diff --git a/examples/fsl_default/report_log.html b/examples/fsl_default/report_log.html deleted file mode 100644 index 9fa11fc8d..000000000 --- a/examples/fsl_default/report_log.html +++ /dev/null @@ -1,185 +0,0 @@ - - - - - -FSL -

Progress Report / Log

-Started at Fri 4 May 08:20:53 BST 2018

-Feat main script

-
-/bin/cp /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/./fsl_default/design.fsf design.fsf
-
-/usr/local/packages/fsl-5.0.10/bin/feat_model design
-
-mkdir .files;cp /usr/local/packages/fsl-5.0.10/doc/fsl.css .files;cp -r /usr/local/packages/fsl-5.0.10/doc/images .files/images
-
-/usr/local/packages/fsl-5.0.10/bin/fsl_sub -T 10 -l logs -N feat0_init   /usr/local/packages/fsl-5.0.10/bin/feat /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/design.fsf -D /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat -I 1 -init
-job
-326901
-
-/usr/local/packages/fsl-5.0.10/bin/fsl_sub -T 40 -l logs -N feat2_pre -j 326901  /usr/local/packages/fsl-5.0.10/bin/feat /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/design.fsf -D /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat -I 1 -prestats
-job
-326902
-
-/usr/local/packages/fsl-5.0.10/bin/fsl_sub -T 1 -l logs -N feat3_film -j 326902  /usr/local/packages/fsl-5.0.10/bin/feat /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/design.fsf -D /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat -I 1 -stats
-job
-326903
-
-/usr/local/packages/fsl-5.0.10/bin/fsl_sub -T 119 -l logs -N feat4_post -j 326903  /usr/local/packages/fsl-5.0.10/bin/feat /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/design.fsf -D /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat -poststats 0 
-job
-326904
-
-/usr/local/packages/fsl-5.0.10/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 326902,326903,326904  /usr/local/packages/fsl-5.0.10/bin/feat /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/design.fsf -D /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat -stop
-job
-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
-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 
-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 -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"
-Option -y ( standard dof ) selected with  argument "12"
-Option -z ( standard search ) selected with  argument "90"
-

Registration
-
-/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 /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w  highres_head
-
-did not find file: example_func2highres.mat. Generating transform.
-
-/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres
-Running FAST segmentation FLIRT pre-alignment Running BBR 0.436200 0.999899 -0.001807 0.014099 0.000000 0.001680 0.999958 0.009056 0.000000 -0.014115 -0.009032 0.999860 0.000000 2.273952 0.940215 1.394828 1.000000
-
-/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat
-
-
-/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 ; /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 ; /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 ; /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 ; /usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png - example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png example_func2highres2.png
-
-
-/bin/rm example_func2highres1.png
-
-

Preprocessing:Stage 2
-
-/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
-
-/bin/mkdir -p mc ; /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
-
-/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 
-
-/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 
-
-/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 
-
-/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func
-
-/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask
-
-/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet
-
-/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
-0.000000 744.585571 
-
-/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char
-
-/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50
-594.438538 
-
-/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask
-
-/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh
-
-/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func
-
-/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
-
-/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth
-
-/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm
-
-/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean
-
-/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt
-
-/usr/local/packages/fsl-5.0.10/bin/imrm tempMean
-
-/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data
-
-/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func
-
-/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 /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/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
-paradigm.getDesignMatrix().Nrows()=104
-paradigm.getDesignMatrix().Ncols()=2
-sizeTS=104
-numTS=38352
-Calculating residuals...
-Completed
-Estimating residual autocorrelation...
-Calculating raw AutoCorrs... Completed
-mode = 9979.81
-sig = 963
-Spatially smoothing auto corr estimates
-.........
-Completed
-Tukey M = 10
-Tukey estimates... Completed
-Completed
-Prewhitening and Computing PEs...
-Percentage done:
-1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,Completed
-Saving results... 
-Completed
-
-/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102   -m mask -r stats/res4d > stats/smoothness
-

