Installation

There are three ways to use qsiprep: in a Docker Container, in a Singularity Container, or in a Manually Prepared Environment (Python 3.6+). 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.

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:ro \
    -v /path/to_output/dir:/out pennbbl/qsiprep:1.0.0 \
    /data /out participant
...

You may also invoke docker directly:

$ docker run -ti --rm \
    -v filepath/to/data/dir:/data:ro \
    -v filepath/to/output/dir:/out \
    pennbbl/qsiprep:latest \
    /data /out participant

For example:

$ docker run -ti --rm \
    -v $HOME/fullds005:/data:ro \
    -v $HOME/dockerout:/out \
    pennbbl/qsiprep:latest \
    /data /out participant \
    --ignore fieldmaps

See External Dependencies for more information (e.g., specific versions) on what is included in the latest Docker images.

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.

Manually Prepared Environment (Python 3.6+)

Warning

This method is not recommended! Make sure you would rather do this than use a Docker Container or a Singularity Container. Also, this method does not work at the moment because there is no package on PyPI.

Make sure all of qsiprep’s External Dependencies are installed. These tools must be installed and their binaries available in the system’s $PATH. A relatively interpretable description of how your environment can be set-up is found in the Dockerfile. As an additional installation setting, FreeSurfer requires a license file.

On a functional Python 3.5 (or above) environment with pip installed, qsiprep can be installed using the habitual command

$ pip install qsiprep

Check your installation with the --version argument

$ qsiprep --version

External Dependencies

qsiprep is written using Python 3.5 (or above), and is based on nipype.

qsiprep requires some other neuroimaging software tools that are not handled by the Python’s packaging system (Pypi) used to deploy the qsiprep package: