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Add a Dockerfile #2

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210 changes: 210 additions & 0 deletions Dockerfile
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# MRIsegmentation Dockerfile
#
# Build: podman build -t mrisegmentation .
#
# Run segmentation:
# podman run -it -v /path/to/data:/data mrisegmentation -batch "start_segmentation_cedalion('/data/T1.nii')"
# Interactive MATLAB:
# podman run -it --shm-size=512M -p 8888:8888 -v /path/to/data:/data mrisegmentation -browser
#
# License: Requires MATLAB license configured for cloud use.
# Individual and Campus-Wide licenses are already configured for cloud use.
# See: https://www.mathworks.com/help/cloudcenter/ug/matlab-container-on-docker-hub.html

# ============================================================================
# Build arguments
# ============================================================================
ARG MATLAB_IMAGE=matlab:r2024b
ARG MATLAB_RELEASE=R2024b
ARG MATLAB_TOOLBOXES="Image_Processing_Toolbox Optimization_Toolbox Parallel_Computing_Toolbox Signal_Processing_Toolbox Statistics_and_Machine_Learning_Toolbox Wavelet_Toolbox"

# ============================================================================
# Base image
# ============================================================================
FROM mathworks/${MATLAB_IMAGE}

ARG MATLAB_RELEASE
ARG MATLAB_TOOLBOXES

LABEL maintainer="Nils Harmening"
LABEL description="MRI Segmentation Pipeline with SPM12, CAT12, FieldTrip, iso2mesh"

# Avoid interactive prompts
ENV DEBIAN_FRONTEND=noninteractive

# Switch to root for installation
USER root

ENV MATLAB_INSTALL_LOCATION=/opt/matlab/${MATLAB_RELEASE}
ENV PATH=${MATLAB_INSTALL_LOCATION}/bin:${PATH}

# ============================================================================
# Install system dependencies
# ============================================================================
RUN sudo apt-get update && sudo apt-get install -y --no-install-recommends \
build-essential \
ca-certificates \
curl \
git \
sudo \
unzip \
wget \
xvfb \
&& rm -rf /var/lib/apt/lists/*


# ============================================================================
# Create working directory
# ============================================================================
ENV MRISEG_HOME=/opt/MRIsegmentation
WORKDIR ${MRISEG_HOME}

# ============================================================================
# Clone MRIsegmentation repository (or copy local files)
# ============================================================================
RUN git clone --depth 1 https://github.com/harmening/MRIsegmentation.git .

# ============================================================================
# Install FieldTrip
# ============================================================================
RUN git clone --depth 1 https://github.com/fieldtrip/fieldtrip.git

# ============================================================================
# Install SPM12
# ============================================================================
#RUN wget -q https://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado/spm12.zip && \

RUN --mount=type=bind,source=spm12.zip,target=/tmp/spm12.zip \
rm -rf ./fieldtrip/external/spm12 && \
unzip -q /tmp/spm12.zip -d ./fieldtrip/external/

# ============================================================================
# Build SPM12 MEX files
# ============================================================================
RUN cd ./fieldtrip/external/spm12/src && \
make distclean && \
make && make install && \
make external-distclean && \
make external && make external-install && \
cd ../../../../

# ============================================================================
# Install CAT12 (version r2159 for compatibility with SPM12)
# ============================================================================
#RUN wget -q http://www.neuro.uni-jena.de/cat12/cat12_r2159.zip && \

RUN --mount=type=bind,source=cat12_r2159.zip,target=/tmp/cat12_r2159.zip \
rm -rf ./fieldtrip/external/spm12/toolbox/cat12 && \
unzip -q /tmp/cat12_r2159.zip -d ./fieldtrip/external/spm12/toolbox/

# ============================================================================
# Install iso2mesh
# ============================================================================
RUN git clone --depth 1 https://github.com/fangq/iso2mesh.git

# ============================================================================
# Install Andy's tools (Huang et al. 2013)
# ============================================================================
RUN --mount=type=bind,source=Huang_et_al_2013.zip,target=/tmp/Huang_et_al_2013.zip \
unzip -q /tmp/Huang_et_al_2013.zip -d ./Huang_et_al_2013

# Apply patch: Make new_segment store the nonlinear warp
RUN sed -i 's/warp\.write = \[0 0\]/warp\.write = \[1 1\]/' Huang_et_al_2013/start_seg.m

# ============================================================================
# Install NIfTI tools
# ============================================================================
RUN wget -q "https://www.mathworks.com/matlabcentral/mlc-downloads/downloads/submissions/8797/versions/28/download/zip" \
-O nifti_tools.zip && \
unzip -q nifti_tools.zip -d ./NIfTI_tools && \
rm nifti_tools.zip || echo "NIfTI tools may need manual installation"

