b3ec9af5da8cc6e59a1d7e8390ae3472441d28192b"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/SPM.mat",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-10/SPM.mat",
         "Label": "sub-10_SPM.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/SPM.mat",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-10/SPM.mat",
         "digest": {
-          "sha256": "e2a3867b076a8f6aa12d20a95057d38221fd5e0da5175e0b5a33b6661e811897"
+          "sha256": "27c346f569177ac9c93bc84d34c7375a540565d0755e9aae4f6f5153f54aee8e"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/SPM.mat",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-11/SPM.mat",
         "Label": "sub-11_SPM.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/SPM.mat",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-11/SPM.mat",
         "digest": {
-          "sha256": "64020b5a770246c406dd26cccf751b053d4ad6179e652f99967a109ea8ce27c0"
+          "sha256": "8937ceea6f689bbe77b9a885e59a035ee8835dd9ed54e72c534015da3f37b9bf"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/SPM.mat",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-12/SPM.mat",
         "Label": "sub-12_SPM.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/SPM.mat",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-12/SPM.mat",
         "digest": {
-          "sha256": "630720d0b74f64a3501da3cbfbc1506affc26df70c85e6ca7f04685f0d6b54cb"
+          "sha256": "5ad1865c53953093b55177487f92e5b9dd8f4f059e2205b28fb8de04a358891a"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/SPM.mat",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-13/SPM.mat",
         "Label": "sub-13_SPM.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/SPM.mat",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-13/SPM.mat",
         "digest": {
-          "sha256": "0d7c0e476a420f026c3664b827681e0cdef9b48833db4b2629293b7ee5acdf4d"
+          "sha256": "de8e6fd0ea79aa7bac1f78f13fb97e970fede0c0fe8cad9df8356df2bd27e5c5"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/SPM.mat",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-14/SPM.mat",
         "Label": "sub-14_SPM.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/SPM.mat",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-14/SPM.mat",
         "digest": {
-          "sha256": "91f643585bc990782d2e1890bc60d454647bc6eec0850aa0e529a9378927df4e"
+          "sha256": "74459bee0eb3411118758c85edefbca8b974fe99272839b0586156031306f36f"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/SPM.mat",
+        "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-05/SPM.mat",
         "Label": "sub-05_SPM.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/SPM.mat",
+        "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-05/SPM.mat",
         "digest": {
-          "sha256": "82553bb332b3133407b1da2fd73527c99691e1fef7445c5ba8c6aa53a97da615"
+          "sha256": "d19456101522384c27a8a89e85edfa0dc62de1a5a69fe52a2a10c13b0a643c10"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_group_wls_batch.png b/examples/from_parsers/spm/spm_group_wls_batch.png
index 82ac1b9e..d52267ec 100644
Binary files a/examples/from_parsers/spm/spm_group_wls_batch.png and b/examples/from_parsers/spm/spm_group_wls_batch.png differ
diff --git a/examples/from_parsers/spm/spm_hrf_fir_batch.jsonld b/examples/from_parsers/spm/spm_hrf_fir_batch.jsonld
index 3d06fe5c..d48e333b 100644
--- a/examples/from_parsers/spm/spm_hrf_fir_batch.jsonld
+++ b/examples/from_parsers/spm/spm_hrf_fir_batch.jsonld
@@ -16,24 +16,24 @@
         "@id": "urn:movefile-yFdmdoKh",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
+          "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-qiv4p9Xd",
-        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+        "AssociatedWith": "urn:spm-qiv4p9Xd",
+        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
         }
       },
       {
         "@id": "urn:movefile-y7t2Z5pu",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz"
+          "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-qiv4p9Xd",
-        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+        "AssociatedWith": "urn:spm-qiv4p9Xd",
+        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
         }
       },
       {
@@ -42,7 +42,7 @@
         "Used": [
           "urn:uuid:9e0ef7b6-f708-4c54-b7d0-0dda9e7b2dcd"
         ],
-        "AssociatedWith": "urn:urn:spm-qiv4p9Xd",
+        "AssociatedWith": "urn:spm-qiv4p9Xd",
         "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -51,7 +51,7 @@
         "Used": [
           "urn:uuid:f10ba202-e81b-4c88-a2e0-da4b10f1081f"
         ],
-        "AssociatedWith": "urn:urn:spm-qiv4p9Xd",
+        "AssociatedWith": "urn:spm-qiv4p9Xd",
         "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -60,7 +60,7 @@
         "Used": [
           "urn:uuid:e36fad5d-dcec-40cf-b6ea-df80a876f12d"
         ],
-        "AssociatedWith": "urn:urn:spm-qiv4p9Xd",
+        "AssociatedWith": "urn:spm-qiv4p9Xd",
         "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
         "Parameters": {
           "eoptions.quality": "0.9",
@@ -84,7 +84,7 @@
           "urn:uuid:b2e934fb-5f1c-40bf-b5b6-51b885d8faff",
           "urn:uuid:e233cc3f-54dc-4464-8f5a-10bb7b09e039"
         ],
-        "AssociatedWith": "urn:urn:spm-qiv4p9Xd",
+        "AssociatedWith": "urn:spm-qiv4p9Xd",
         "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
         "Parameters": {
           "other": "{''}",
@@ -100,7 +100,7 @@
         "Used": [
           "urn:uuid:b2e934fb-5f1c-40bf-b5b6-51b885d8faff"
         ],
-        "AssociatedWith": "urn:urn:spm-qiv4p9Xd",
+        "AssociatedWith": "urn:spm-qiv4p9Xd",
         "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
         "Parameters": {
           "channel.biasreg": "0.001",
@@ -143,10 +143,10 @@
         "@id": "urn:normaliz-Keen4iD8",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz",
+          "bids::c1anat_sub-01_T1w.nii",
           "urn:uuid:e233cc3f-54dc-4464-8f5a-10bb7b09e039"
         ],
-        "AssociatedWith": "urn:urn:spm-qiv4p9Xd",
+        "AssociatedWith": "urn:spm-qiv4p9Xd",
         "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -159,9 +159,9 @@
         "@id": "urn:normaliz-grJqrlDm",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz"
+          "bids::c1anat_sub-01_T1w.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-qiv4p9Xd",
+        "AssociatedWith": "urn:spm-qiv4p9Xd",
         "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -176,7 +176,7 @@
         "Used": [
           "urn:uuid:cb881a9c-46a8-4c17-a093-4ff7d167e3a6"
         ],
-        "AssociatedWith": "urn:urn:spm-qiv4p9Xd",
+        "AssociatedWith": "urn:spm-qiv4p9Xd",
         "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
         "Parameters": {
           "fwhm": "[6, 6, 6]",
@@ -190,10 +190,10 @@
         "Label": "Stat Design",
         "Used": [
           "urn:uuid:d6abb162-b880-4a28-9176-a59c7e5e4b63",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
+          "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
         ],
-        "AssociatedWith": "urn:urn:spm-qiv4p9Xd",
-        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FIR_basis'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.fir.length = 20;\nmatlabbatch{11}.spm.stats.fmri_spec.bases.fir.order = 10;\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+        "AssociatedWith": "urn:spm-qiv4p9Xd",
+        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FIR_basis'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.fir.length = 20;\nmatlabbatch{11}.spm.stats.fmri_spec.bases.fir.order = 10;\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FIR_basis'}",
           "timing.units": "'secs'",
@@ -220,7 +220,7 @@
         "Used": [
           "urn:uuid:0c7b1d5c-c38e-40bd-a371-ee1b23b22d29"
         ],
-        "AssociatedWith": "urn:urn:spm-qiv4p9Xd",
+        "AssociatedWith": "urn:spm-qiv4p9Xd",
         "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -233,7 +233,7 @@
         "Used": [
           "urn:uuid:75a17631-bcb4-4160-bd04-3eaef4c79383"
         ],
-        "AssociatedWith": "urn:urn:spm-qiv4p9Xd",
