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": "urn:464be845-c5d0-4365-a47b-a17e0c37c851",
- "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",
- "used": [
- "urn:a637ad31-66b3-48d2-ab77-f36277bf862d"
- ]
- },
- {
- "@id": "urn:24d14993-3412-43a7-baa2-2c948fb52e70",
- "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/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
- "used": [
- "urn:38d3088a-a55e-401f-ae0d-f136631019bf"
- ]
- },
- {
- "@id": "urn:90d50e51-2469-4746-a527-6f8fc580f466",
- "label": "epi_reg",
- "associatedWith": "urn:464be845-c5d0-4365-a47b-a17e0c37c851",
- "command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
- "used": [
- "urn:20206c16-f4de-4eb6-906e-439777b29b99",
- "urn:9e0e57a6-b49b-4cf9-9408-910f5c8c77c6",
- "urn:d4d5d59d-c11d-4573-92b5-cb47ded7b575"
- ]
- },
- {
- "@id": "urn:70eb6e5d-18c1-4cf6-bc3f-4fcf0154aeef",
- "label": "convert_xfm",
- "associatedWith": "urn:464be845-c5d0-4365-a47b-a17e0c37c851",
- "command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
- "used": [
- "urn:0098d9e4-942f-428b-a3b3-abb4c58c9790"
- ]
- },
- {
- "@id": "urn:3dd29616-13ee-4d88-8f50-e88e33df56c3",
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- "label": "sub-01_tone_counting.txt",
- "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt"
- },
- {
- "@id": "urn:80ae7cee-deb7-4cb0-b61d-95bb573570cb",
- "label": "ev1.txt",
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- "generatedBy": "urn:92204d7f-44ae-44e5-9809-40f5f8e43f31"
- },
- {
- "@id": "urn:e5e62a29-f02c-4c93-9585-5ad149d22120",
- "label": "sub-01_tone_counting_probe.txt",
- "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt"
- },
- {
- "@id": "urn:d3e975e7-25b5-43c7-a6b6-2326f7642dc7",
- "label": "ev2.txt",
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- "generatedBy": "urn:51114b07-0f2a-4a66-8fe5-13ab68ee7a71"
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- "label": "stats",
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- {
- "@id": "urn:7037e6ad-d35c-4f36-98c2-a10cfbbfe142",
- "label": "design.mat",
- "prov:atLocation": "design.mat"
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- "label": "design.con",
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- "@id": "urn:84d0fc14-86ff-4d6b-9a85-9da9cd66b8e2",
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- }
- ]
- }
-}
\ No newline at end of file
diff --git a/examples/spm_default/batch.jsonld b/examples/spm_default/batch.jsonld
deleted file mode 100644
index aae029d2e..000000000
--- a/examples/spm_default/batch.jsonld
+++ /dev/null
@@ -1,334 +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:46fa4656-04ff-4815-9924-630ade8c68a1",
- "RRID": "RRID:SCR_007037",
- "@type": "prov:SoftwareAgent",
- "label": "SPM",
- "version": "SPM12r7224"
- }
- ],
- "prov:Activity": [
- {
- "@id": "urn:166dce06-394f-4efd-bff9-89e21cd0530e",
- "label": "Move file",
- "used": [
- "urn:e3cbcb3c-bafe-41cc-b381-cc208c96da0c"
- ],
- "associatedWith": "urn:46fa4656-04ff-4815-9924-630ade8c68a1",
- "parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
- }
- },
- {
- "@id": "urn:f3ac49e0-6cee-4ad5-a241-0a0003c59605",
- "label": "Move file",
- "used": [
- "urn:25117bf5-5a0a-4b9a-b398-31b0ccdccd1d"
- ],
- "associatedWith": "urn:46fa4656-04ff-4815-9924-630ade8c68a1",
- "parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
- }
- },
- {
- "@id": "urn:44d46866-152d-41ed-bd63-9aa703518cfc",
- "label": "Gunzip",
- "used": [
- "urn:3cc12c9a-b2a8-4f28-a93c-9f217d881fb3"
- ],
- "associatedWith": "urn:46fa4656-04ff-4815-9924-630ade8c68a1"
- },
- {
- "@id": "urn:3a0afe4a-8fd2-471f-b5f3-775548f5dd60",
- "label": "Gunzip",
- "used": [
- "urn:70658eb1-7e23-410d-b783-7794f0bd74c8"
- ],
- "associatedWith": "urn:46fa4656-04ff-4815-9924-630ade8c68a1"
- },
- {
- "@id": "urn:00b5a19a-32b1-4419-ace4-18d3a0b012d0",
- "label": "Realign",
- "used": [
- "urn:cee0e17e-0fbf-49d4-b9d8-7c78a5258d7d"
- ],
