FIX: Ignore sourcedata and derivatives when fetching data #1788
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@yarikoptic Would you care to give this branch a try? |
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oh... I run fmriprep as released in a container. would take me a bit to do otherwise. if you have such environment ready, could you please just try running that script (removing singularity shimming) I provided in #1787 -- it should be quite straightforward |
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If you use fmriprep-docker <all> <my> <usual> <args> -f /data/projects/fmriprep/fmriprep(Note that you need to target the Python source directory, not the repository root.) |
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(I'll give your script a try, though.) |
that is neat! haven't used |
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Updated script to: > cat replicate-fmriprepkaboom.sh
#!/bin/bash
set -eu
datalad install ///labs/haxby/life
datalad get life/sub-rid000001 # one subject to start with
export FS_LICENSE=/Users/markiewicz/Documents/freesurfer_license.txt
mkdir -p derivatives/{work,fmriprep-1.5.0}
# manual execution to ease troubleshooting
# --skip-bids-validation since we did not get/process all the subjects, and
# https://github.com/bids-standard/bids-validator/issues/769 still scares me a lot ;)
fmriprep-docker life derivatives/fmriprep-1.5.0/ participant --skip-bids-validation \
--participant-label rid000001 -w derivatives/work \
--notrack --skull-strip-fixed-seed \
--ignore slicetiming --fs-license-file="$FS_LICENSE" \
--bold2t1w-dof 9 --output-space fsaverage5 T1w \
--n_cpus 2 --omp-nthreads 1 $@To get to the error, I ran: > bash replicate-fmriprepkaboom.sh --anat-onlyProducing (click to expand)Running with > bash replicate-fmriprepkaboom.sh --anat-only -f /Users/markiewicz/Projects/crn/fmriprep/fmriprepContinues past that point. So I'll go ahead and merge this once tests pass. @oesteban A note that rerunning with the fix and a working directory that has a crashfile in it produced Deleting the working directory resolved it. fMRIPrep reports using Nipype 1.2.2. |
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so, the fix came without a test to solidify correct behavior... I guess it might come back to bite us. |
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Changes proposed in this pull request
Closes #1787.
Documentation that should be reviewed