+        "AssociatedWith": "urn:spm-qiv4p9Xd",
         "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.name = 'Tone Counting vs Baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.weights = [1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1];\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.fcon.name": "'Tone Counting vs Baseline'",
@@ -248,7 +248,7 @@
         "Used": [
           "urn:uuid:bd54c40a-bea2-4186-86c3-b863563f214f"
         ],
-        "AssociatedWith": "urn:urn:spm-qiv4p9Xd",
+        "AssociatedWith": "urn:spm-qiv4p9Xd",
         "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -266,19 +266,19 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "digest": {
-          "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+          "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
         "Label": "anat_sub-01_T1w.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
         "digest": {
-          "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+          "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
         }
       },
       {
@@ -307,7 +307,7 @@
         "GeneratedBy": "urn:gunzip4-lqCoqCpN"
       },
       {
-        "@id": "bids::c1xxx.nii.gz",
+        "@id": "bids::c1anat_sub-01_T1w.nii",
         "Label": "segment1",
         "AtLocation": "c1anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-e8tpZVIm",
@@ -316,7 +316,7 @@
         }
       },
       {
-        "@id": "bids::c2xxx.nii.gz",
+        "@id": "bids::c2anat_sub-01_T1w.nii",
         "Label": "segment2",
         "AtLocation": "c2anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-e8tpZVIm",
@@ -330,11 +330,11 @@
         "GeneratedBy": "urn:normaliz-Keen4iD8"
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "Label": "ONSETS_sub-01-MultiCond.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "digest": {
-          "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+          "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_hrf_fir_batch.png b/examples/from_parsers/spm/spm_hrf_fir_batch.png
index 8139cc59..b05a9bf1 100644
Binary files a/examples/from_parsers/spm/spm_hrf_fir_batch.png and b/examples/from_parsers/spm/spm_hrf_fir_batch.png differ
diff --git a/examples/from_parsers/spm/spm_non_sphericity_batch.jsonld b/examples/from_parsers/spm/spm_non_sphericity_batch.jsonld
index d6cecfee..24edb106 100644
--- a/examples/from_parsers/spm/spm_non_sphericity_batch.jsonld
+++ b/examples/from_parsers/spm/spm_non_sphericity_batch.jsonld
@@ -16,7 +16,7 @@
         "@id": "urn:statsfac-cEPGgC8F",
         "Label": "stats.factorial_design",
         "Used": [],
-        "AssociatedWith": "urn:urn:spm-VoEw1onB",
+        "AssociatedWith": "urn:spm-VoEw1onB",
         "Command": "matlabbatch{1}.spm.stats.factorial_design.dir = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Group/Informed'};\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.name = 'Basis';\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.levels = 3;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.dept = 1;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.variance = 1;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.gmsca = 0;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.ancova = 0;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(1).levels = 1;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(1).scans = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub01/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub02/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub03/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub04/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub05/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub06/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub07/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub08/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub09/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub10/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub11/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub12/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub13/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub14/CanonicalHRF/con_0001.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(2).levels = 2;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(2).scans = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub01/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub02/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub03/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub04/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub05/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub06/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub07/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub08/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub09/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub10/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub11/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub12/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub13/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub14/CanonicalHRF/con_0005.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(3).levels = 3;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(3).scans = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub01/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub02/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub03/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub04/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub05/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub06/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub07/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub08/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub09/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub10/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub11/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub12/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub13/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub14/CanonicalHRF/con_0009.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.contrasts = 1;\nmatlabbatch{1}.spm.stats.factorial_design.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.im = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.em = {''};\nmatlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Group/Informed'}",
@@ -49,7 +49,7 @@
         "Used": [
           "urn:uuid:e7a5c2e4-5784-49b4-bc5c-43f34a712c0e"
         ],
-        "AssociatedWith": "urn:urn:spm-VoEw1onB",
+        "AssociatedWith": "urn:spm-VoEw1onB",
         "Command": "matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('Factorial design specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -62,7 +62,7 @@
         "Used": [
           "urn:uuid:4a2aa5a5-953a-4787-a638-d162b4fce3e0"
         ],
-        "AssociatedWith": "urn:urn:spm-VoEw1onB",
+        "AssociatedWith": "urn:spm-VoEw1onB",
         "Command": "matlabbatch{3}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.name = 'mr vs plain informed basis';\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.weights = 1;\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{3}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'mr vs plain informed basis'",
@@ -77,7 +77,7 @@
         "Used": [
           "urn:uuid:b5676206-f275-4e9c-a547-dfc05f32afdf"
         ],
-        "AssociatedWith": "urn:urn:spm-VoEw1onB",
+        "AssociatedWith": "urn:spm-VoEw1onB",
         "Command": "matlabbatch{4}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{4}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{4}.spm.stats.results.conspec.contrasts = 1;\nmatlabbatch{4}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{4}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{4}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{4}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{4}.spm.stats.results.units = 1;\nmatlabbatch{4}.spm.stats.results.print = 'pdf';\nmatlabbatch{4}.spm.stats.results.write.none = 1;",
         "Parameters": {
           "conspec.titlestr": "''",
