BAMF MR Brain tumor segmentation

models/bamf_mr_brain_tumor/config/default.yml

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+general:
+  data_base_dir: /app/data
+  version: 1.0
+  description: Default configuration for Bamf NNUnet Brain tumor segmentation on MR scans (dicom to dicom)
+
+segdb:
+    triplets:
+        T_EDEMA_MABNORMALITY:
+            code: 79654002
+            meaning: Edema
+            scheme_designator: SCT
+        T_NECROSIS_MABNORMALITY:
+            code: 6574001
+            meaning: Necrosis
+            scheme_designator: SCT
+        T_ENHANCING_MABNORMALITY:
+            code: C113842
+            meaning: Enhancing Lesion
+            scheme_designator: NCIt
+    segments:
+        EDEMA:
+            name: Edema
+            category: C_MORPHOLOGICALLY_ABNORMAL_STRUCTURE
+            type: T_EDEMA_MABNORMALITY
+            color: [140, 224, 228]
+        NECROSIS:
+            name: Necrosis
+            category: C_MORPHOLOGICALLY_ABNORMAL_STRUCTURE
+            type: T_EDEMA_MABNORMALITY
+            color: [216, 191, 216]
+        ENHANCING:
+            name: Enhancing Lesion
+            category: C_MORPHOLOGICALLY_ABNORMAL_STRUCTURE
+            type: T_ENHANCING_MABNORMALITY
+            color: [128, 174, 128]
+
+execute:
+- FileStructureImporter
+- NiftiConverter
+- ReOrientationRunner
+- BiasCorrectionRunner
+- FLIRTRegistrationRunner
+- SkullStripRunner
+- StdRegistrationRunner
+- NNUnetRunnerV2
+- InverseStdRegistrationRunner
+- InverseRegistrationRunner
+- module: DsegConverter
+  target_dicom: dicom:mod=mr:type=t1
+  source_segs: nifti:mod=mr:type=t1:task=inverse
+- module: DsegConverter
+  target_dicom: dicom:mod=mr:type=t1ce
+  source_segs: nifti:mod=mr:type=t1ce:task=inverse
+- module: DsegConverter
+  target_dicom: dicom:mod=mr:type=t2
+  source_segs: nifti:mod=mr:type=t2:task=inverse
+- module: DsegConverter
+  target_dicom: dicom:mod=mr:type=flair
+  source_segs: nifti:mod=mr:type=flair:task=inverse
+- DataOrganizer
+
+modules:
+  FileStructureImporter:
+    input_dir: 'input_data'
+    structures:
+      - $patientID@instance/$type@dicom:mod=mr
+    import_id: patientID
+
+  NiftiConverter:
+    allow_multi_input: True
+    out_datas: nifti:mod=mr:task=conversion
+    engine: dcm2niix
+
+  ReOrientationRunner:
+    in_datas: nifti:mod=mr
+
+  BiasCorrectionRunner:
+    in_datas: nifti:mod=mr:task=reorientation
+
+  FLIRTRegistrationRunner:
+    in_datas: nifti:mod=mr:task=bias_corrected
+    reference_data: nifti:mod=mr:task=bias_corrected:type=t1ce
+
+  SkullStripRunner:
+    in_datas: nifti:mod=mr:task=registration
+
+  StdRegistrationRunner:
+    in_datas: nifti:mod=mr:task=skull_stripped
+
+  NNUnetRunnerV2:
+    in_t1_data: nifti:mod=mr:task=std_registration:type=t1
+    in_t1ce_data: nifti:mod=mr:task=std_registration:type=t1ce
+    in_t2_data: nifti:mod=mr:task=std_registration:type=t2
+    in_flair_data: nifti:mod=mr:task=std_registration:type=flair
+
+  InverseStdRegistrationRunner:
+    in_seg_data: nifti:mod=seg:model=nnunet:nnunet_dataset=Dataset002_BRATS19
+    in_mat_datas: txt:task=std_registration_transform_mat
+    in_registration_datas: nifti:mod=mr:task=registration
+
+  InverseRegistrationRunner:
+    in_seg_datas: nifti:mod=mr:task=std_inverse
+    in_mat_datas: txt:task=registration_transform_mat
+    in_registration_datas: nifti:mod=mr:task=bias_corrected
+
+  DsegConverter:
+    model_name: Bamf NNUnet Brain segmentation
+    skip_empty_slices: True
+
+  DataOrganizer:
+    targets:
+    - dicomseg:type=t1ce-->[i:patientID]/t1ce.seg.dcm
+    - dicomseg:type=t1-->[i:patientID]/t1.seg.dcm
+    - dicomseg:type=t2-->[i:patientID]/t2.seg.dcm
+    - dicomseg:type=flair-->[i:patientID]/flair.seg.dcm

