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FROM python:3.10.2-slim
RUN apt-get update && apt-get install -y \
apt-utils git \
&& rm -rf /var/lib/apt/lists/*
RUN mkdir -p /envs && python -m venv /envs/fastsurfer
RUN mkdir /repos && \
git clone https://github.com/Deep-MI/FastSurfer.git /repos/FastSurfer \
&& cd /repos/FastSurfer \
&& git checkout v2.0.1
ENV FASTSURFER_HOME=/repos/FastSurfer
# Install requirements. The SimpleITK version in requirements.txt is yanked,
# so we need to install it manually and remove it from requirements.txt.
RUN /envs/fastsurfer/bin/pip install --upgrade pip && \
/envs/fastsurfer/bin/pip install simpleitk==2.1.1.2 --upgrade && \
sed -i '/simpleitk/d' ${FASTSURFER_HOME}/requirements.txt && \
/envs/fastsurfer/bin/pip install -r ${FASTSURFER_HOME}/requirements.txt
#COPY ${CHECKPOINTS_FOLDER} ${FASTSURFER_HOME}/FastSurferCNN/checkpoints
COPY checkpoints/fastsurfer ${FASTSURFER_HOME}/FastSurferCNN/checkpoints
RUN mkdir /scripts
COPY scripts/preprocess.sh /scripts/preprocess.sh
CMD ["/bin/sh", "/scripts/preprocess.sh", \
"--license", "/licenses/freesurfer.txt", \
"--python", "/envs/fastsurfer/bin/python", \
"/input", "/output/fastsurfer"]
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