Update freesurfer

.dockerignore

@@ -0,0 +1,50 @@
+# Git files
+.git
+.gitignore
+.gitattributes
+
+# Documentation
+*.md
+!README.md
+UPDATING_FREESURFER.md
+MODERNIZATION_PLAN.md
+
+# Docker files (except those needed for build)
+docker-compose*.yml
+MultiStage_Dockerfile
+
+# Validation and test data
+validation/
+Fariba_full_pipeline/TVB1/
+
+# Python cache
+**/__pycache__
+**/*.pyc
+**/*.pyo
+**/*.pyd
+.Python
+*.so
+*.egg
+*.egg-info
+dist/
+build/
+
+# IDE and editor files
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+.DS_Store
+
+# Temporary files
+*.tmp
+*.log
+.cache/
+
+# Jupyter notebook checkpoints
+.ipynb_checkpoints/
+
+# Only include specific notebooks needed in the image
+validation/workspace/*.ipynb
+!README.ipynb

.github/workflows/check-image.yml

@@ -13,11 +13,11 @@ jobs:
       - name: Checkout repo content
         uses: actions/checkout@v3
       - name: ooil version
-        uses: docker://itisfoundation/ci-service-integration-library:v2.0.10
+        uses: docker://itisfoundation/ci-service-integration-library:v2.1.27
         with:
           args: ooil --version
       - name: Assemble docker compose spec
-        uses: docker://itisfoundation/ci-service-integration-library:v2.0.10
+        uses: docker://itisfoundation/ci-service-integration-library:v2.1.27
         with:
           args: ooil compose
       - name: create new dir
@@ -44,8 +44,8 @@ jobs:
       - name: check disk space before image build
         run: df -h
       - name: Build all images if multiple
-        uses: docker://itisfoundation/ci-service-integration-library:v2.0.10
+        uses: docker://itisfoundation/ci-service-integration-library:v2.1.27
         with:
-          args: docker compose build --quiet
+          args: docker compose build --progress=plain
       - name: print docker image info
-        run: docker images
+        run: docker images

Dockerfile

@@ -1,5 +1,7 @@
-## Refactor as normal (ie no multistage) dockerfile
-## also have a smaller base image
+## Multi-stage build: use FreeSurfer official Docker image to avoid slow server downloads
+FROM freesurfer/freesurfer:7.4.1@sha256:10b6468cbd9fcd2db3708f4651d59ad75d4da849a2c5d8bb6dba217f08b8c46b as freesurfer-source
+
+## Main build stage
 FROM itisfoundation/jupyter-math:2.0.9 as main
 LABEL maintainer="ordonez"
 USER root
@@ -17,7 +19,10 @@ RUN apt-get -qq update \
   libqt5opengl5-dev \
   libqt5svg5-dev \
   libtiff5-dev \
-  qt5-default \
+  qtbase5-dev \
+  qtchooser \
+  qt5-qmake \
+  qtbase5-dev-tools \
   zlib1g-dev \
   && rm -rf /var/lib/apt/lists/*
 
@@ -40,19 +45,22 @@ ENV ANTSPATH="$HOME/ants/bin" \
   PATH="$HOME/mrtrix3/bin:$HOME/ants/bin:$HOME/art/bin:$PATH"
 
 ############################################################
-## Freesurfer
+## Freesurfer v7.4.1 (copied from official Docker image to avoid slow download)
 WORKDIR ${HOME}
+# Install FreeSurfer runtime dependencies
 RUN apt-get update && apt-get install -y tcsh bc libgomp1 perl-modules \
   && rm -rf /var/lib/apt/lists/*
-RUN wget -N -qO- ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar -xzv -C ${HOME} 
-# \ && rm -rf ${HOME}/freesurfer/subjects  # we actually need subjects/fsaverage for recon-all
-ENV FREESURFER_HOME ${HOME}/freesurfer
-COPY freesurfer_license.txt ${FREESURFER_HOME}/license.txt
-ENV FSFAST_HOME==$FREESURFER_HOME/fsfast \
-  MINC_BIN_DIR=$FREESURFER_HOME/mni/bin \
-  MNI_DIR=$FREESURFER_HOME/mni \
-  PERL5LIB=$FREESURFER_HOME/mni/share/perl5
+# Copy FreeSurfer installation from official Docker image
+COPY --from=freesurfer-source /usr/local/freesurfer /usr/local/freesurfer
+# Set up FreeSurfer environment variables
+ENV FREESURFER_HOME=/usr/local/freesurfer/7.4.1 \
+    FSFAST_HOME=$FREESURFER_HOME/fsfast \
+    MINC_BIN_DIR=$FREESURFER_HOME/mni/bin \
+    MNI_DIR=$FREESURFER_HOME/mni \
+    PERL5LIB=$FREESURFER_HOME/mni/share/perl5
 ENV PATH=$FREESURFER_HOME/bin:$MINC_BIN_DIR:$PATH
+# Copy license file to FreeSurfer home (v7 method)
+COPY freesurfer_license.txt $FREESURFER_HOME/license.txt
 
 ############################################################
 ## FSL
@@ -119,17 +127,19 @@ ENV PATH=$PATH:$HOME/c3d-1.0.0-Linux-x86_64/bin/
 
 ############################################################
 ## python packages in requirements.in
-## before pip install fsleyes, we need to install wxPython:
+## fsleyes requires wxPython, which has pre-built wheels available
 WORKDIR ${HOME}
-RUN .venv/bin/pip --no-cache install -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04 wxpython &&\
-  .venv/bin/pip install attrdict
 
