The pyAFQ docker image

Every time a new commit is made to master the pyAFQ github, a new image is pushed to the NRDG github. This image contains an installation of the latest version of pyAFQ with fslpy. This image also contains an entrypoint, and can be run with:

docker run -v bids_dir:/bids_dir:rw ghcr.io/nrdg/pyafq path/to/dwi path/to/t1 path/to/output_folder

or, for a whole BIDS dataset, with the BIDS App style entrypoint:

docker run -v bids_dir:/bids_dir:rw --entrypoint pyAFQ-bids ghcr.io/nrdg/pyafq /bids_dir participant --dwi-preproc-pipeline qsiprep

These use the CLIs which you can read about in The pyAFQ CLI. You can also launch python inside the container and use the normal pyAFQ.