Installation

There are two easy ways to use QSIPrep: as a Python library with PyPi or as a container with Docker or Singularity/Apptainer. Using a local container method is highly recommended.

Once you are ready to run QSIPrep, see Usage for details.

Python Library

To install the QSIPrep Python library, use pip:

$ pip install --user --upgrade qsiprep

We strongly discourage installing QSIPrep this way, as QSIPrep relies on a number of non-Python dependencies that are difficult to install and configure on a local system. Pip will not install these dependencies for you. Instead, we recommend using the Docker or Singularity/Apptainer containers, wherein all of the necessary dependencies will come pre-installed and configured.

Docker Container

In order to run QSIPrep in a Docker container, Docker must be installed.

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.

You may 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 \
    pennlinc/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 \
    pennlinc/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 \
    pennlinc/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.

Apptainer Container

The easiest way to get an Apptainer (formerly Singularity) image is to run:

$ apptainer build qsiprep-<version>.sif docker://pennlinc/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 Apptainer

$ apptainer 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

Note

Running QSIPrep with Apptainer on Non-Internet Nodes

QSIPrep relies on TemplateFlow to provide standard anatomical templates. By default, it downloads necessary files into the $TEMPLATEFLOW_HOME directory (default: $HOME/.cache/templateflow). However, when running with --containall, the default location may not be accessible, and any missing templates will be tentatively downloaded into the temporary QSIPrep working directory instead. To avoid this, you must always set and bind TEMPLATEFLOW_HOME explicitly.

Steps to ensure successful execution:

1. On an internet-enabled node, set and bind the TEMPLATEFLOW_HOME variable to a persistent directory before running QSIPrep. This will ensure all necessary templates are downloaded into the specified location:

   export TEMPLATEFLOW_HOME=/path/to/persistent/templateflow
   apptainer run --cleanenv --containall \
     -B ${TEMPLATEFLOW_HOME}:${TEMPLATEFLOW_HOME} \
     --env "TEMPLATEFLOW_HOME=$TEMPLATEFLOW_HOME" \
     /path/to/qsiprep_<VERSION>.sif <your commands>
   

2. If the TEMPLATEFLOW_HOME directory is not accessible on your target HPC node, manually copy it to the target system after the first run.

3. On nodes without internet access, bind the copied TEMPLATEFLOW_HOME directory and set the environment variable as described above before running QSIPrep.

4. It may help to run a single subject or session on its own before running many jobs that access the templates. The single run will download the necessary templates and prevent multiple jobs from attempting to download the templates simultaneously.

For additional troubleshooting, see fmriprep docs or this thread on Neurostars.

External Dependencies

QSIPrep is written using Python 3.10 (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.