models/bamf_mr_brain_tumor/dockerfiles/Dockerfile

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+FROM mhubai/base:latest
+
+ENV DEBIAN_FRONTEND "noninteractive"
+ENV LANG            "en_GB.UTF-8"
+
+# 1. Install gcc-14 and build ants
+RUN apt-get update && apt-get install -y cmake make ninja-build git bzip2 flex manpages-dev g++ wget unzip file
+RUN wget https://github.com/gcc-mirror/gcc/archive/refs/tags/releases/gcc-11.4.0.zip \
+    && unzip gcc-11.4.0.zip && cd gcc-releases-gcc-11.4.0 && ./contrib/download_prerequisites \
+    && mkdir /app/gcc-build && cd /app/gcc-build \
+    && ../gcc-releases-gcc-11.4.0/configure -v --target=x86_64-linux-gnu --prefix=/usr/local/gcc-11.4.0 --enable-checking=release --enable-languages=c,c++ --disable-multilib --program-suffix=-11.4 \
+    && make -j$(nproc) && make install-strip \
+    && update-alternatives --install /usr/bin/gcc gcc /usr/local/gcc-11.4.0/bin/gcc-11.4 11 --slave /usr/bin/g++ g++ /usr/local/gcc-11.4.0/bin/g++-11.4 \
+    && rm -rf /app/gcc-*
+
+ENV PATH=/usr/local/gcc-11.4.0/bin:$PATH
+ENV LD_LIBRARY_PATH="/usr/local/gcc-11.4.0/lib64:$LD_LIBRARY_PATH"
+
+RUN git clone https://github.com/ANTsX/ANTs.git /usr/local/src/ants \
+    && mkdir /app/build && cd /app/build && cmake -DBUILD_TESTING=ON \
+    -DRUN_LONG_TESTS=OFF \
+    -DRUN_SHORT_TESTS=ON \
+    -DBUILD_SHARED_LIBS=OFF \
+    -DCMAKE_INSTALL_PREFIX=/opt/ants \
+    /usr/local/src/ants \
+    && cmake --build . --parallel \
+    && cd /app/build/ANTS-build && cmake --build . --target test \
+    && cmake --install . && rm -rf /app/build
+
+# 2. Install mri_convert
+ENV FREESURFER_HOME="/freesurfer"
+RUN git clone https://github.com/freesurfer/freesurfer.git && cd freesurfer/mri_synthstrip \
+    git+https://github.com/freesurfer/surfa.git@0d83332351083b33c4da221e9d10a63a93ae7f52 \
+    && mkdir -p $FREESURFER_HOME/models/ \
+    && git remote add datasrc https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git \
+    && apt-get update -y && apt-get install -y git-annex \
+    && git fetch datasrc && git-annex get . \
+    && cp mri_synthstrip $FREESURFER_HOME \
+    && cp synthstrip.*.pt $FREESURFER_HOME/models/
+
+# 3. Install fsl
+RUN wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py && \
+    python3 ./fslinstaller.py -V 6.0.7.11 -d /usr/local/fsl/ && rm fslinstaller.py
+
+ENV PATH="/opt/ants/bin:$PATH:/$FREESURFER_HOME:/usr/local/fsl/bin" \
+LD_LIBRARY_PATH="/opt/ants/lib:$LD_LIBRARY_PATH"
+
+# 3. Install nnunet
+# FIXME: set this environment variable as a shortcut to avoid nnunet crashing the build
+# by pulling sklearn instead of scikit-learn
+# N.B. this is a known issue:
+# https://github.com/MIC-DKFZ/nnUNet/issues/1281
+# https://github.com/MIC-DKFZ/nnUNet/pull/1209
+ENV SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True
+
+# 4. Install nnunet and surfa
+RUN pip3 install --no-cache-dir torch surfa==0.6
+RUN apt-get update && apt-get install -y python3.9 python3-pip && apt-get clean  && rm -rf /var/lib/apt/lists/*
+RUN python3.9 -m pip install nnunetv2==2.4.1
+RUN apt-get update && apt-get install -y bc
+
+# Clone the main branch of MHubAI/models
+ARG MHUB_MODELS_REPO
+RUN buildutils/import_mhub_model.sh bamf_mr_brain_tumor ${MHUB_MODELS_REPO}
+
+# Pull nnUNet model weights into the container
+ENV WEIGHTS_DIR=/root/.nnunet/nnUNet_models/
+RUN mkdir -p $WEIGHTS_DIR
+ENV WEIGHTS_FN=Dataset002_BRATS19.zip
+ENV WEIGHTS_URL=https://zenodo.org/records/11582627/files/$WEIGHTS_FN
+RUN wget --directory-prefix ${WEIGHTS_DIR} ${WEIGHTS_URL}
+RUN unzip ${WEIGHTS_DIR}${WEIGHTS_FN} -d ${WEIGHTS_DIR}
+RUN rm ${WEIGHTS_DIR}${WEIGHTS_FN}
+
+# specify nnunet specific environment variables
+ENV WEIGHTS_FOLDER=$WEIGHTS_DIR
+
+# Default run script
+ENTRYPOINT ["mhub.run"]
+CMD ["--config", "/app/models/bamf_mr_brain_tumor/config/default.yml"]