diff --git a/examples/from_parsers/spm/spm_partial_conjunction_batch.jsonld b/examples/from_parsers/spm/spm_partial_conjunction_batch.jsonld
index 7c6cd67f..768f2a56 100644
--- a/examples/from_parsers/spm/spm_partial_conjunction_batch.jsonld
+++ b/examples/from_parsers/spm/spm_partial_conjunction_batch.jsonld
@@ -16,24 +16,24 @@
         "@id": "urn:movefile-E9SUEKGJ",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
+          "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-kRUWK166",
-        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+        "AssociatedWith": "urn:spm-kRUWK166",
+        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
         }
       },
       {
         "@id": "urn:movefile-UEkIbFqL",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz"
+          "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-kRUWK166",
-        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+        "AssociatedWith": "urn:spm-kRUWK166",
+        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
         }
       },
       {
@@ -42,7 +42,7 @@
         "Used": [
           "urn:uuid:020b2bdf-e472-42a1-9e43-8c9f9fbeb376"
         ],
-        "AssociatedWith": "urn:urn:spm-kRUWK166",
+        "AssociatedWith": "urn:spm-kRUWK166",
         "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -51,7 +51,7 @@
         "Used": [
           "urn:uuid:b0e1709d-5501-4e9a-bd09-0f2c82c09610"
         ],
-        "AssociatedWith": "urn:urn:spm-kRUWK166",
+        "AssociatedWith": "urn:spm-kRUWK166",
         "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -60,7 +60,7 @@
         "Used": [
           "urn:uuid:e7827303-0d45-40a1-a675-c59efc4101fc"
         ],
-        "AssociatedWith": "urn:urn:spm-kRUWK166",
+        "AssociatedWith": "urn:spm-kRUWK166",
         "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
         "Parameters": {
           "eoptions.quality": "0.9",
@@ -84,7 +84,7 @@
           "urn:uuid:705569ce-f0f4-4551-b596-8e52a4b35e54",
           "urn:uuid:dad38e4b-0886-4822-ba34-c1bffa39acc8"
         ],
-        "AssociatedWith": "urn:urn:spm-kRUWK166",
+        "AssociatedWith": "urn:spm-kRUWK166",
         "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
         "Parameters": {
           "other": "{''}",
@@ -100,7 +100,7 @@
         "Used": [
           "urn:uuid:705569ce-f0f4-4551-b596-8e52a4b35e54"
         ],
-        "AssociatedWith": "urn:urn:spm-kRUWK166",
+        "AssociatedWith": "urn:spm-kRUWK166",
         "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
         "Parameters": {
           "channel.biasreg": "0.001",
@@ -143,10 +143,10 @@
         "@id": "urn:normaliz-prV8DwTN",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz",
+          "bids::c1anat_sub-01_T1w.nii",
           "urn:uuid:dad38e4b-0886-4822-ba34-c1bffa39acc8"
         ],
-        "AssociatedWith": "urn:urn:spm-kRUWK166",
+        "AssociatedWith": "urn:spm-kRUWK166",
         "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -159,9 +159,9 @@
         "@id": "urn:normaliz-t1VMS4pO",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz"
+          "bids::c1anat_sub-01_T1w.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-kRUWK166",
+        "AssociatedWith": "urn:spm-kRUWK166",
         "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -176,7 +176,7 @@
         "Used": [
           "urn:uuid:383bcc26-9c00-47ec-8a5b-78af546c286c"
         ],
-        "AssociatedWith": "urn:urn:spm-kRUWK166",
+        "AssociatedWith": "urn:spm-kRUWK166",
         "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
         "Parameters": {
           "fwhm": "[6, 6, 6]",
@@ -190,10 +190,10 @@
         "Label": "Stat Design",
         "Used": [
           "urn:uuid:bbcd8fb6-282c-4086-8603-fee526502c2d",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
+          "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
         ],
-        "AssociatedWith": "urn:urn:spm-kRUWK166",
-        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_conjunction'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+        "AssociatedWith": "urn:spm-kRUWK166",
+        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_conjunction'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_conjunction'}",
           "timing.units": "'secs'",
@@ -219,7 +219,7 @@
         "Used": [
           "urn:uuid:d6974014-232a-4fc3-93ff-dd5858b45621"
         ],
-        "AssociatedWith": "urn:urn:spm-kRUWK166",
+        "AssociatedWith": "urn:spm-kRUWK166",
         "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -232,7 +232,7 @@
         "Used": [
           "urn:uuid:eb53674f-1bce-414f-86e0-c3d525f9033d"
         ],
-        "AssociatedWith": "urn:urn:spm-kRUWK166",
+        "AssociatedWith": "urn:spm-kRUWK166",
         "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.name = 'tone counting probe vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.weights = [0 1];\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -250,7 +250,7 @@
         "Used": [
           "urn:uuid:89d4303e-f6be-45e0-a9a9-0e04440761a4"
         ],
-        "AssociatedWith": "urn:urn:spm-kRUWK166",
+        "AssociatedWith": "urn:spm-kRUWK166",
         "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = [1 2];\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 2;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -268,19 +268,19 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "digest": {
-          "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+          "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
         "Label": "anat_sub-01_T1w.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
         "digest": {
-          "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+          "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
         }
       },
       {
@@ -309,7 +309,7 @@
         "GeneratedBy": "urn:gunzip4-X87P6yn3"
       },
       {
-        "@id": "bids::c1xxx.nii.gz",
+        "@id": "bids::c1anat_sub-01_T1w.nii",
         "Label": "segment1",
         "AtLocation": "c1anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-wIsiP0z9",
@@ -318,7 +318,7 @@
         }
       },
       {
-        "@id": "bids::c2xxx.nii.gz",
+        "@id": "bids::c2anat_sub-01_T1w.nii",
         "Label": "segment2",
         "AtLocation": "c2anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-wIsiP0z9",
@@ -332,11 +332,11 @@
         "GeneratedBy": "urn:normaliz-prV8DwTN"
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "Label": "ONSETS_sub-01-MultiCond.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "digest": {
-          "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+          "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_partial_conjunction_batch.png b/examples/from_parsers/spm/spm_partial_conjunction_batch.png
index 1c390fd7..8657c0fe 100644
Binary files a/examples/from_parsers/spm/spm_partial_conjunction_batch.png and b/examples/from_parsers/spm/spm_partial_conjunction_batch.png differ
diff --git a/examples/from_parsers/spm/spm_temporal_derivative_batch.jsonld b/examples/from_parsers/spm/spm_temporal_derivative_batch.jsonld
index 2590cea4..18941ef2 100644
--- a/examples/from_parsers/spm/spm_temporal_derivative_batch.jsonld
+++ b/examples/from_parsers/spm/spm_temporal_derivative_batch.jsonld
@@ -16,24 +16,24 @@
         "@id": "urn:movefile-8gz2vYDp",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
+          "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-Iqi6cYes",
-        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+        "AssociatedWith": "urn:spm-Iqi6cYes",
+        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
         }
       },
       {
         "@id": "urn:movefile-ciNJaxWf",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz"
+          "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-Iqi6cYes",
-        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+        "AssociatedWith": "urn:spm-Iqi6cYes",
+        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
         }
       },
       {
@@ -42,7 +42,7 @@
         "Used": [
           "urn:uuid:d28c66ee-9df4-4f48-bcdb-5cc80f2c82b8"
         ],
-        "AssociatedWith": "urn:urn:spm-Iqi6cYes",
