Section23 prep-script for VM image

I made a new variant of the prep-script. Using VM path for images (avoids some downloads) and disables all the stuff meant for interactive demos. What follows is the code I ran inside the VM after importing the pristine OVA (e789b13556ca0f517743e6a1da4f3fe0 /tmp/reprotraining.ova):

All executed in $HOME inside the image

git config --global user.email johndoe@example.com
git config --global user.name "John Doe"
source activate section2

# neuroimaging extension install was missing dependencies
pip install --upgrade datalad-neuroimaging

# not really needed, but nice: install datalad stable release
pip install --upgrade datalad

# for the next one I actually did
#datalad install https://github.com/myyoda/ohbm2018-training
# to get this PR, but really it would be, after the PR is merged
datalad install https://github.com/ReproNim/ohbm2018-training

# it is super useful to have gitk and/or tig to inspect Git history
sudo apt-get install gitk tig

# replace broken FSL image in the VM with current one
singularity pull -n fsl.simg shub://ReproNim/ohbm2018-training:fsln
mv fsl.simg images/

# and run the beast
bash -x ohbm2018-training/section23/fsl_glm_in_image.sh

Notice that I could not use the FSL singularity image in the VM, but had to use shub://ReproNim/ohbm2018-training:fsln (the local one has no proper PATH environment setup).

Here is the full log of running the script:

