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fix: Set FSL environment variables because conda install doesn't #322

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Oct 2, 2023
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10 changes: 10 additions & 0 deletions Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,16 @@ RUN micromamba install -y -n base -f $RABIES/rabies_environment.yml && \
micromamba run -n base pip install -e $RABIES && \
micromamba clean --all --yes

# FSL conda packages don't properly setup FSL, do it manually
ENV FSLDIR=/opt/conda
ENV FSLWISH=/opt/conda/bin/fslwish
ENV FSLTCLSH=/opt/conda/bin/fsltclsh
ENV FSLMULTIFILEQUIT=TRUE
ENV FSL_LOAD_NIFTI_EXTENSIONS=0
ENV FSLGECUDAQ=
ENV FSL_SKIP_GLOBAL=0
ENV FSLOUTPUTTYPE=NIFTI_GZ

# adding 'agg' as default backend to avoid matplotlib errors
ENV MPLBACKEND agg

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