+        "AssociatedWith": "urn:spm-Iqi6cYes",
         "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -51,7 +51,7 @@
         "Used": [
           "urn:uuid:12c70fce-50a2-4587-a377-83845161d6f0"
         ],
-        "AssociatedWith": "urn:urn:spm-Iqi6cYes",
+        "AssociatedWith": "urn:spm-Iqi6cYes",
         "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -60,7 +60,7 @@
         "Used": [
           "urn:uuid:b9734a59-46f3-4366-aac7-ce4e18652307"
         ],
-        "AssociatedWith": "urn:urn:spm-Iqi6cYes",
+        "AssociatedWith": "urn:spm-Iqi6cYes",
         "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
         "Parameters": {
           "eoptions.quality": "0.9",
@@ -84,7 +84,7 @@
           "urn:uuid:9bfb0b4b-b351-4f87-b425-5ab23b28e8b8",
           "urn:uuid:bdd303a3-95b8-429d-be7c-5526b3701b1b"
         ],
-        "AssociatedWith": "urn:urn:spm-Iqi6cYes",
+        "AssociatedWith": "urn:spm-Iqi6cYes",
         "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
         "Parameters": {
           "other": "{''}",
@@ -100,7 +100,7 @@
         "Used": [
           "urn:uuid:bdd303a3-95b8-429d-be7c-5526b3701b1b"
         ],
-        "AssociatedWith": "urn:urn:spm-Iqi6cYes",
+        "AssociatedWith": "urn:spm-Iqi6cYes",
         "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
         "Parameters": {
           "channel.biasreg": "0.001",
@@ -143,10 +143,10 @@
         "@id": "urn:normaliz-gxMyUxTC",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz",
+          "bids::c1anat_sub-01_T1w.nii",
           "urn:uuid:9bfb0b4b-b351-4f87-b425-5ab23b28e8b8"
         ],
-        "AssociatedWith": "urn:urn:spm-Iqi6cYes",
+        "AssociatedWith": "urn:spm-Iqi6cYes",
         "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -159,9 +159,9 @@
         "@id": "urn:normaliz-HSrOJAko",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz"
+          "bids::c1anat_sub-01_T1w.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-Iqi6cYes",
+        "AssociatedWith": "urn:spm-Iqi6cYes",
         "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -176,7 +176,7 @@
         "Used": [
           "urn:uuid:640338ab-1dde-494c-a012-ee8afd479306"
         ],
-        "AssociatedWith": "urn:urn:spm-Iqi6cYes",
+        "AssociatedWith": "urn:spm-Iqi6cYes",
         "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
         "Parameters": {
           "fwhm": "[6, 6, 6]",
@@ -190,10 +190,10 @@
         "Label": "Stat Design",
         "Used": [
           "urn:uuid:ae76fb47-5ccd-4dfc-8142-411e1b1b129f",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
+          "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
         ],
-        "AssociatedWith": "urn:urn:spm-Iqi6cYes",
-        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_temporal_derivative'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [1 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+        "AssociatedWith": "urn:spm-Iqi6cYes",
+        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_temporal_derivative'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [1 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_temporal_derivative'}",
           "timing.units": "'secs'",
@@ -219,7 +219,7 @@
         "Used": [
           "urn:uuid:4a6db4b0-3c55-4daa-83b4-3fce50530896"
         ],
-        "AssociatedWith": "urn:urn:spm-Iqi6cYes",
+        "AssociatedWith": "urn:spm-Iqi6cYes",
         "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -232,7 +232,7 @@
         "Used": [
           "urn:uuid:1ef58f22-1c60-40c8-a8cc-32c360c3b073"
         ],
-        "AssociatedWith": "urn:urn:spm-Iqi6cYes",
+        "AssociatedWith": "urn:spm-Iqi6cYes",
         "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0 0 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -247,7 +247,7 @@
         "Used": [
           "urn:uuid:24f0054d-e998-40fc-8931-a30b14234f5b"
         ],
-        "AssociatedWith": "urn:urn:spm-Iqi6cYes",
+        "AssociatedWith": "urn:spm-Iqi6cYes",
         "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -265,19 +265,19 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "digest": {
-          "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+          "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
         "Label": "anat_sub-01_T1w.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
         "digest": {
-          "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+          "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
         }
       },
       {
@@ -306,7 +306,7 @@
         "GeneratedBy": "urn:gunzip4-Pq5ZEXnx"
       },
       {
-        "@id": "bids::c1xxx.nii.gz",
+        "@id": "bids::c1anat_sub-01_T1w.nii",
         "Label": "segment1",
         "AtLocation": "c1anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-TxjeajaC",
@@ -315,7 +315,7 @@
         }
       },
       {
-        "@id": "bids::c2xxx.nii.gz",
+        "@id": "bids::c2anat_sub-01_T1w.nii",
         "Label": "segment2",
         "AtLocation": "c2anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-TxjeajaC",
@@ -329,11 +329,11 @@
         "GeneratedBy": "urn:normaliz-gxMyUxTC"
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "Label": "ONSETS_sub-01-MultiCond.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "digest": {
-          "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+          "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_temporal_derivative_batch.png b/examples/from_parsers/spm/spm_temporal_derivative_batch.png
index af96df8e..0b6e146e 100644
Binary files a/examples/from_parsers/spm/spm_temporal_derivative_batch.png and b/examples/from_parsers/spm/spm_temporal_derivative_batch.png differ
diff --git a/examples/from_parsers/spm/spm_thr_clustfwep05_batch.jsonld b/examples/from_parsers/spm/spm_thr_clustfwep05_batch.jsonld
index 051ee6e9..5ba0324e 100644
--- a/examples/from_parsers/spm/spm_thr_clustfwep05_batch.jsonld
+++ b/examples/from_parsers/spm/spm_thr_clustfwep05_batch.jsonld
@@ -16,24 +16,24 @@
         "@id": "urn:movefile-xEUWiFIX",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
+          "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-0M07DSW9",
-        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+        "AssociatedWith": "urn:spm-0M07DSW9",
+        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
         }
       },
       {
         "@id": "urn:movefile-NRl0j05C",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz"
+          "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-0M07DSW9",
-        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+        "AssociatedWith": "urn:spm-0M07DSW9",
+        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
         }
       },
       {
@@ -42,7 +42,7 @@
         "Used": [
           "urn:uuid:3a1d3aaa-f467-4762-8b65-74efb94acbdc"
         ],
-        "AssociatedWith": "urn:urn:spm-0M07DSW9",
+        "AssociatedWith": "urn:spm-0M07DSW9",
         "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -51,7 +51,7 @@
         "Used": [
           "urn:uuid:73cdb74c-9f64-4789-81b9-0e5bf20d453b"
         ],
-        "AssociatedWith": "urn:urn:spm-0M07DSW9",
+        "AssociatedWith": "urn:spm-0M07DSW9",
         "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -60,7 +60,7 @@
         "Used": [
           "urn:uuid:e4dff923-f549-4834-b48a-b363ba87bbf6"
         ],
-        "AssociatedWith": "urn:urn:spm-0M07DSW9",
+        "AssociatedWith": "urn:spm-0M07DSW9",
         "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
         "Parameters": {
           "eoptions.quality": "0.9",
@@ -84,7 +84,7 @@
           "urn:uuid:c991394e-1a6b-4dec-af39-37e0ce004fae",
           "urn:uuid:ea2bad58-0c22-447c-8b66-1aeb5499512f"
         ],
-        "AssociatedWith": "urn:urn:spm-0M07DSW9",
+        "AssociatedWith": "urn:spm-0M07DSW9",
         "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
         "Parameters": {
           "other": "{''}",
@@ -100,7 +100,7 @@
         "Used": [
           "urn:uuid:ea2bad58-0c22-447c-8b66-1aeb5499512f"
         ],
-        "AssociatedWith": "urn:urn:spm-0M07DSW9",
+        "AssociatedWith": "urn:spm-0M07DSW9",
