fMRIPrep¶

background about fmriprep

Local fmriprep¶

fmriprep-docker \
    "/path/to/bids" \
    "/path/to/derivatives" \
    participant \
    --fs-license-file "/path/to/fs/license.txt"

docker run --rm -e DOCKER_VERSION_8395080871=20.10.8 -it \
    -v "path/to/filter.json:/files/filter.json:ro" \
    -v "path/to/fs/license.txt:/opt/freesurfer/license.txt:ro" \
    -v "path/to/bids:/data:ro" \
    -v "path/to/derivatives:/out" \
    nipreps/fmriprep:<tag> \
    /data /out participant \
    --bids-filter-file /files/filter.json \
    --fs-license-file /opt/freesurfer/license.txt

Output of fMRIPrep¶

output of fMRIPrep documentation

output_directory
├── fmriprep
│   ├── dataset_description.json
│   ├── ...
│   ├── sub-<subject_label>
│   │   ├── ...
│   │   └── ses-<session_label>
│   │       ├── anat
│   │       └── func
│   └── sub-<subject_label>.html
└── freesurfer
    ├── fsaverage
    └── sub-<subject_label>

fMRIPRep Output on Flywheel¶

errors on flywheel

include license.txt

Last update: October 21, 2021