The pyAFQ singularity image

You can build a singularity image for pyAFQ from the Docker image using this command:

apptainer build pyafq_latest.sif docker://ghcr.io/nrdg/pyafq:latest

We have a singularity definition file for building pyAFQ for the GPU specifically, which can be found here.

Assuming the singularity image pyafq_latest.sif exists, trigger the entrypoint pyafq to run the workflow with:

apptainer run \
    --bind bids_dir:bids_dir \
    pyafq_latest.sif /path/to/dwi /path/to/t1 /path/to/output_folder

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

Note

It may be necessary to set the global variable TEMPLATEFLOW_HOME to reference a pull of TemplateFlow:

export TEMPLATEFLOW_HOME=/path/to/templateflow