         "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
         "Parameters": {
           "channel.biasreg": "0.001",
@@ -143,10 +143,10 @@
         "@id": "urn:normaliz-9GRC3VyJ",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz",
+          "bids::c1anat_sub-01_T1w.nii",
           "urn:uuid:c991394e-1a6b-4dec-af39-37e0ce004fae"
         ],
-        "AssociatedWith": "urn:urn:spm-0M07DSW9",
+        "AssociatedWith": "urn:spm-0M07DSW9",
         "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -159,9 +159,9 @@
         "@id": "urn:normaliz-a6YDDjrt",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz"
+          "bids::c1anat_sub-01_T1w.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-0M07DSW9",
+        "AssociatedWith": "urn:spm-0M07DSW9",
         "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -176,7 +176,7 @@
         "Used": [
           "urn:uuid:34637116-2460-4e0d-a7f3-d79b7feb3fc8"
         ],
-        "AssociatedWith": "urn:urn:spm-0M07DSW9",
+        "AssociatedWith": "urn:spm-0M07DSW9",
         "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
         "Parameters": {
           "fwhm": "[6, 6, 6]",
@@ -190,10 +190,10 @@
         "Label": "Stat Design",
         "Used": [
           "urn:uuid:d939ba15-a30f-4d48-a4c2-9d3ca0eb2972",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
+          "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
         ],
-        "AssociatedWith": "urn:urn:spm-0M07DSW9",
-        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_cluster_p005'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+        "AssociatedWith": "urn:spm-0M07DSW9",
+        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_cluster_p005'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_cluster_p005'}",
           "timing.units": "'secs'",
@@ -219,7 +219,7 @@
         "Used": [
           "urn:uuid:641e9a46-6810-4125-b85c-1aa5bb8119e7"
         ],
-        "AssociatedWith": "urn:urn:spm-0M07DSW9",
+        "AssociatedWith": "urn:spm-0M07DSW9",
         "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -232,7 +232,7 @@
         "Used": [
           "urn:uuid:ddb595a9-6134-47dd-a3db-47d426702f79"
         ],
-        "AssociatedWith": "urn:urn:spm-0M07DSW9",
+        "AssociatedWith": "urn:spm-0M07DSW9",
         "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -247,7 +247,7 @@
         "Used": [
           "urn:uuid:4bd3cab0-ba16-490e-b334-ca7c036cec4f"
         ],
-        "AssociatedWith": "urn:urn:spm-0M07DSW9",
+        "AssociatedWith": "urn:spm-0M07DSW9",
         "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 116;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -265,19 +265,19 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "digest": {
-          "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+          "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
         "Label": "anat_sub-01_T1w.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
         "digest": {
-          "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+          "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
         }
       },
       {
@@ -306,7 +306,7 @@
         "GeneratedBy": "urn:gunzip4-D4JR7Bc6"
       },
       {
-        "@id": "bids::c1xxx.nii.gz",
+        "@id": "bids::c1anat_sub-01_T1w.nii",
         "Label": "segment1",
         "AtLocation": "c1anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-hPpFAHil",
@@ -315,7 +315,7 @@
         }
       },
       {
-        "@id": "bids::c2xxx.nii.gz",
+        "@id": "bids::c2anat_sub-01_T1w.nii",
         "Label": "segment2",
         "AtLocation": "c2anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-hPpFAHil",
@@ -329,11 +329,11 @@
         "GeneratedBy": "urn:normaliz-9GRC3VyJ"
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "Label": "ONSETS_sub-01-MultiCond.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "digest": {
-          "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+          "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_thr_clustfwep05_batch.png b/examples/from_parsers/spm/spm_thr_clustfwep05_batch.png
index 36e0ccf7..046b1575 100644
Binary files a/examples/from_parsers/spm/spm_thr_clustfwep05_batch.png and b/examples/from_parsers/spm/spm_thr_clustfwep05_batch.png differ
diff --git a/examples/from_parsers/spm/spm_thr_clustunck10_batch.jsonld b/examples/from_parsers/spm/spm_thr_clustunck10_batch.jsonld
index b5f3b00e..3c16abf8 100644
--- a/examples/from_parsers/spm/spm_thr_clustunck10_batch.jsonld
+++ b/examples/from_parsers/spm/spm_thr_clustunck10_batch.jsonld
@@ -16,24 +16,24 @@
         "@id": "urn:movefile-6M2dWydM",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
+          "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-Eyt4IuQT",
-        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+        "AssociatedWith": "urn:spm-Eyt4IuQT",
+        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
         }
       },
       {
         "@id": "urn:movefile-lMbd62mT",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz"
+          "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-Eyt4IuQT",
-        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+        "AssociatedWith": "urn:spm-Eyt4IuQT",
+        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
         }
       },
       {
@@ -42,7 +42,7 @@
         "Used": [
           "urn:uuid:aeb68c71-9731-4d2d-9ea0-12c4b3cfaea2"
         ],
-        "AssociatedWith": "urn:urn:spm-Eyt4IuQT",
+        "AssociatedWith": "urn:spm-Eyt4IuQT",
         "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -51,7 +51,7 @@
         "Used": [
           "urn:uuid:f5dceeb4-5e21-462a-9be8-d084ddbf7932"
         ],
-        "AssociatedWith": "urn:urn:spm-Eyt4IuQT",
+        "AssociatedWith": "urn:spm-Eyt4IuQT",
         "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -60,7 +60,7 @@
         "Used": [
           "urn:uuid:1fdcb68d-e374-4d38-bcc6-20e33e2b5d16"
         ],
-        "AssociatedWith": "urn:urn:spm-Eyt4IuQT",
+        "AssociatedWith": "urn:spm-Eyt4IuQT",
         "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
         "Parameters": {
           "eoptions.quality": "0.9",
@@ -84,7 +84,7 @@
           "urn:uuid:0d8b8014-e217-4f92-a442-a7d19c708320",
           "urn:uuid:5a8a8ad7-73f8-456f-afe3-ac53d237dfd1"
         ],
-        "AssociatedWith": "urn:urn:spm-Eyt4IuQT",
+        "AssociatedWith": "urn:spm-Eyt4IuQT",
         "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
         "Parameters": {
           "other": "{''}",
@@ -100,7 +100,7 @@
         "Used": [
           "urn:uuid:5a8a8ad7-73f8-456f-afe3-ac53d237dfd1"
         ],
-        "AssociatedWith": "urn:urn:spm-Eyt4IuQT",
+        "AssociatedWith": "urn:spm-Eyt4IuQT",
         "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
         "Parameters": {
           "channel.biasreg": "0.001",
@@ -143,10 +143,10 @@
         "@id": "urn:normaliz-vR7z5lUJ",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz",
+          "bids::c1anat_sub-01_T1w.nii",
           "urn:uuid:0d8b8014-e217-4f92-a442-a7d19c708320"
         ],
-        "AssociatedWith": "urn:urn:spm-Eyt4IuQT",
+        "AssociatedWith": "urn:spm-Eyt4IuQT",
         "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -159,9 +159,9 @@
         "@id": "urn:normaliz-ZinH9mGC",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz"
+          "bids::c1anat_sub-01_T1w.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-Eyt4IuQT",
+        "AssociatedWith": "urn:spm-Eyt4IuQT",
         "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -176,7 +176,7 @@
         "Used": [
           "urn:uuid:6865890c-2e7f-4d7b-846d-40e2034cb7a9"
         ],
-        "AssociatedWith": "urn:urn:spm-Eyt4IuQT",
+        "AssociatedWith": "urn:spm-Eyt4IuQT",
         "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
         "Parameters": {
           "fwhm": "[6, 6, 6]",
@@ -190,10 +190,10 @@
         "Label": "Stat Design",
         "Used": [
           "urn:uuid:c9a1d982-a774-4e4a-b4de-119da8e1ddc2",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
+          "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
