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Local#

Run MEGPrep#

The example below runs the default full MEG workflow with an existing FreeSurfer/DeepPrep SUBJECTS_DIR. Add --steps all if structural MRI processing should run in the same command.

docker run --rm -it \
    -v /data/datasets/SMN4Lang:/input \
    -v /data/datasets/SMN4Lang/megprep_out:/output \
    -v /data/datasets/SMN4Lang/smri:/smri \
    -v /data/megprep/license.txt:/fs_license.txt \
    -v /data/nextflow.config:/program/nextflow/nextflow.config \
    cmrlab/megprep:0.0.3 \
    -i /input \
    -o /output \
    --fs_license_file /fs_license.txt \
    --fs_subjects_dir /smri \
    --steps meg_all \
    --resume

In this command:

  • -it

    Run in interactive mode, allowing users to interact within the container.

  • --rm

    This option automatically removes the container after it exits, ensuring no residual containers remain.

  • Output ownership

    The container entrypoint starts as root only long enough to prepare mounted output permissions, then runs Nextflow as the host UID/GID inferred from /input. Report-only runs that only mount /output infer ownership from /output instead. You do not need Docker’s --user flag or a pre-created output directory. If neither mount has the desired output owner, add -e LOCAL_UID="$(id -u)" -e LOCAL_GID="$(id -g)" to the docker run command.

  • -v /data/datasets/SMN4Lang:/input

    This option creates a volume mount, mapping the host directory /data/datasets/SMN4Lang to the container’s /input directory, allowing the container to access input data.

  • -v /data/datasets/SMN4Lang/megprep_out:/output

    This maps the output directory in the host to the container’s /output directory for saving processed data.

  • -v /data/datasets/SMN4Lang/smri:/smri

    This mounts a directory containing SMRI data(T1w, Freesurfer’s SUBJECTS_DIR) to the container’s /smri directory for application use.

  • -v /data/megprep/license.txt:/fs_license.txt

    This mounts the FreeSurfer license file into the container, ensuring it has access to the necessary permissions.

  • -v /data/nextflow.config:/program/nextflow/nextflow.config

    This mounts the Nextflow configuration file so the program inside the container can use it.

  • cmrlab/megprep:0.0.3

    This specifies the Docker image and version to run, where megprep is the image name, and 0.0.3 is the version.

  • -i /input

    This is a parameter passed to the program, specifying the input data directory as /input.

  • -o /output

    This parameter specifies the output data directory as /output.

  • --fs_license_file /fs_license.txt

    This passes the path to the FreeSurfer license file to the program, ensuring it can be recognized correctly.

  • --fs_subjects_dir /smri

    This specifies the separate SMRI data directory for use by the program.

  • --steps meg_all

    This selects full MEG processing using the existing anatomy in /smri. See Configuration Reference for all stage options.

  • --resume

    This flag allows the process to resume execution from the last completed step, which is useful for long-running tasks to avoid re-running completed steps.

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