# ============================================================================
# Install weighted-SPHARM (optional)
# ============================================================================
RUN mkdir -p ./weighted-SPHARM && \
wget -q https://pages.stat.wisc.edu/~mchung/research/amygdala/SPHARMsmooth2.m \
-O ./weighted-SPHARM/SPHARMsmooth2.m && \
wget -q https://pages.stat.wisc.edu/~mchung/softwares/weighted-SPHARM/SPHARMvectorize.m \
-O ./weighted-SPHARM/SPHARMvectorize.m || \
echo "weighted-SPHARM download failed - optional component"

# ============================================================================
# ATRA (Automatic Temporal Registration Algorithm) - OPTIONAL
# Due to license restrictions, must be downloaded manually from:
# https://www.nitrc.org/frs/download.php/10393/atra1.0_LinuxCentOS6.7.tar.gz
#
# To include ATRA:
# 1. Download and place atra1.0_LinuxCentOS6.7.tar.gz in build context
# 2. Uncomment the following lines:
# ============================================================================
RUN mkdir -p ./art
# COPY atra1.0_LinuxCentOS6.7.tar.gz ./art/
# RUN cd ./art && \
# gunzip atra1.0_LinuxCentOS6.7.tar.gz && \
# tar -xvf atra1.0_LinuxCentOS6.7.tar && \
# rm -f atra1.0_*.tar

ENV ARTHOME=${MRISEG_HOME}/art
ENV PATH=${ARTHOME}/bin:${PATH}

# ============================================================================
# Install MATLAB using mpm (MathWorks Package Manager)
# https://github.com/mathworks-ref-arch/matlab-dockerfile
# Placed after other downloads so toolbox changes don't invalidate cache
# ============================================================================

RUN wget -q https://www.mathworks.com/mpm/glnxa64/mpm && \
chmod +x mpm && \
./mpm install \
--release=${MATLAB_RELEASE} \
--destination=${MATLAB_INSTALL_LOCATION} \
--products MATLAB ${MATLAB_TOOLBOXES} \
|| (cat /tmp/mathworks_root.log && false) && \
rm -f mpm /tmp/mathworks_root.log


# ============================================================================
# Fix FieldTrip compatibility issues (see README troubleshooting)
# ============================================================================
RUN find ./fieldtrip/compat -mindepth 1 -maxdepth 1 -type d -name "matlablt*" \
-exec rm -rf {} + 2>/dev/null || true && \
find ./fieldtrip/external/spm12/external/fieldtrip/compat -mindepth 1 -maxdepth 1 \
-type d -name "matlablt*" -exec rm -rf {} + 2>/dev/null || true

# ============================================================================
# Copy startup.m for MATLAB path configuration
# ============================================================================
RUN mkdir -p /home/matlab/Documents/MATLAB
COPY docker/startup.m /home/matlab/Documents/MATLAB/startup.m

# Set MATLABPATH so paths are available in batch mode
# Note: startup.m is still needed for ft_defaults and other initialization
ENV MATLABPATH=${MRISEG_HOME}:${MRISEG_HOME}/MRIsegmentation:${MRISEG_HOME}/fieldtrip:${MRISEG_HOME}/iso2mesh:${MRISEG_HOME}/Huang_et_al_2013:${MRISEG_HOME}/NIfTI_tools:${MRISEG_HOME}/weighted-SPHARM:${MRISEG_HOME}/Schaefer2018_Parcellations

# ============================================================================
# Set permissions
# ============================================================================
RUN chown -R matlab:matlab ${MRISEG_HOME} && \
chown -R matlab:matlab /home/matlab

# ============================================================================
# Switch to matlab user
# ============================================================================
USER matlab

# ============================================================================
# Data volume mount point
# ============================================================================
VOLUME ["/data"]

# ============================================================================
# Working directory for MATLAB
# ============================================================================
WORKDIR ${MRISEG_HOME}

# ============================================================================
# Use the MathWorks run.sh for license validation
# ============================================================================
ENTRYPOINT ["/bin/run.sh"]
CMD ["-help"]
23 changes: 23 additions & 0 deletions docker/startup.m
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% MRIsegmentation MATLAB startup script
disp('Loading MRIsegmentation environment...');

% Change to MRIsegmentation directory (scripts expect this as working dir)
cd('/opt/MRIsegmentation');

% Add paths
addpath('/opt/MRIsegmentation');
addpath(genpath('/opt/MRIsegmentation/MRIsegmentation'));
addpath(genpath('/opt/MRIsegmentation/fieldtrip'));
addpath(genpath('/opt/MRIsegmentation/iso2mesh'));
addpath(genpath('/opt/MRIsegmentation/Huang_et_al_2013'));
addpath(genpath('/opt/MRIsegmentation/NIfTI_tools'));
addpath(genpath('/opt/MRIsegmentation/weighted-SPHARM'));
addpath(genpath('/opt/MRIsegmentation/Schaefer2018_Parcellations'));

% Initialize FieldTrip (adds necessary subfolders)
ft_defaults;

% Configure iso2mesh
setenv('ISO2MESH_BIN', '/opt/MRIsegmentation/iso2mesh/bin');

disp('MRIsegmentation environment loaded.');