         ],
-        "AssociatedWith": "urn:urn:spm-Eyt4IuQT",
-        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_cluster_k10'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+        "AssociatedWith": "urn:spm-Eyt4IuQT",
+        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_cluster_k10'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_cluster_k10'}",
           "timing.units": "'secs'",
@@ -219,7 +219,7 @@
         "Used": [
           "urn:uuid:b097d4f8-8924-49fc-b7bf-d36e399f4f21"
         ],
-        "AssociatedWith": "urn:urn:spm-Eyt4IuQT",
+        "AssociatedWith": "urn:spm-Eyt4IuQT",
         "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -232,7 +232,7 @@
         "Used": [
           "urn:uuid:8fdee69d-4f68-4c41-9e25-d5bc958272db"
         ],
-        "AssociatedWith": "urn:urn:spm-Eyt4IuQT",
+        "AssociatedWith": "urn:spm-Eyt4IuQT",
         "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -247,7 +247,7 @@
         "Used": [
           "urn:uuid:7a4e0b61-870e-4ea1-804a-c5cb1dcca2d2"
         ],
-        "AssociatedWith": "urn:urn:spm-Eyt4IuQT",
+        "AssociatedWith": "urn:spm-Eyt4IuQT",
         "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 10;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -265,19 +265,19 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "digest": {
-          "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+          "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
         "Label": "anat_sub-01_T1w.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
         "digest": {
-          "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+          "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
         }
       },
       {
@@ -306,7 +306,7 @@
         "GeneratedBy": "urn:gunzip4-hjYeNgdg"
       },
       {
-        "@id": "bids::c1xxx.nii.gz",
+        "@id": "bids::c1anat_sub-01_T1w.nii",
         "Label": "segment1",
         "AtLocation": "c1anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-2TUAqTwk",
@@ -315,7 +315,7 @@
         }
       },
       {
-        "@id": "bids::c2xxx.nii.gz",
+        "@id": "bids::c2anat_sub-01_T1w.nii",
         "Label": "segment2",
         "AtLocation": "c2anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-2TUAqTwk",
@@ -329,11 +329,11 @@
         "GeneratedBy": "urn:normaliz-vR7z5lUJ"
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "Label": "ONSETS_sub-01-MultiCond.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "digest": {
-          "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+          "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_thr_clustunck10_batch.png b/examples/from_parsers/spm/spm_thr_clustunck10_batch.png
index 9a7320f5..475eb634 100644
Binary files a/examples/from_parsers/spm/spm_thr_clustunck10_batch.png and b/examples/from_parsers/spm/spm_thr_clustunck10_batch.png differ
diff --git a/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.jsonld b/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.jsonld
index 81b3f300..8c34e40d 100644
--- a/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.jsonld
+++ b/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.jsonld
@@ -16,24 +16,24 @@
         "@id": "urn:movefile-oKHoqlpV",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
+          "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-9bcWvatM",
-        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+        "AssociatedWith": "urn:spm-9bcWvatM",
+        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
         }
       },
       {
         "@id": "urn:movefile-Wjq8qqkf",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz"
+          "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-9bcWvatM",
-        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+        "AssociatedWith": "urn:spm-9bcWvatM",
+        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
         }
       },
       {
@@ -42,7 +42,7 @@
         "Used": [
           "urn:uuid:8fa22cb9-7c76-486f-9d5b-8cba8bd3acee"
         ],
-        "AssociatedWith": "urn:urn:spm-9bcWvatM",
+        "AssociatedWith": "urn:spm-9bcWvatM",
         "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -51,7 +51,7 @@
         "Used": [
           "urn:uuid:b8523047-5639-4e6e-adec-6daec8a60280"
         ],
-        "AssociatedWith": "urn:urn:spm-9bcWvatM",
+        "AssociatedWith": "urn:spm-9bcWvatM",
         "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -60,7 +60,7 @@
         "Used": [
           "urn:uuid:d93c3829-c444-49f3-a3c6-6f836e61bd6a"
         ],
-        "AssociatedWith": "urn:urn:spm-9bcWvatM",
+        "AssociatedWith": "urn:spm-9bcWvatM",
         "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
         "Parameters": {
           "eoptions.quality": "0.9",
@@ -84,7 +84,7 @@
           "urn:uuid:858135c7-7aac-4fee-9ffb-2109e784abc0",
           "urn:uuid:d8124621-a9cb-4ed9-b26d-0adfb02e6e84"
         ],
-        "AssociatedWith": "urn:urn:spm-9bcWvatM",
+        "AssociatedWith": "urn:spm-9bcWvatM",
         "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
         "Parameters": {
           "other": "{''}",
@@ -100,7 +100,7 @@
         "Used": [
           "urn:uuid:d8124621-a9cb-4ed9-b26d-0adfb02e6e84"
         ],
-        "AssociatedWith": "urn:urn:spm-9bcWvatM",
+        "AssociatedWith": "urn:spm-9bcWvatM",
         "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
         "Parameters": {
           "channel.biasreg": "0.001",
@@ -143,10 +143,10 @@
         "@id": "urn:normaliz-XNMcYmPX",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz",
+          "bids::c1anat_sub-01_T1w.nii",
           "urn:uuid:858135c7-7aac-4fee-9ffb-2109e784abc0"
         ],
-        "AssociatedWith": "urn:urn:spm-9bcWvatM",
+        "AssociatedWith": "urn:spm-9bcWvatM",
         "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -159,9 +159,9 @@
         "@id": "urn:normaliz-YUhm2lc5",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz"
+          "bids::c1anat_sub-01_T1w.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-9bcWvatM",
+        "AssociatedWith": "urn:spm-9bcWvatM",
         "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -176,7 +176,7 @@
         "Used": [
           "urn:uuid:11e832e4-d52e-4d41-aa63-1013364f30be"
         ],
-        "AssociatedWith": "urn:urn:spm-9bcWvatM",
+        "AssociatedWith": "urn:spm-9bcWvatM",
         "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
         "Parameters": {
           "fwhm": "[6, 6, 6]",
@@ -190,10 +190,10 @@
         "Label": "Stat Design",
         "Used": [
           "urn:uuid:f6b16b8e-ba13-4b03-957f-fbe68afe59df",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
+          "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
         ],
-        "AssociatedWith": "urn:urn:spm-9bcWvatM",
-        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FDR_p005'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+        "AssociatedWith": "urn:spm-9bcWvatM",
+        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FDR_p005'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FDR_p005'}",
           "timing.units": "'secs'",
@@ -219,7 +219,7 @@
         "Used": [
           "urn:uuid:30abb4c8-1be8-45e1-8509-67d5ed09efed"
         ],
-        "AssociatedWith": "urn:urn:spm-9bcWvatM",
+        "AssociatedWith": "urn:spm-9bcWvatM",
         "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -232,7 +232,7 @@
         "Used": [
           "urn:uuid:c0fb8d7f-a541-432b-a819-abdc9366765e"
         ],
-        "AssociatedWith": "urn:urn:spm-9bcWvatM",
+        "AssociatedWith": "urn:spm-9bcWvatM",
         "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -247,7 +247,7 @@
         "Used": [
           "urn:uuid:2864188c-4e65-4ac4-acd8-096759441ba7"
         ],
-        "AssociatedWith": "urn:urn:spm-9bcWvatM",
+        "AssociatedWith": "urn:spm-9bcWvatM",
         "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'FDR';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.05;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -265,19 +265,19 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "digest": {
