Installation

There are two easy ways to use qsiprep: in a Docker Container, or in a Singularity Container. Using a local container method is highly recommended. Once you are ready to run qsiprep, see Usage for details.

To install:

$ pip install --user --upgrade qsiprep-container

Docker Container

In order to run qsiprep in a Docker container, Docker must be installed. Once Docker is installed, the recommended way to run qsiprep is to use the qsiprep-docker wrapper, which requires Python and an Internet connection and that you install the qsiprep-container package with pip.

Note

If running Docker Desktop on MacOS (or via Docker Desktop), be sure to set the memory to 6 or more GB. Too little memory assigned to Docker Desktop can result in a message like Killed.

When run, qsiprep-docker will generate a Docker command line for you, print it out for reporting purposes, and then run the command, e.g.:

$ qsiprep-docker /path/to/data/dir /path/to/output/dir participant
RUNNING: docker run --rm -it -v /path/to/data/dir:/data \
    -v /path/to_output/dir:/out pennbbl/qsiprep:latest \
    /data /out participant
...

You may also invoke docker directly:

$ docker run -ti --rm \
    -v /filepath/to/data/dir \
    -v /filepath/to/output/dir \
    -v ${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
    pennbbl/qsiprep:latest \
    /filepath/to/data/dir /filepath/to/output/dir participant \
    --fs-license-file /opt/freesurfer/license.txt

For example:

$ docker run -ti --rm \
    -v $HOME/fullds005 \
    -v $HOME/dockerout \
    -v ${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
    pennbbl/qsiprep:latest \
    $HOME/fullds005 $HOME/dockerout participant \
    --ignore fieldmaps \
    --fs-license-file /opt/freesurfer/license.txt

If you are running Freesurfer as part of QSIPrep, you will need to mount your Freesurfer license.txt file when invoking docker

$ docker run -ti --rm \
    -v $HOME/fullds005 \
    -v $HOME/dockerout \
    -v ${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
    pennbbl/qsiprep:latest \
    $HOME/fullds005 -v $HOME/dockerout participant \
    --fs-license-file /opt/freesurfer/license.txt

See External Dependencies for more information on what is included in the Docker image and how it’s built.

Singularity Container

The easiest way to get a Sigularity image is to run:

$ singularity build qsiprep-<version>.sif docker://pennbbl/qsiprep:<version>

Where <version> should be replaced with the desired version of qsiprep that you want to download. Do not use latest or unstable unless you are performing limited testing.

As with Docker, you will need to bind the Freesurfer license.txt when running Singularity

$ singularity run --containall --writable-tmpfs \
    -B $HOME/fullds005,$HOME/dockerout,${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
    qsiprep-<version>.sif \
    $HOME/fullds005 $HOME/dockerout participant \
    --fs-license-file /opt/freesurfer/license.txt

External Dependencies

qsiprep is written using Python 3.8 (or above), and is based on nipype. The external dependencies are built in the qsiprep_build repository. There you can find the URLs used to download the dependency source code and the steps to compile each dependency.