 COPY --chown=$NB_UID:$NB_GID requirements.in ${NOTEBOOK_BASE_DIR}/requirements.in
 RUN .venv/bin/pip --no-cache install pip-tools &&\
   ## rename the previously existing "requirements.txt" from the jupyter-math service (we want to keep it for user reference)
   mv ${NOTEBOOK_BASE_DIR}/requirements.txt ${NOTEBOOK_BASE_DIR}/requirements_base_math.txt   &&\
+  ## Run pip-compile with find-links and only-binary to ensure wxpython wheel is used
+  PIP_FIND_LINKS=https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04 \
+  PIP_ONLY_BINARY=wxpython \
   .venv/bin/pip-compile --build-isolation --output-file ${NOTEBOOK_BASE_DIR}/requirements.txt ${NOTEBOOK_BASE_DIR}/requirements.in   &&\
-  .venv/bin/pip --no-cache install -r ${NOTEBOOK_BASE_DIR}/requirements.txt && \
+  ## Install all packages, ensuring wxpython comes from the wheel
+  .venv/bin/pip --no-cache install --only-binary=wxpython --find-links https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04 -r ${NOTEBOOK_BASE_DIR}/requirements.txt && \
   rm ${NOTEBOOK_BASE_DIR}/requirements.in && \
   echo "Your environment contains these python packages:" && \
   .venv/bin/pip list 

Makefile

@@ -5,13 +5,14 @@ SHELL = /bin/sh
 
 export DOCKER_IMAGE_NAME ?= jupyter-medimproc
 export DOCKER_IMAGE_TAG ?= 1.2.1
+export CI_SERVICE_INTEGRATION_LIBRARY ?= itisfoundation/ci-service-integration-library:v2.1.25
 
 
 define _bumpversion
 	# upgrades as $(subst $(1),,$@) version, commits and tags
 	@docker run -it --rm -v $(PWD):/${DOCKER_IMAGE_NAME} \
 		-u $(shell id -u):$(shell id -g) \
-		itisfoundation/ci-service-integration-library:v2.0.10 \
+		${CI_SERVICE_INTEGRATION_LIBRARY} \
 		sh -c "cd /${DOCKER_IMAGE_NAME} && bump2version --verbose --config-file $(1) $(subst $(2),,$@)"
 endef
 
@@ -25,7 +26,7 @@ version-patch version-minor version-major: .bumpversion.cfg ## increases service
 compose-spec: ## runs ooil to assemble the docker-compose.yml file
 	@docker run -it --rm -v $(PWD):/${DOCKER_IMAGE_NAME} \
 		-u $(shell id -u):$(shell id -g) \
-		itisfoundation/ci-service-integration-library:v2.0.10 \
+		${CI_SERVICE_INTEGRATION_LIBRARY} \
 		sh -c "cd /${DOCKER_IMAGE_NAME} && ooil compose"
 
 .PHONY: build

README.md

@@ -1,11 +1,20 @@
 # JupyterLab for Medical Image Processing (MedImProc)
 
+<!-- TODO'S
+- DONE fix build process
+- bump version to 2.2.0 after bump in FreeSurfer + make sure pipeline Fariba runs end to end
+- add version details in the README
+- add badges
+- then keep going through modernization plan (reduce image size, build time etc); add these learning to my Obsidian notes
+- in future, download FreeSurfer 8.1.0 .deb and put in filesrv and fetch from there (like in ASCENT service) so we can have the latest version without increasing build time
+ -->
+
 This is the source code of the JupyterLab Medical Image Processing OSPARC service. It is mostly centered on MRI data, and contains the following packages:
   "[JupyterLab](https://jupyter.org/) with a variety of Medical Image Processing packages pre-installed, mostly centered on MRI data:
   - [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki), a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
-  - [FreeSurfer](https://surfer.nmr.mgh.harvard.edu/), an open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images-
+  - [FreeSurfer](https://surfer.nmr.mgh.harvard.edu/) version 7.4.1 (June 2023), an open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images.
   - [MRtrix3](https://www.mrtrix.org/) provides a set of tools to perform various types of diffusion MRI analyses.
-  - [Spinal Cord Toolbox](https://spinalcordtoolbox.com/), a comprehensive, free and open-source set of command-line tools dedicated to the processing and analysis of spinal cord MRI data.
+  <!-- - [Spinal Cord Toolbox](https://spinalcordtoolbox.com/), a comprehensive, free and open-source set of command-line tools dedicated to the processing and analysis of spinal cord MRI data. -->
   - [Synb0 Disco](https://github.com/MASILab/Synb0-DISCO#readme), for distortion correction of diffusion weighted MRI without reverse phase-encoding scans or field-maps.
   - Python packages like [nibabel](https://nipy.org/nibabel/), [pyvista](https://docs.pyvista.org/version/stable/), [fsleyes](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes) and [cc3d](https://github.com/seung-lab/connected-components-3d#readme).
 

requirements.in

@@ -1,7 +1,9 @@
-nibabel
-pyvista
+# Medical image processing and visualization packages
+# Pinned versions for reproducibility (checked December 2025)
 
-PyOpenGL
-PyOpenGL_accelerate
-fsleyes
-connected-components-3d
+nibabel==5.3.2  # 23 Oct 2024
+pyvista==0.46.4  # 30 Oct 2025
+PyOpenGL==3.1.10  # 18 Aug 2025
+PyOpenGL_accelerate==3.1.10  # 18 Aug 2025
+fsleyes==1.16.3  # 21 Nov 2025
+connected-components-3d==3.26.1 # 3 Nov 2025