(section2) vagrant@nitrcce:~$ bash -x ohbm2018-training/section23/fsl_glm_in_image.sh 
+ set -e -u
++ pwd
+ srcdir=/home/vagrant
+ wdir=demo
+ mkdir -p demo
+ cd demo
++ pwd
+ echo 'Workdir at /home/vagrant/demo'
Workdir at /home/vagrant/demo
+ datalad create bids
[INFO   ] Creating a new annex repo at /home/vagrant/demo/bids 
create(ok): /home/vagrant/demo/bids (dataset)                                                    
+ cd bids
+ datalad install -d . -s https://github.com/datalad/example-dicom-functional.git inputs/rawdata
[INFO   ] Cloning https://github.com/datalad/example-dicom-functional.git to '/home/vagrant/demo/bids/inputs/rawdata' 
install(ok): inputs/rawdata (dataset)                                                            
action summary:
  add (notneeded: 2, ok: 1)
  install (ok: 1)
  save (ok: 1)
+ datalad containers-add heudiconv -u /home/vagrant/images/heudiconv.simg --call-fmt 'singularity exec -B /tmp --bind {{pwd}} -H {{pwd}} {img} {cmd}'
save(ok): /home/vagrant/demo/bids (dataset)                                                      
containers_add(ok): /home/vagrant/demo/bids/.datalad/environments/heudiconv/image (file)
action summary:
  containers_add (ok: 1)
  save (ok: 1)
+ datalad containers-run -m 'Convert sub-02 DICOMs into BIDS' --input inputs/rawdata/dicoms --output . heudiconv -f reproin -s 02 -c dcm2niix -b -l '' --minmeta -a . -o /tmp/heudiconv.sub-02 --files inputs/rawdata/dicoms
[INFO   ] == Command start (output follows) ===== 
WARNING: Not mounting requested bind point (already mounted in container): /home/vagrant/demo/bids
INFO: Running heudiconv version 0.5.dev1
INFO: Analyzing 5460 dicoms
INFO: Filtering out 0 dicoms based on their filename
WARNING: dcmstack without support of pydicom >= 1.0 is detected. Adding a plug
INFO: Generated sequence info for 1 studies with 1 entries total
INFO: Processing sequence infos to deduce study/session
INFO: Study session for {'locator': 'Hanke/Stadler/0083_transrep2', 'subject': '02', 'session': None}
INFO: Need to process 1 study sessions
INFO: PROCESSING STARTS: {'subject': '02', 'outdir': '/tmp/heudiconv.sub-02/', 'session': None}
INFO: Processing 1 pre-sorted seqinfo entries
INFO: Reloading existing filegroup.json because /tmp/heudiconv.sub-02/.heudiconv/02/02.edit.txt exists
INFO: Doing conversion using dcm2niix
INFO: Converting ./sub-02/func/sub-02_task-oneback_run-01_bold (5460 DICOMs) -> ./sub-02/func . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')
INFO: Generating grammar tables from /usr/lib/python3.5/lib2to3/Grammar.txt
INFO: Generating grammar tables from /usr/lib/python3.5/lib2to3/PatternGrammar.txt
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixmrs31zqi/convert".
INFO: [Node] Running "convert" ("nipype.interfaces.dcm2nii.Dcm2niix"), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f func -o . -s n -v n /tmp/dcm2niixmrs31zqi/convert
INFO: stdout 2018-06-12T18:28:23.930486:Chris Rorden's dcm2niiX version v1.0.20171215 (OpenJPEG build) GCC6.3.0 (64-bit Linux)
INFO: stdout 2018-06-12T18:28:23.930486:Found 5460 DICOM image(s)
INFO: stdout 2018-06-12T18:28:23.930486:swizzling 3rd and 4th dimensions (XYTZ -> XYZT), assuming interslice distance is 3.300000
INFO: stdout 2018-06-12T18:28:23.930486:Convert 5460 DICOM as ./func (80x80x35x156)
INFO: stdout 2018-06-12T18:28:23.930486:Philips Precise RS:RI:SS = 4.00757:0:0.0132383 (see PMC3998685)
INFO: stdout 2018-06-12T18:28:23.930486: R = raw value, P = precise value, D = displayed value
INFO: stdout 2018-06-12T18:28:23.930486: RS = rescale slope, RI = rescale intercept,  SS = scale slope
INFO: stdout 2018-06-12T18:28:23.930486: D = R * RS + RI    , P = D/(RS * SS)
INFO: stdout 2018-06-12T18:28:23.930486: D scl_slope:scl_inter = 4.00757:0
INFO: stdout 2018-06-12T18:28:23.930486: P scl_slope:scl_inter = 75.5384:0
INFO: stdout 2018-06-12T18:28:23.930486: Using P values ('-p n ' for D values)
INFO: stdout 2018-06-12T18:28:25.933874:compress: "/usr/bin/pigz" -n -f -6 "./func.nii"
INFO: stdout 2018-06-12T18:28:25.933874:Conversion required 3.857223 seconds (0.920270 for core code).
INFO: [Node] Finished "convert".
INFO: Populating template files under ./
INFO: PROCESSING DONE: {'subject': '02', 'outdir': '/tmp/heudiconv.sub-02/', 'session': None}
[INFO   ] == Command exit (modification check follows) ===== 
get(notneeded): .datalad/environments/heudiconv/image (file) [already present]                   
get(notneeded): inputs/rawdata/dicoms [no dataset annex, content already present]
unlock(ok): .datalad/environments/heudiconv/image (file)
add(ok): CHANGES (file)
add(ok): README (file)
add(ok): dataset_description.json (file)
add(ok): participants.tsv (file)
add(ok): sourcedata/README (file)
add(ok): sourcedata/sub-02/func/sub-02_task-oneback_run-01_bold.dicom.tgz (file)
add(ok): sub-02/func/sub-02_task-oneback_run-01_bold.json (file)
add(ok): sub-02/func/sub-02_task-oneback_run-01_bold.nii.gz (file)
