Minor changes to coordinate delimiter, ciftify container binding #28
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jerdra
requested changes
Oct 21, 2022
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| -v $(pwd)/fmriprep:/fmriprep \ | ||
| -v $(pwd)/freesurfer:/freesurfer \ |
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Suggested change
| -v $(pwd)/fmriprep:/fmriprep \ | |
| -v $(pwd)/freesurfer:/freesurfer \ |
Your invocation file is probably mis-specified here if you need to bind to the root directory of the container!
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Make sure that in ciftify that your fmriprep workdir is set to /output
| mri2mesh( | ||
| fmriprep_anat_wf.out.preproc_t1.map { s, t1 -> | ||
| [ s, t1, try_fetch_t2("${params.bids}/${s}/**/*T2w.nii.gz") ] | ||
| [ s, t1, try_fetch_t2("${params.bids}/${s}/*/*/*T2w.nii.gz") ] |
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Ok this one is strange cause I tested it w/the double star to recursively check directories. Mind if I test this real quick?
Only asking because I'd prefer ** since it removes dependencies on how the directory under subject is organized
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A few changes that I put in to help the workflow get running on my side for the pilots! Lmk if these make sense to include