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Extend PATH to include FastSurfer
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Currently, the fastsurfer folder (/fastsurfer) is not part of PATH. Adding this will make singularity and docker commands potentially easier:

singularity exec [options] run_fastsurfer.sh [options]

instead of

singularity exec [options] /fastsurfer/run_fastsurfer.sh [options]
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dkuegler authored Sep 19, 2024
1 parent ef3843c commit d9e8657
Showing 1 changed file with 3 additions and 2 deletions.
5 changes: 3 additions & 2 deletions Docker/Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -195,7 +195,8 @@ RUN if [[ "$DEVICE" == "cu118" ]] ; then cd /venv/python3.10/site-packages/torch
# Copy fastsurfer over from the build context and add PYTHONPATH
COPY . /fastsurfer/
ENV PYTHONPATH=/fastsurfer:/opt/freesurfer/python/packages \
FASTSURFER_HOME=/fastsurfer
FASTSURFER_HOME=/fastsurfer \
PATH=/fastsurfer:$PATH

# Download all remote network checkpoints already, compile all FastSurfer scripts into
# bytecode and update the build file with checkpoints md5sums and pip packages.
Expand Down Expand Up @@ -232,4 +233,4 @@ FROM runtime AS runtime_cuda

ENV NVIDIA_VISIBLE_DEVICES=all \
NVIDIA_DRIVER_CAPABILITIES=compute,utility \
NVIDIA_REQUIRE_CUDA="cuda>=8.0"
NVIDIA_REQUIRE_CUDA="cuda>=8.0"

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