add(ok): sub-02/func/sub-02_task-oneback_run-01_events.tsv (file)
add(ok): sub-02/sub-02_scans.tsv (file)
add(ok): task-oneback_bold.json (file)
add(ok): .datalad/environments/heudiconv/image (file)
save(ok): /home/vagrant/demo/bids (dataset)
action summary:
  add (ok: 12)
  get (notneeded: 2)
  save (ok: 1)
  unlock (ok: 1)
+ datalad run -m 'Import stimulation events' --input inputs/rawdata/events.tsv --output sub-02/func/sub-02_task-oneback_run-01_events.tsv cp '{inputs}' '{outputs}'
get(notneeded): inputs/rawdata/events.tsv [no dataset annex, content already present]
unlock(ok): sub-02/func/sub-02_task-oneback_run-01_events.tsv (file)
[INFO   ] == Command start (output follows) ===== 
[INFO   ] == Command exit (modification check follows) ===== 
add(ok): sub-02/func/sub-02_task-oneback_run-01_events.tsv (file)                                
save(ok): /home/vagrant/demo/bids (dataset)
action summary:
  add (ok: 1)
  get (notneeded: 1)
  save (ok: 1)
  unlock (ok: 1)
+ cd ..
+ datalad create glm_analysis
[INFO   ] Creating a new annex repo at /home/vagrant/demo/glm_analysis 
create(ok): /home/vagrant/demo/glm_analysis (dataset)                                            
+ cd glm_analysis
+ datalad install -d . -s ../bids inputs/rawdata
[INFO   ] Cloning ../bids to '/home/vagrant/demo/glm_analysis/inputs/rawdata' 
install(ok): inputs/rawdata (dataset)                                                            
action summary:
  add (notneeded: 2, ok: 1)
  install (ok: 1)
  save (ok: 1)
+ datalad run-procedure setup_yoda_dataset
[INFO   ] == Command start (output follows) ===== 
[INFO   ] == Command exit (modification check follows) =====                                     
add(notneeded): /home/vagrant/demo/glm_analysis (dataset)
+ datalad download-url -O code/events2ev3.sh https://raw.githubusercontent.com/ReproNim/ohbm2018-training/master/section23/scripts/events2ev3.sh
[INFO   ] Downloading 'https://raw.githubusercontent.com/ReproNim/ohbm2018-training/master/section23/scripts/events2ev3.sh' into 'code/events2ev3.sh' 
https://raw.githubusercontent.com/ReproNim/ohbm2018-training/master/section23/scripts/events2ev3.                                                                                                 download_url(ok): code/events2ev3.sh (file)
add(ok): code/events2ev3.sh (file) [non-large file; adding content to git repository]            
save(ok): /home/vagrant/demo/glm_analysis (dataset)
action summary:
  add (ok: 1)
  download_url (ok: 1)
  save (ok: 1)
+ datalad download-url -O code/ffa_design.fsf https://raw.githubusercontent.com/ReproNim/ohbm2018-training/master/section23/scripts/ffa_design.fsf
[INFO   ] Downloading 'https://raw.githubusercontent.com/ReproNim/ohbm2018-training/master/section23/scripts/ffa_design.fsf' into 'code/ffa_design.fsf' 
https://raw.githubusercontent.com/ReproNim/ohbm2018-training/master/section23/scripts/ffa_design.                                                                                                 download_url(ok): code/ffa_design.fsf (file)
add(ok): code/ffa_design.fsf (file) [non-large file; adding content to git repository]           
save(ok): /home/vagrant/demo/glm_analysis (dataset)
action summary:
  add (ok: 1)
  download_url (ok: 1)
  save (ok: 1)
+ datalad run -m 'Build FSL EV3 design files' --input inputs/rawdata/sub-02/func/sub-02_task-oneback_run-01_events.tsv --output sub-02/onsets bash code/events2ev3.sh sub-02 '{inputs}'
get(ok): inputs/rawdata/sub-02/func/sub-02_task-oneback_run-01_events.tsv (file) [from origin...]
[INFO   ] == Command start (output follows) ===== 
sub-02
1
[INFO   ] == Command exit (modification check follows) ===== 
add(ok): sub-02/onsets/run-1/body.txt (file)                                                     
add(ok): sub-02/onsets/run-1/face.txt (file)
add(ok): sub-02/onsets/run-1/house.txt (file)
add(ok): sub-02/onsets/run-1/object.txt (file)
add(ok): sub-02/onsets/run-1/scene.txt (file)
add(ok): sub-02/onsets/run-1/scramble.txt (file)
save(ok): /home/vagrant/demo/glm_analysis (dataset)
action summary:
  add (ok: 6)
  get (ok: 1)
  save (ok: 1)
+ datalad run -m 'FSL FEAT analysis config script' --output sub-02/1stlvl_design.fsf bash -c 'sed -e "s,##BASEPATH##,{pwd},g" -e "s,##SUB##,sub-02,g" \
         code/ffa_design.fsf > {outputs}'
unlock(ok): sub-02/onsets/run-1/body.txt (file)
unlock(ok): sub-02/onsets/run-1/face.txt (file)
unlock(ok): sub-02/onsets/run-1/house.txt (file)
unlock(ok): sub-02/onsets/run-1/object.txt (file)
unlock(ok): sub-02/onsets/run-1/scene.txt (file)
unlock(ok): sub-02/onsets/run-1/scramble.txt (file)
[INFO   ] == Command start (output follows) ===== 
[INFO   ] == Command exit (modification check follows) ===== 
add(ok): sub-02/1stlvl_design.fsf (file)                                                         
add(ok): sub-02/onsets/run-1/body.txt (file)
add(ok): sub-02/onsets/run-1/face.txt (file)
