.. include:: links.rst
.. _Usage :
-----
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 :abbr:`BIDS (Brain Imaging Data
Structure)` format, and it must include at least one T1w structural image and
(unless disabled with a flag) one :abbr:`DWI (diffusion weighted imaging)` 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
----------------------
.. argparse::
:ref: dmriprep.cli.run.get_parser
:prog: dmriprep
:nodefault:
:nodefaultconst:
.. _fs_license:
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