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Description
Here's the workflow I use for development:
for REPO in nipreps/{fmriprep,smriprep,niworkflows,sdcflows}; do
git clone https://github.com/$REPO
done
mamba env create -f fmriprep/env.yml
mamba env config vars set -n fmriprep FSLDIR=$CONDA_PREFIX
mamba activate fmriprep
pip install --no-deps -e ./fmriprep -e ./smriprep -e ./niworkflows -e ./sdcflows
Separately install AFNI, Connectome Workbench, FreeSurfer and msm.
Pretty much only use fmriprep-docker --patch
to test fixes to specific released versions these days.