add(ok): sub-02/onsets/run-1/house.txt (file)
add(ok): sub-02/onsets/run-1/object.txt (file)
add(ok): sub-02/onsets/run-1/scene.txt (file)
add(ok): sub-02/onsets/run-1/scramble.txt (file)
save(ok): /home/vagrant/demo/glm_analysis (dataset)
action summary:
  add (ok: 7)
  save (ok: 1)
  unlock (ok: 6)
+ datalad containers-add fsl -u shub://ReproNim/ohbm2018-training:fsln --call-fmt 'singularity exec -B /tmp --bind {{pwd}} -H {{pwd}} {img} {cmd}'
save(ok): /home/vagrant/demo/glm_analysis (dataset)                                              
containers_add(ok): /home/vagrant/demo/glm_analysis/.datalad/environments/fsl/image (file)
action summary:
  containers_add (ok: 1)
  save (ok: 1)
+ datalad containers-run -m 'sub-02 1st-level GLM' --input sub-02/1stlvl_design.fsf --input sub-02/onsets --input inputs/rawdata/sub-02/func/sub-02_task-oneback_run-01_bold.nii.gz --output sub-02/1stlvl_glm.feat feat '{inputs[0]}'
[INFO   ] == Command start (output follows) =====                                                
WARNING: Not mounting requested bind point (already mounted in container): /home/vagrant/demo/glm_analysis
To view the FEAT progress and final report, point your web browser at /home/vagrant/demo/glm_analysis/sub-02/1stlvl_glm.feat/report_log.html
[INFO   ] == Command exit (modification check follows) ===== 
get(notneeded): sub-02/1stlvl_design.fsf (file) [already present]                                
get(notneeded): sub-02/onsets (directory) [nothing to get from /home/vagrant/demo/glm_analysis/sub-02/onsets]
get(notneeded): .datalad/environments/fsl/image (file) [already present]
get(ok): inputs/rawdata/sub-02/func/sub-02_task-oneback_run-01_bold.nii.gz (file) [from origin...]
unlock(ok): .datalad/environments/fsl/image (file)
unlock(ok): sub-02/1stlvl_design.fsf (file)
unlock(ok): sub-02/onsets/run-1/body.txt (file)
unlock(ok): sub-02/onsets/run-1/face.txt (file)
unlock(ok): sub-02/onsets/run-1/house.txt (file)
unlock(ok): sub-02/onsets/run-1/object.txt (file)
unlock(ok): sub-02/onsets/run-1/scene.txt (file)
unlock(ok): sub-02/onsets/run-1/scramble.txt (file)
add(ok): sub-02/1stlvl_glm.feat/absbrainthresh.txt (file)
add(ok): sub-02/1stlvl_glm.feat/cluster_mask_zstat1.nii.gz (file)
add(ok): sub-02/1stlvl_glm.feat/cluster_zstat1.html (file)
add(ok): sub-02/1stlvl_glm.feat/cluster_zstat1.txt (file)
add(ok): sub-02/1stlvl_glm.feat/confoundevs.txt (file)
add(ok): sub-02/1stlvl_glm.feat/custom_timing_files/ev1.txt (file)
add(ok): sub-02/1stlvl_glm.feat/custom_timing_files/ev2.txt (file)
add(ok): sub-02/1stlvl_glm.feat/custom_timing_files/ev3.txt (file)
add(ok): sub-02/1stlvl_glm.feat/custom_timing_files/ev4.txt (file)
add(ok): sub-02/1stlvl_glm.feat/custom_timing_files/ev5.txt (file)
add(ok): sub-02/1stlvl_glm.feat/custom_timing_files/ev6.txt (file)
add(ok): sub-02/1stlvl_glm.feat/design.con (file)
add(ok): sub-02/1stlvl_glm.feat/design.frf (file)
add(ok): sub-02/1stlvl_glm.feat/design.fsf (file)
add(ok): sub-02/1stlvl_glm.feat/design.mat (file)
add(ok): sub-02/1stlvl_glm.feat/design.min (file)
add(ok): sub-02/1stlvl_glm.feat/design.png (file)
add(ok): sub-02/1stlvl_glm.feat/design.ppm (file)
add(ok): sub-02/1stlvl_glm.feat/design.trg (file)
add(ok): sub-02/1stlvl_glm.feat/design_cov.png (file)
add(ok): sub-02/1stlvl_glm.feat/design_cov.ppm (file)
add(ok): sub-02/1stlvl_glm.feat/example_func.nii.gz (file)
add(ok): sub-02/1stlvl_glm.feat/filtered_func_data.nii.gz (file)
add(ok): sub-02/1stlvl_glm.feat/lmax_zstat1.txt (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat0 (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat0_init.e11990 (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat0_init.o11990 (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat1 (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat1a_init (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat2_pre (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat2_pre.e12072 (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat2_pre.o12072 (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat3_film.e12519 (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat3_film.o12519 (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat3_stats (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat4_post (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat4_post.e12876 (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat4_post.o12876 (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat5_stop.e13513 (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat5_stop.o13513 (file)
add(ok): sub-02/1stlvl_glm.feat/logs/feat9 (file)
add(ok): sub-02/1stlvl_glm.feat/mask.nii.gz (file)
