Installation

The official source of QSIRecon is the Docker repository.

Running QSIRecon via containers

Docker

In order to run QSIRecon 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.

A Docker command line may look like:

docker run -ti --rm \
    -v /filepath/to/data/dir \
    -v /filepath/to/output/dir \
    -v ${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
    pennlinc/qsirecon:latest \
    /filepath/to/data/dir /filepath/to/output/dir participant \
    --fs-license-file /opt/freesurfer/license.txt \
    --recon-spec pyafq_tractometry

Singularity/Apptainer

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

apptainer build qsirecon-<version>.sif docker://pennlinc/qsirecon:<version>

Where <version> should be replaced with the desired version of QSIRecon 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 :

apptainer run \
    --containall \
    --writable-tmpfs \
    -B "${PWD}","${FREESURFER_HOME}"/license.txt:/opt/freesurfer/license.txt \
    qsirecon-<version>.sif \
    "${PWD}"/derivatives/qsiprep \
    "${PWD}"/derivatives/qsirecon \
    participant \
    --fs-license-file /opt/freesurfer/license.txt \
    --recon-spec ss3t_autotrack \
    -w "${PWD}/work" \
    -v -v

External Dependencies

QSIRecon is written using Python 3.10, and is based on nipype. The external dependencies are built in the qsirecon_build repository. There you can find the URLs used to download the dependency source code and the steps to compile each dependency.