The MRSIPrep on Docker wrapper

MRSIPrep is distributed as a Docker image; there is no supported host installation of the pipeline itself. This is a lightweight, dependency-free Python wrapper (mirroring the fmriprep-docker wrapper) that builds and runs the appropriate docker run command using the normal MRSIPrep BIDS App syntax. Docker must be installed and running (check with docker info).

Install

pip install mrsiprep-docker

Use

mrsiprep-docker /path/to/bids /path/to/derivatives participant \
  --participant-label S001 --session-label V1 \
  --mode mni-norm --nthreads 8 \
  --fs-license-file /path/to/freesurfer/license.txt

This generates and runs the equivalent of:

docker run --rm -it -u "$(id -u):$(id -g)" \
  -e TZ="$(cat /etc/timezone)" \
  -v /path/to/freesurfer/license.txt:/opt/freesurfer/license.txt:ro \
  -e FS_LICENSE=/opt/freesurfer/license.txt \
  -v /path/to/bids:/data:ro \
  -v /path/to/derivatives:/out \
  mrsiup/mrsiprep:cpu \
  /data /out participant \
  --participant-label S001 --session-label V1 \
  --mode mni-norm --nthreads 8

All ordinary mrsiprep arguments (--mode, --participant-label, --tissue-backend, --parcellation-mode, --nproc, --verbose, ...) are passed straight through to the container unchanged. The wrapper only special-cases the few options that need a bind mount or an environment variable: --fs-license-file, --fs-subjects-dir, --work-dir, and --participants.

-u "$(id -u):$(id -g)" (the default; override with -u/--user) plus the container's own permission-fixing entrypoint means output files are owned by the invoking user, not root. -e TZ=... (skip with --no-tz) keeps console and logbook timestamps in sync with the host clock.

See the main repository's documentation for the full MRSIPrep CLI reference: https://mrsiprep.readthedocs.io/