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Usage Notes

Warning

As of fMRIPRep 1.0.12, the software includes a tracking system to report usage statistics and errors. Users can opt-out using the --notrack command line argument.

Execution and the BIDS format

The fMRIPRep workflow takes as principal input the path of the dataset that is to be processed. The input dataset is required to be in valid :abbr:`BIDS (Brain Imaging Data Structure)` format, and it must include at least one T1w structural image and (unless disabled with a flag) a BOLD series. We highly recommend that you validate your dataset with the free, online BIDS Validator.

The exact command to run fMRIPRep depends on the Installation_ method. The common parts of the command follow the BIDS-Apps definition. Example:

fmriprep data/bids_root/ out/ participant -w work/

Command-Line Arguments

.. argparse::
   :ref: fmriprep.cli.run.get_parser
   :prog: fmriprep
   :nodefault:
   :nodefaultconst:

The command-line interface of the docker wrapper

.. argparse::
   :ref: fmriprep_docker.get_parser
   :prog: fmriprep-docker
   :nodefault:
   :nodefaultconst:

The FreeSurfer license

fMRIPRep uses FreeSurfer tools, which require a license to run.

To obtain a FreeSurfer license, simply register for free at https://surfer.nmr.mgh.harvard.edu/registration.html.

When using manually-prepared environments or singularity, FreeSurfer will search for a license key file first using the $FS_LICENSE environment variable and then in the default path to the license key file ($FREESURFER_HOME/license.txt). If using the --cleanenv flag and $FS_LICENSE is set, use --fs-license-file $FS_LICENSE to pass the license file location to fMRIPRep.

It is possible to run the docker container pointing the image to a local path where a valid license file is stored. For example, if the license is stored in the $HOME/.licenses/freesurfer/license.txt file on the host system:

$ docker run -ti --rm \
    -v $HOME/fullds005:/data:ro \
    -v $HOME/dockerout:/out \
    -v $HOME/.licenses/freesurfer/license.txt:/opt/freesurfer/license.txt \
    poldracklab/fmriprep:latest \
    /data /out/out \
    participant \
    --ignore fieldmaps

Using FreeSurfer can also be enabled when using fmriprep-docker:

$ fmriprep-docker --fs-license-file $HOME/.licenses/freesurfer/license.txt \
    /path/to/data/dir /path/to/output/dir participant
RUNNING: docker run --rm -it -v /path/to/data/dir:/data:ro \
    -v /home/user/.licenses/freesurfer/license.txt:/opt/freesurfer/license.txt \
    -v /path/to_output/dir:/out poldracklab/fmriprep:1.0.0 \
    /data /out participant
...

If the environment variable $FS_LICENSE is set in the host system, then it will automatically used by fmriprep-docker. For instance, the following would be equivalent to the latest example:

$ export FS_LICENSE=$HOME/.licenses/freesurfer/license.txt
$ fmriprep-docker /path/to/data/dir /path/to/output/dir participant
RUNNING: docker run --rm -it -v /path/to/data/dir:/data:ro \
    -v /home/user/.licenses/freesurfer/license.txt:/opt/freesurfer/license.txt \
    -v /path/to_output/dir:/out poldracklab/fmriprep:1.0.0 \
    /data /out participant
...

Troubleshooting

Logs and crashfiles are outputted into the <output dir>/fmriprep/sub-<participant_label>/log directory. Information on how to customize and understand these files can be found on the nipype debugging page.

Support and communication. The documentation of this project is found here: http://fmriprep.readthedocs.org/en/latest/.

All bugs, concerns and enhancement requests for this software can be submitted here: https://github.com/poldracklab/fmriprep/issues.

If you have a problem or would like to ask a question about how to use fMRIPRep, please submit a question to NeuroStars.org with an fmriprep tag. NeuroStars.org is a platform similar to StackOverflow but dedicated to neuroinformatics.

Previous questions about fMRIPRep are available here: http://neurostars.org/tags/fmriprep/

To participate in the fMRIPRep development-related discussions please use the following mailing list: http://mail.python.org/mailman/listinfo/neuroimaging Please add [fmriprep] to the subject line when posting on the mailing list.