-          "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+          "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
         "Label": "anat_sub-01_T1w.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
         "digest": {
-          "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+          "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
         }
       },
       {
@@ -306,7 +306,7 @@
         "GeneratedBy": "urn:gunzip4-aws2OWPG"
       },
       {
-        "@id": "bids::c1xxx.nii.gz",
+        "@id": "bids::c1anat_sub-01_T1w.nii",
         "Label": "segment1",
         "AtLocation": "c1anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-1oFMwhYt",
@@ -315,7 +315,7 @@
         }
       },
       {
-        "@id": "bids::c2xxx.nii.gz",
+        "@id": "bids::c2anat_sub-01_T1w.nii",
         "Label": "segment2",
         "AtLocation": "c2anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-1oFMwhYt",
@@ -329,11 +329,11 @@
         "GeneratedBy": "urn:normaliz-XNMcYmPX"
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "Label": "ONSETS_sub-01-MultiCond.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "digest": {
-          "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+          "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.png b/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.png
index f0886d1c..5dfb550d 100644
Binary files a/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.png and b/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.png differ
diff --git a/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.jsonld b/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.jsonld
index c67b363c..dfa1ad3c 100644
--- a/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.jsonld
+++ b/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.jsonld
@@ -16,24 +16,24 @@
         "@id": "urn:movefile-jgpFGx7p",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
+          "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-yjAds0ke",
-        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+        "AssociatedWith": "urn:spm-yjAds0ke",
+        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
         }
       },
       {
         "@id": "urn:movefile-oi25dFW5",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz"
+          "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-yjAds0ke",
-        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+        "AssociatedWith": "urn:spm-yjAds0ke",
+        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
         }
       },
       {
@@ -42,7 +42,7 @@
         "Used": [
           "urn:uuid:66498c32-4cc1-4b35-8a3b-7ef1e48f870b"
         ],
-        "AssociatedWith": "urn:urn:spm-yjAds0ke",
+        "AssociatedWith": "urn:spm-yjAds0ke",
         "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -51,7 +51,7 @@
         "Used": [
           "urn:uuid:be46fe75-48d3-4aec-b827-72eb76cf3e4b"
         ],
-        "AssociatedWith": "urn:urn:spm-yjAds0ke",
+        "AssociatedWith": "urn:spm-yjAds0ke",
         "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -60,7 +60,7 @@
         "Used": [
           "urn:uuid:0e8c2114-421b-4c1f-9770-b7ec22289e5b"
         ],
-        "AssociatedWith": "urn:urn:spm-yjAds0ke",
+        "AssociatedWith": "urn:spm-yjAds0ke",
         "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
         "Parameters": {
           "eoptions.quality": "0.9",
@@ -84,7 +84,7 @@
           "urn:uuid:116af5c8-b8ba-4dc0-8992-24147d8fa74f",
           "urn:uuid:a921f85d-f605-4362-954a-0cb2364b9106"
         ],
-        "AssociatedWith": "urn:urn:spm-yjAds0ke",
+        "AssociatedWith": "urn:spm-yjAds0ke",
         "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
         "Parameters": {
           "other": "{''}",
@@ -100,7 +100,7 @@
         "Used": [
           "urn:uuid:116af5c8-b8ba-4dc0-8992-24147d8fa74f"
         ],
-        "AssociatedWith": "urn:urn:spm-yjAds0ke",
+        "AssociatedWith": "urn:spm-yjAds0ke",
         "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
         "Parameters": {
           "channel.biasreg": "0.001",
@@ -143,10 +143,10 @@
         "@id": "urn:normaliz-qr8A88OY",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz",
+          "bids::c1anat_sub-01_T1w.nii",
           "urn:uuid:a921f85d-f605-4362-954a-0cb2364b9106"
         ],
-        "AssociatedWith": "urn:urn:spm-yjAds0ke",
+        "AssociatedWith": "urn:spm-yjAds0ke",
         "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -159,9 +159,9 @@
         "@id": "urn:normaliz-RHavIjbG",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz"
+          "bids::c1anat_sub-01_T1w.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-yjAds0ke",
+        "AssociatedWith": "urn:spm-yjAds0ke",
         "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -176,7 +176,7 @@
         "Used": [
           "urn:uuid:be60ffac-85d7-4c57-b3a3-64e06e72d7b6"
         ],
-        "AssociatedWith": "urn:urn:spm-yjAds0ke",
+        "AssociatedWith": "urn:spm-yjAds0ke",
         "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
         "Parameters": {
           "fwhm": "[6, 6, 6]",
@@ -190,10 +190,10 @@
         "Label": "Stat Design",
         "Used": [
           "urn:uuid:4380232a-e050-464e-8f0f-3bd6d53cd023",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
+          "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
         ],
-        "AssociatedWith": "urn:urn:spm-yjAds0ke",
-        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FWE_p005'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+        "AssociatedWith": "urn:spm-yjAds0ke",
+        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FWE_p005'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FWE_p005'}",
           "timing.units": "'secs'",
@@ -219,7 +219,7 @@
         "Used": [
           "urn:uuid:1ce4a608-dfe0-4e27-ac4f-77f4f7897c8d"
         ],
-        "AssociatedWith": "urn:urn:spm-yjAds0ke",
+        "AssociatedWith": "urn:spm-yjAds0ke",
         "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -232,7 +232,7 @@
         "Used": [
           "urn:uuid:63e6bd7b-8840-4c4a-8706-995cdcdecacb"
         ],
-        "AssociatedWith": "urn:urn:spm-yjAds0ke",
+        "AssociatedWith": "urn:spm-yjAds0ke",
         "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -247,7 +247,7 @@
         "Used": [
           "urn:uuid:449e7341-030f-47de-ab61-25a597c0a2fc"
         ],
-        "AssociatedWith": "urn:urn:spm-yjAds0ke",
+        "AssociatedWith": "urn:spm-yjAds0ke",
         "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'FWE';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.05;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -265,19 +265,19 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "digest": {
-          "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+          "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
         "Label": "anat_sub-01_T1w.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
         "digest": {
-          "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+          "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
         }
       },
       {
@@ -306,7 +306,7 @@
         "GeneratedBy": "urn:gunzip4-unV7YNDw"
       },
       {
-        "@id": "bids::c1xxx.nii.gz",
+        "@id": "bids::c1anat_sub-01_T1w.nii",
         "Label": "segment1",
         "AtLocation": "c1anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-kfGSAqvJ",
@@ -315,7 +315,7 @@
         }
       },
       {
-        "@id": "bids::c2xxx.nii.gz",
+        "@id": "bids::c2anat_sub-01_T1w.nii",
         "Label": "segment2",
         "AtLocation": "c2anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-kfGSAqvJ",
@@ -329,11 +329,11 @@
         "GeneratedBy": "urn:normaliz-qr8A88OY"
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "Label": "ONSETS_sub-01-MultiCond.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "digest": {
-          "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+          "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.png b/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.png
index cd9a93d5..a2dd7a9b 100644
Binary files a/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.png and b/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.png differ
diff --git a/examples/from_parsers/spm/spm_thr_voxelunct4_batch.jsonld b/examples/from_parsers/spm/spm_thr_voxelunct4_batch.jsonld
index 86d96c82..71d198e5 100644
--- a/examples/from_parsers/spm/spm_thr_voxelunct4_batch.jsonld
+++ b/examples/from_parsers/spm/spm_thr_voxelunct4_batch.jsonld
@@ -16,24 +16,24 @@
         "@id": "urn:movefile-ROutyaPT",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
+          "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-VHiUsL5F",
-        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+        "AssociatedWith": "urn:spm-VHiUsL5F",
+        "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
         }
       },
       {
         "@id": "urn:movefile-4PSvH3CK",
         "Label": "Move file",
         "Used": [
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz"
+          "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
         ],
-        "AssociatedWith": "urn:urn:spm-VHiUsL5F",
-        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+        "AssociatedWith": "urn:spm-VHiUsL5F",
+        "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
         "Parameters": {
-          "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+          "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
         }
       },
       {
@@ -42,7 +42,7 @@
         "Used": [
           "urn:uuid:b9c13da5-bd20-4982-8e24-84e88a4ae030"
         ],
-        "AssociatedWith": "urn:urn:spm-VHiUsL5F",
+        "AssociatedWith": "urn:spm-VHiUsL5F",
         "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -51,7 +51,7 @@
         "Used": [
           "urn:uuid:e8972264-3d5c-41e9-9e79-3aa2517f2787"
         ],
-        "AssociatedWith": "urn:urn:spm-VHiUsL5F",
+        "AssociatedWith": "urn:spm-VHiUsL5F",
         "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
       },
       {
@@ -60,7 +60,7 @@
         "Used": [
           "urn:uuid:b9238bd2-fa85-4bcb-a4c2-08d2eec5e697"
         ],
-        "AssociatedWith": "urn:urn:spm-VHiUsL5F",
+        "AssociatedWith": "urn:spm-VHiUsL5F",
         "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
         "Parameters": {
           "eoptions.quality": "0.9",
@@ -84,7 +84,7 @@
           "urn:uuid:9e132fb5-837a-4e40-b107-656f6b9a41f4",
           "urn:uuid:fc1e9970-e3d1-4041-98fc-93127b2276d3"
         ],
-        "AssociatedWith": "urn:urn:spm-VHiUsL5F",
+        "AssociatedWith": "urn:spm-VHiUsL5F",
         "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
         "Parameters": {
           "other": "{''}",
@@ -100,7 +100,7 @@
         "Used": [
           "urn:uuid:9e132fb5-837a-4e40-b107-656f6b9a41f4"
         ],
-        "AssociatedWith": "urn:urn:spm-VHiUsL5F",
+        "AssociatedWith": "urn:spm-VHiUsL5F",
         "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
         "Parameters": {
           "channel.biasreg": "0.001",
@@ -143,10 +143,10 @@
         "@id": "urn:normaliz-EnYVW6ta",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz",
+          "bids::c1anat_sub-01_T1w.nii",
           "urn:uuid:fc1e9970-e3d1-4041-98fc-93127b2276d3"
         ],
-        "AssociatedWith": "urn:urn:spm-VHiUsL5F",
+        "AssociatedWith": "urn:spm-VHiUsL5F",
         "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -159,9 +159,9 @@
         "@id": "urn:normaliz-6rnR9WUq",
         "Label": "Normalize",
         "Used": [
-          "bids::c1xxx.nii.gz"
+          "bids::c1anat_sub-01_T1w.nii"
         ],
-        "AssociatedWith": "urn:urn:spm-VHiUsL5F",
+        "AssociatedWith": "urn:spm-VHiUsL5F",
         "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
         "Parameters": {
           "woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -176,7 +176,7 @@
         "Used": [
           "urn:uuid:6ebfdade-3218-4c37-abda-28ad1f81b578"
         ],
-        "AssociatedWith": "urn:urn:spm-VHiUsL5F",
+        "AssociatedWith": "urn:spm-VHiUsL5F",
         "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
         "Parameters": {
           "fwhm": "[6, 6, 6]",
@@ -190,10 +190,10 @@
         "Label": "Stat Design",
         "Used": [
           "urn:uuid:f5296976-630d-4243-885f-f11f9ea2027d",
-          "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
+          "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
         ],
-        "AssociatedWith": "urn:urn:spm-VHiUsL5F",
-        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_t4'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+        "AssociatedWith": "urn:spm-VHiUsL5F",
+        "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_t4'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
         "Parameters": {
           "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_t4'}",
           "timing.units": "'secs'",
@@ -219,7 +219,7 @@
         "Used": [
           "urn:uuid:dc23b217-4d4d-4f85-8976-c35f199399ec"
         ],
-        "AssociatedWith": "urn:urn:spm-VHiUsL5F",
+        "AssociatedWith": "urn:spm-VHiUsL5F",
         "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
         "Parameters": {
           "write_residuals": "0",
@@ -232,7 +232,7 @@
         "Used": [
           "urn:uuid:74440f61-3749-47ff-bde5-b4c8a1a60240"
         ],
-        "AssociatedWith": "urn:urn:spm-VHiUsL5F",
+        "AssociatedWith": "urn:spm-VHiUsL5F",
         "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
         "Parameters": {
           "consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -247,7 +247,7 @@
         "Used": [
           "urn:uuid:18fe4543-ccde-4309-8280-1f29622ad95f"
         ],
-        "AssociatedWith": "urn:urn:spm-VHiUsL5F",
+        "AssociatedWith": "urn:spm-VHiUsL5F",
         "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 4;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
         "Parameters": {
           "conspec.titlestr": "''",
@@ -265,19 +265,19 @@
     ],
     "Entities": [
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "Label": "func_sub-01_task-tonecounting_bold.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+        "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
         "digest": {
-          "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+          "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
         }
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
         "Label": "anat_sub-01_T1w.nii.gz",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+        "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
         "digest": {
-          "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+          "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
         }
       },
       {
@@ -306,7 +306,7 @@
         "GeneratedBy": "urn:gunzip4-u7pnp8ps"
       },
       {
-        "@id": "bids::c1xxx.nii.gz",
+        "@id": "bids::c1anat_sub-01_T1w.nii",
         "Label": "segment1",
         "AtLocation": "c1anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-w1flk7eY",
@@ -315,7 +315,7 @@
         }
       },
       {
-        "@id": "bids::c2xxx.nii.gz",
+        "@id": "bids::c2anat_sub-01_T1w.nii",
         "Label": "segment2",
         "AtLocation": "c2anat_sub-01_T1w.nii",
         "GeneratedBy": "urn:segment7-w1flk7eY",
@@ -329,11 +329,11 @@
         "GeneratedBy": "urn:normaliz-EnYVW6ta"
       },
       {
-        "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "Label": "ONSETS_sub-01-MultiCond.mat",
-        "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+        "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
         "digest": {
-          "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+          "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
         }
       },
       {
diff --git a/examples/from_parsers/spm/spm_thr_voxelunct4_batch.png b/examples/from_parsers/spm/spm_thr_voxelunct4_batch.png
index a9856095..a265034f 100644
Binary files a/examples/from_parsers/spm/spm_thr_voxelunct4_batch.png and b/examples/from_parsers/spm/spm_thr_voxelunct4_batch.png differ