Warning: This document is for an old version of dmriprep. The main version is master.

Usage

Execution and the BIDS format

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

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

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

Command-Line Arguments

The FreeSurfer license

dMRIPrep 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 dMRIPrep.

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 \
    nipreps/dmriprep:latest \
    /data /out/out \
    participant \
    --ignore fieldmaps