- "associatedWith": "urn:46fa4656-04ff-4815-9924-630ade8c68a1",
- "parameters": {
- "eoptions.quality": "0.9",
- "eoptions.sep": "4",
- "eoptions.fwhm": "5",
- "eoptions.rtm": "1",
- "eoptions.interp": "2",
- "eoptions.wrap": "[0, 0, 0]",
- "eoptions.weight": "''",
- "roptions.which": "[0, 1]",
- "roptions.interp": "4",
- "roptions.wrap": "[0, 0, 0]",
- "roptions.mask": "1",
- "roptions.prefix": "'r'"
- }
- },
- {
- "@id": "urn:a0faa270-06ad-4714-a268-18f071bd31c8",
- "label": "Coregister",
- "used": [
- "urn:0faa82fd-a82d-4cc6-92bc-92d073721e96",
- "urn:3ecd9684-e52e-4b0f-9d48-0fc559a2fa1f"
- ],
- "associatedWith": "urn:46fa4656-04ff-4815-9924-630ade8c68a1",
- "parameters": {
- "other": "{''}",
- "eoptions.cost_fun": "'nmi'",
- "eoptions.sep": "[4, 2]",
- "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]",
- "eoptions.fwhm": "[7, 7]"
- }
- },
- {
- "@id": "urn:afd882cf-12ab-45ce-b10f-e53c5d9c9f1d",
- "label": "Segment",
- "used": [
- "urn:3ecd9684-e52e-4b0f-9d48-0fc559a2fa1f"
- ],
- "associatedWith": "urn:46fa4656-04ff-4815-9924-630ade8c68a1",
- "parameters": {
- "channel.biasreg": "0.001",
- "channel.biasfwhm": "60",
- "channel.write": "[0, 1]",
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- "tissue(1).ngaus": "1",
- "tissue(1).native": "[1, 0]",
- "tissue(1).warped": "[0, 0]",
- "tissue(2).tpm": "{'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'}",
- "tissue(2).ngaus": "1",
- "tissue(2).native": "[1, 0]",
- "tissue(2).warped": "[0, 0]",
- "tissue(3).tpm": "{'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'}",
- "tissue(3).ngaus": "2",
- "tissue(3).native": "[1, 0]",
- "tissue(3).warped": "[0, 0]",
- "tissue(4).tpm": "{'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'}",
- "tissue(4).ngaus": "3",
- "tissue(4).native": "[1, 0]",
- "tissue(4).warped": "[0, 0]",
- "tissue(5).tpm": "{'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'}",
- "tissue(5).ngaus": "4",
- "tissue(5).native": "[1, 0]",
- "tissue(5).warped": "[0, 0]",
- "tissue(6).tpm": "{'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'}",
- "tissue(6).ngaus": "2",
- "tissue(6).native": "[0, 0]",
- "tissue(6).warped": "[0, 0]",
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- "warp.affreg": "'mni'",
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- }
- },
- {
- "@id": "urn:bdd7aefe-c624-473d-b02d-70e9f992e872",
- "label": "Normalize",
- "used": [
- "urn:a976c2d4-9085-4136-8255-c2bb6853a286",
- "urn:0faa82fd-a82d-4cc6-92bc-92d073721e96"
- ],
- "associatedWith": "urn:46fa4656-04ff-4815-9924-630ade8c68a1",
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- "woptions.vox": "[2, 2, 2]",
- "woptions.interp": "4",
- "woptions.prefix": "'w'"
- }
- },
- {
- "@id": "urn:cd29997a-7696-47d6-85c5-1fcfc6b64da0",
- "label": "Normalize",
- "used": [
- "urn:a976c2d4-9085-4136-8255-c2bb6853a286",
- "urn:a976c2d4-9085-4136-8255-c2bb6853a286"
- ],
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- "parameters": {
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- "woptions.prefix": "'w'"
- }
- },
- {
- "@id": "urn:3a79bde1-8944-460a-b492-f42e6cea7457",
- "label": "Smooth",
- "used": [
- "urn:a30c6b73-85ab-49f3-8236-c2247331042b"
- ],
- "associatedWith": "urn:46fa4656-04ff-4815-9924-630ade8c68a1",
- "parameters": {
- "fwhm": "[6, 6, 6]",
- "dtype": "0",
- "im": "0",
- "prefix": "'s'"
- }
- },
- {
- "@id": "urn:12285f0b-f74b-49b2-b3fa-b8f149a41a6f",
- "label": "Stat Design",
- "used": [
- "urn:c5ad3e75-61fa-463d-87fc-c3c56facf623",
- "urn:a81992ff-2747-4efb-8483-c578db401f65"
- ],
- "associatedWith": "urn:46fa4656-04ff-4815-9924-630ade8c68a1",
- "parameters": {
- "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_p0001'}",
- "timing.units": "'secs'",
- "timing.RT": "2",
- "timing.fmri_t": "16",
- "timing.fmri_t0": "8",
- "sess.cond": "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": [
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- ],
- "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';