Post-stats
-
-/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1
-
-echo 38352 > thresh_zstat1.vol
-zstat1: DLH=0.70114 VOLUME=38352 RESELS=6.60665
-
-/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001
-3.090232
-
-/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
-
-/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1 
-
-/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null
-3.090524 7.488793 
-Rendering using zmin=3.090524 zmax=7.488793
-
-/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090524 7.488793 rendered_thresh_zstat1
-
-/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png
-
-/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif
-
-mkdir -p tsplot ; /usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot
-

























diff --git a/examples/fsl_default/report_log.jsonld b/examples/fsl_default/report_log.jsonld deleted file mode 100644 index 8b739ae23..000000000 --- a/examples/fsl_default/report_log.jsonld +++ /dev/null @@ -1,1139 +0,0 @@ -{ - "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json", - "BIDSProvVersion": "dev", - "@id": "http://example.org/ds00000X", - "records": { - "prov:Agent": [ - { - "@id": "urn:464be845-c5d0-4365-a47b-a17e0c37c851", - "RRID": "RRID:SCR_007037", - "@type": "prov:SoftwareAgent", - "label": "FSL", - "version": "xxx" - } - ], - "prov:Activity": [ - { - "@id": "urn:7b4cc7a3-77d8-4a6f-a4d9-d391ed15902d", - "label": "fslmaths", - "associatedWith": "urn:464be845-c5d0-4365-a47b-a17e0c37c851", - "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", - "used": [ - "urn:10d74558-dd9f-4b24-84be-91d38f32d1a1" - ] - }, - { - "@id": "urn:e57b1809-0a72-4836-b019-92bf0ef6c9e3", - "label": "fslroi", - "associatedWith": "urn:464be845-c5d0-4365-a47b-a17e0c37c851", - "command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1", - "used": [ - "urn:a10cc9e0-1851-40a3-9ba1-babb9f06fbaa" - ] - }, - { - "@id": "urn:524413b4-640c-49cd-9ae4-f38ad0936d41", - "label": "mainfeatreg", - "associatedWith": "urn:464be845-c5d0-4365-a47b-a17e0c37c851", - "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", - "used": [ - "urn:1d4e6395-268e-4037-9a88-c89c2cde0318", - "urn:a637ad31-66b3-48d2-ab77-f36277bf862d", - "urn:311425ff-8824-45f2-a933-71bc20540d9a" - ] - }, - { - "@id": "urn:ff4f96c7-3bc9-4b33-a529-92dc051aac16", - "label": "Make directory", - "associatedWith": "urn:464be845-c5d0-4365-a47b-a17e0c37c851", - "command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/reg", - "used": [] - }, - { - "@id": "urn:cbcfd381-3748-4192-8abb-34f2f3e98edd", - "label": "fslmaths", - "associatedWith": 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"struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {})", - "sess.regress": "struct('name', {}, 'val', {})", - "sess.multi_reg": "{''}", - "sess.hpf": "128", - "fact": "struct('name', {}, 'levels', {})", - "bases.hrf.derivs": "[0, 0]", - "volt": "1", - "global": "'None'", - "mthresh": "0.8", - "mask": "{''}", - "cvi": "'AR(1)'" - } - }, - { - "@id": "urn:41c2651d-3c6f-4a73-acb0-b27a83e9f260", - "label": "Estimate stat.", - "used": [ - "urn:99917d06-d721-4a5d-b2c2-840c05fcc74a" - ], - "associatedWith": "urn:46fa4656-04ff-4815-9924-630ade8c68a1", - "parameters": { - "write_residuals": "0", - "method.Classical": "1" - } - }, - { - "@id": "urn:b5da6d4e-ec48-4b1c-97a0-6a1f3a7e44d2", - "label": "Estimate contrast", - "used": [ - "urn:178b1021-d703-4223-a6bc-140088fd42b7" - ], - "associatedWith": "urn:46fa4656-04ff-4815-9924-630ade8c68a1", - "parameters": { - "consess{1}.tcon.name": "'tone counting vs baseline'", - "consess{1}.tcon.weights": "[1, 0]", - "consess{1}.tcon.sessrep": "'none'", - "delete": "0" - } - }, - { - "@id": "urn:d229064f-517b-4908-bb15-e0dcd8ae3fed", - "label": "Threshold", - "used": [ - "urn:cf588147-6489-489b-8fb1-35976dc05824" - ], - "associatedWith": "urn:46fa4656-04ff-4815-9924-630ade8c68a1", - "parameters": { - "conspec.titlestr": "''", - "conspec.contrasts": "Inf", - "conspec.threshdesc": "'none'", - "conspec.thresh": "0.001", - "conspec.extent": "0", - "conspec.conjunction": "1", - "conspec.mask.none": "1", - "units": "1", - "print": "'pdf'", - "write.tspm.basename": "'thresh'" - } - } - ], - "prov:Entity": [ - { - "@id": "urn:e3cbcb3c-bafe-41cc-b381-cc208c96da0c", - "label": "func_sub-01_task-tonecounting_bold.nii.gz", - "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz" - }, - { - "@id": "urn:25117bf5-5a0a-4b9a-b398-31b0ccdccd1d", - "label": "anat_sub-01_T1w.nii.gz", - "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz" - }, - { - "@id": "urn:3cc12c9a-b2a8-4f28-a93c-9f217d881fb3", - "label": "func_sub-01_task-tonecounting_bold.nii.gz", - "generatedBy": "urn:166dce06-394f-4efd-bff9-89e21cd0530e" - }, - { - "@id": "urn:70658eb1-7e23-410d-b783-7794f0bd74c8", - "label": "anat_sub-01_T1w.nii.gz", - "generatedBy": "urn:f3ac49e0-6cee-4ad5-a241-0a0003c59605" - }, - { - "@id": "urn:cee0e17e-0fbf-49d4-b9d8-7c78a5258d7d", - "label": "func_sub-01_task-tonecounting_bold.nii", - "generatedBy": "urn:44d46866-152d-41ed-bd63-9aa703518cfc" - }, - { - "@id": "urn:0faa82fd-a82d-4cc6-92bc-92d073721e96", - "label": "meanfunc_sub-01_task-tonecounting_bold.nii", - "generatedBy": "urn:00b5a19a-32b1-4419-ace4-18d3a0b012d0" - }, - { - "@id": "urn:3ecd9684-e52e-4b0f-9d48-0fc559a2fa1f", - "label": "anat_sub-01_T1w.nii", - "generatedBy": "urn:3a0afe4a-8fd2-471f-b5f3-775548f5dd60" - }, - { - "@id": "urn:a976c2d4-9085-4136-8255-c2bb6853a286", - "label": "segment1", - "prov:atLocation": "c1anat_sub-01_T1w.nii", - "generatedBy": "urn:afd882cf-12ab-45ce-b10f-e53c5d9c9f1d" - }, - { - "@id": "urn:45f570ad-55e6-40cf-b382-6f61ca371a0c", - "label": "segment2", - "prov:atLocation": "c2anat_sub-01_T1w.nii", - "generatedBy": "urn:afd882cf-12ab-45ce-b10f-e53c5d9c9f1d" - }, - { - "@id": "urn:a30c6b73-85ab-49f3-8236-c2247331042b", - "label": "wsegment1", - "generatedBy": "urn:bdd7aefe-c624-473d-b02d-70e9f992e872" - }, - { - "@id": "urn:a81992ff-2747-4efb-8483-c578db401f65", - "label": "ONSETS_sub-01-MultiCond.mat", - "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat" - }, - { - "@id": "urn:c5ad3e75-61fa-463d-87fc-c3c56facf623", - "label": "swsegment1", - "generatedBy": "urn:3a79bde1-8944-460a-b492-f42e6cea7457" - }, - { - "@id": "urn:99917d06-d721-4a5d-b2c2-840c05fcc74a", - "label": "SPM.mat", - "generatedBy": "urn:12285f0b-f74b-49b2-b3fa-b8f149a41a6f" - }, - { - "@id": "urn:178b1021-d703-4223-a6bc-140088fd42b7", - "label": "SPM.mat", - "generatedBy": "urn:41c2651d-3c6f-4a73-acb0-b27a83e9f260" - }, - { - "@id": "urn:cf588147-6489-489b-8fb1-35976dc05824", - "label": "SPM.mat", - "generatedBy": "urn:b5da6d4e-ec48-4b1c-97a0-6a1f3a7e44d2" - } - ] - } -} \ No newline at end of file diff --git a/examples/spm_default/batch.m b/examples/spm_default/batch.m deleted file mode 100644 index 4b22e99f4..000000000 --- a/examples/spm_default/batch.m +++ /dev/null @@ -1,122 +0,0 @@ -%----------------------------------------------------------------------- -% Job saved on 15-Mar-2016 14:20:25 by cfg_util (rev $Rev: 6460 $) -% spm SPM - SPM12 (12.1) -% cfg_basicio BasicIO - Unknown -%----------------------------------------------------------------------- -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'}; -matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}; -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'}; -matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}; -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')); -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')); -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('()',{':'})); -matlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9; -matlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4; -matlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5; -matlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1; -matlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2; -matlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0]; -matlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = ''; -matlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1]; -matlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4; -matlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0]; -matlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1; -matlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r'; -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')); -matlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'})); -matlabbatch{6}.spm.spatial.coreg.estimate.other = {''}; -matlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi'; -matlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2]; -matlabbatch{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]; -matlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7]; -matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'})); -matlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001; -matlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60; -matlabbatch{7}.spm.spatial.preproc.channel.write = [0 