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.
$ pip install --user --upgrade qsiprep-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.
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 run -ti --rm \ -v filepath/to/data/dir:/data:ro \ -v filepath/to/output/dir:/out \ pennbbl/qsiprep:latest \ /data /out participant
$ 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.
The easiest way to get a Sigularity image is to run:
$ singularity build qsiprep-<version>.sif docker://pennbbl/qsiprep:<version>
<version> should be replaced with the desired version of qsiprep that you want to download.
Do not use
Manually Prepared Environment (Python 3.6+)¶
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
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
qsiprep can be installed using the habitual command
$ pip install qsiprep
Check your installation with the
$ qsiprep --version
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