add(ok): sub-02/1stlvl_glm.feat/mc/disp.png (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0000 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0001 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0002 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0003 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0004 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0005 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0006 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0007 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0008 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0009 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0010 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0011 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0012 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0013 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0014 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0015 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0016 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0017 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0018 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0019 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0020 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0021 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0022 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0023 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0024 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0025 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0026 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0027 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0028 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0029 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0030 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0031 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0032 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0033 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0034 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0035 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0036 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0037 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0038 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0039 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0040 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0041 (file)
add(ok): sub-02/1stlvl_glm.feat/mc/prefiltered_func_data_mcf.mat/MAT_0042 (file)
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add(ok): sub-02/1stlvl_glm.feat/tsplot/ps_tsplotc_zstat1_ev2.txt (file)
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add(ok): sub-02/1stlvl_glm.feat/tsplot/tsplot_zstat1.png (file)
add(ok): sub-02/1stlvl_glm.feat/tsplot/tsplot_zstat1.txt (file)
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add(ok): sub-02/1stlvl_glm.feat/.files/fsl.css (file)
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add(ok): sub-02/1stlvl_glm.feat/.files/images/fsl-bg (file)
add(ok): sub-02/1stlvl_glm.feat/.files/images/fsl-bg.jpg (file)
add(ok): sub-02/1stlvl_glm.feat/.files/images/fsl-logo-big.jpg (file)
add(ok): sub-02/1stlvl_glm.feat/.files/images/fsl-logo.gif (file)
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add(ok): sub-02/1stlvl_glm.feat/.files/images/vert2.png (file)
add(ok): sub-02/1stlvl_glm.feat/.ramp.gif (file)
add(ok): .datalad/environments/fsl/image (file)
add(ok): sub-02/1stlvl_design.fsf (file)
add(ok): sub-02/onsets/run-1/body.txt (file)
add(ok): sub-02/onsets/run-1/face.txt (file)
add(ok): sub-02/onsets/run-1/house.txt (file)
add(ok): sub-02/onsets/run-1/object.txt (file)
add(ok): sub-02/onsets/run-1/scene.txt (file)
add(ok): sub-02/onsets/run-1/scramble.txt (file)
save(ok): /home/vagrant/demo/glm_analysis (dataset)
action summary:
  add (ok: 352)
  get (notneeded: 3, ok: 1)
  save (ok: 1)
  unlock (ok: 8)
+ datalad run-procedure cfg_metadatatypes nifti1
[INFO   ] == Command start (output follows) ===== 
[INFO   ] == Command exit (modification check follows) =====                                     
add(notneeded): /home/vagrant/demo/glm_analysis (dataset)
+ datalad aggregate-metadata
[INFO   ] Aggregate metadata for dataset /home/vagrant/demo/glm_analysis 
Metadata extraction: 100%|███████████████████████████| 3.00/3.00 [00:01<00:00, 2.04 extractors/s/home/vagrant/miniconda2/envs/section2/lib/python3.6/site-packages/nibabel/parrec.py:508: UserWarning: PAR/REC version 'None' is currently not supported -- making an attempt to read nevertheless. Please email the NiBabel mailing list, if you are interested in adding support for this version. 
  """.format(version)))
[INFO   ] Update aggregate metadata in dataset at: /home/vagrant/demo/glm_analysis               
aggregate_metadata(ok): /home/vagrant/demo/glm_analysis (dataset)                                
[INFO   ] Attempting to save 6 files/datasets 
save(ok): /home/vagrant/demo/glm_analysis (dataset)                                              
action summary:
  aggregate_metadata (ok: 1)
  save (ok: 1)

ReproNim / ohbm2018-training

Section23 prep-script for VM image #33