1]; -matlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'}; -matlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1; -matlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0]; -matlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0]; -matlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'}; -matlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1; -matlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0]; -matlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0]; -matlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'}; -matlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2; -matlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0]; -matlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0]; -matlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'}; -matlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3; -matlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0]; -matlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0]; -matlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'}; -matlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4; -matlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0]; -matlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0]; -matlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'}; -matlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2; -matlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0]; -matlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0]; -matlabbatch{7}.spm.spatial.preproc.warp.mrf = 1; -matlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1; -matlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2]; -matlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni'; -matlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0; -matlabbatch{7}.spm.spatial.preproc.warp.samp = 3; -matlabbatch{7}.spm.spatial.preproc.warp.write = [0 1]; -matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'})); -matlabbatch{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')); -matlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 - 78 76 85]; -matlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2]; -matlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4; -matlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w'; -matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'})); -matlabbatch{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', '()',{':'})); -matlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 - 78 76 85]; -matlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2]; -matlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4; -matlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w'; -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')); -matlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6]; -matlabbatch{10}.spm.spatial.smooth.dtype = 0; -matlabbatch{10}.spm.spatial.smooth.im = 0; -matlabbatch{10}.spm.spatial.smooth.prefix = 's'; -matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_p0001'}; -matlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs'; -matlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2; -matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16; -matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8; -matlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files')); -matlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {}); -matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'}; -matlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {}); -matlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''}; -matlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128; -matlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {}); -matlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0]; -matlabbatch{11}.spm.stats.fmri_spec.volt = 1; -matlabbatch{11}.spm.stats.fmri_spec.global = 'None'; -matlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8; -matlabbatch{11}.spm.stats.fmri_spec.mask = {''}; -matlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)'; -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')); -matlabbatch{12}.spm.stats.fmri_est.write_residuals = 0; -matlabbatch{12}.spm.stats.fmri_est.method.Classical = 1; -matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat')); -matlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline'; -matlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0]; -matlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none'; -matlabbatch{13}.spm.stats.con.delete = 0; -matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat')); -matlabbatch{14}.spm.stats.results.conspec.titlestr = ''; -matlabbatch{14}.spm.stats.results.conspec.contrasts = Inf; -matlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none'; -matlabbatch{14}.spm.stats.results.conspec.thresh = 0.001; -matlabbatch{14}.spm.stats.results.conspec.extent = 0; -matlabbatch{14}.spm.stats.results.conspec.conjunction = 1; -matlabbatch{14}.spm.stats.results.conspec.mask.none = 1; -matlabbatch{14}.spm.stats.results.units = 1; -matlabbatch{14}.spm.stats.results.print = 'pdf'; -matlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';