FIX: Improve segmentation for < 3 months using bibsnet + infantfs

.github/actions/nf-test/action.yml

@@ -71,8 +71,10 @@ runs:
           PROFILE=${{ inputs.profile }}
         fi
 
+        # Increase the java memory
+        export _JAVA_OPTIONS="-Xmx4g"
         nf-test test \
-          --profile=${PROFILE},test \
+          --profile=+${PROFILE} \
           $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
           --ci \
           --changed-since HEAD^ \

.nf-core.yml

@@ -1,5 +1,4 @@
 lint:
-  container_configs: false
   files_exist:
     - CODE_OF_CONDUCT.md
     - assets/nf-core-sf_pediatric_logo_light.png
@@ -37,6 +36,9 @@ lint:
   nextflow_config: false
   schema_params: false
   template_strings: false
+  container_configs: false
+  nf_test_content:
+    - tests/gpu.nf.test
 nf_core_version: 4.0.3
 repository_type: pipeline
 template:

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- Changed segmentation in young participants to use BIBSnet and infant freesurfer ([#128](https://github.com/scilus/sf-pediatric/pull/128))
 - Now use `nf-bids` plugin to read BIDS dataset for faster and more efficient data collection ([#124](https://github.com/scilus/sf-pediatric/pull/124))
 - Add GPU support via a config profile for module `eddy` and `localtracking` ([#121](https://github.com/scilus/sf-pediatric/pull/121))
 - Add support for user-defined external atlases in ‘fsLR‘ 32k space and simply mapping from template to subject space ([#120](https://github.com/scilus/sf-pediatric/pull/120))
@@ -28,6 +29,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Move to parameter typing and bump minimal nextflow version to `26.04.0` ([#122](https://github.com/scilus/sf-pediatric/pull/122))
 - Update to nf-core template `4.0.2` ([#117](https://github.com/scilus/sf-pediatric/pull/117))
 
+### `Removed`
+
+- Remove M-CRIB-S as a segmentation method for younger participants in favor of BIBSnet and infantfs ([#128](https://github.com/scilus/sf-pediatric/pull/128))
+
 ## [0.2.2] - [2026-02-09]
 
 ### `Added`

assets/Docker/infantfs/fsl.yml

@@ -0,0 +1,6 @@
+name: fsl
+channels:
+  - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
+  - conda-forge
+dependencies:
+  - fsl-avwutils

assets/Docker/infantfs/sf-pediatric-infantfs.Dockerfile

@@ -0,0 +1,121 @@
+FROM rockylinux:8.9 AS build-fsl
+
+RUN dnf -y update && \
+    dnf -y install --nogpgcheck \
+        curl \
+        bzip2 \
+        && dnf clean all
+
+WORKDIR /
+RUN echo "2024.04.25" && curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj
+ENV MAMBA_ROOT_PREFIX="/opt/conda"
+
+# Fetch the FSL environment
+COPY fsl.yml fsl.yml
+RUN micromamba create -y -f fsl.yml && \
+    micromamba clean --all --yes
+ENV PATH="/opt/conda/envs/fsl/bin:$PATH"
+
+FROM freesurfer/freesurfer:8.2.0 AS build_freesurfer
+# Bring over freesurfer from official release
+RUN rm -rf \
+        /usr/local/freesurfer/8.2.0-1/average/AAN \
+        /usr/local/freesurfer/8.2.0-1/average/3T18yoSchwartz* \
+        /usr/local/freesurfer/8.2.0-1/average/711-2B* \
+        /usr/local/freesurfer/8.2.0-1/average/SVIP* \
+        /usr/local/freesurfer/8.2.0-1/average/RLB700* \
+        /usr/local/freesurfer/8.2.0-1/average/RB_all* \
+        /usr/local/freesurfer/8.2.0-1/average/aseg+spmhead* \
+        /usr/local/freesurfer/8.2.0-1/average/face.gca \
+        /usr/local/freesurfer/8.2.0-1/average/label_scales.dat \
+        /usr/local/freesurfer/8.2.0-1/average/mideface-atlas \
+        /usr/local/freesurfer/8.2.0-1/average/wmsa_new_eesmith.gca \
+        /usr/local/freesurfer/8.2.0-1/average/talairach_mixed_with_skull.gca \
+        /usr/local/freesurfer/8.2.0-1/average/BrainstemSS \
+        /usr/local/freesurfer/8.2.0-1/average/HippoSF \
+        /usr/local/freesurfer/8.2.0-1/average/PALS_B12.readme \
+        /usr/local/freesurfer/8.2.0-1/average/ThalamicNuclei \
+        /usr/local/freesurfer/8.2.0-1/average/samseg \
+        /usr/local/freesurfer/8.2.0-1/average/mni_icbm152_nlin_asym_09c \
+        /usr/local/freesurfer/8.2.0-1/average/mult-comp-cor \
+        /usr/local/freesurfer/8.2.0-1/average/Choi_JNeurophysiol12_MNI152 \
+        /usr/local/freesurfer/8.2.0-1/average/Buckner_JNeurophysiol11_MNI152 \
+        /usr/local/freesurfer/8.2.0-1/average/Yeo_Brainmap_MNI152 \
+        /usr/local/freesurfer/8.2.0-1/average/Yeo_JNeurophysiol11_MNI152 \
+        /usr/local/freesurfer/8.2.0-1/bin/freeview \
+        /usr/local/freesurfer/8.2.0-1/diffusion \
+        /usr/local/freesurfer/8.2.0-1/matlab \
+        /usr/local/freesurfer/8.2.0-1/models/easyreg* \
+        /usr/local/freesurfer/8.2.0-1/sessions \
+        /usr/local/freesurfer/8.2.0-1/fsfast \
+        /usr/local/freesurfer/8.2.0-1/fsafd \
+        /usr/local/freesurfer/8.2.0-1/subjects/bert \
+        /usr/local/freesurfer/8.2.0-1/subjects/V1_average \
+        /usr/local/freesurfer/8.2.0-1/subjects/cvs_avg35 \
+        /usr/local/freesurfer/8.2.0-1/subjects/cvs_avg35_inMNI152 \
+        /usr/local/freesurfer/8.2.0-1/subjects/fsaverage3 \
+        /usr/local/freesurfer/8.2.0-1/subjects/fsaverage4 \
+        /usr/local/freesurfer/8.2.0-1/subjects/fsaverage5 \
+        /usr/local/freesurfer/8.2.0-1/subjects/fsaverage6 \
+        /usr/local/freesurfer/8.2.0-1/subjects/fsaverage_sym \
+        /usr/local/freesurfer/8.2.0-1/subjects/lh.EC_average \
+        /usr/local/freesurfer/8.2.0-1/subjects/rh.EC_average \
+        /usr/local/freesurfer/8.2.0-1/subjects/sample* \
+        /usr/local/freesurfer/8.2.0-1/trctrain \
+        /usr/local/freesurfer/8.2.0-1/MCRv97 \
+        /usr/local/freesurfer/8.2.0-1/models \
+        /usr/local/freesurfer/8.2.0-1/python/lib/python3.8/site-packages/tensorflow*
+
+# Set the runtime stage
+FROM rockylinux:8.9 AS runtime
+
+# Install freesurfer dependencies
+RUN dnf -y update && \
+    dnf -y install --nogpgcheck \
+        libgomp \
+        procps-ng \
+        libXt \
+        libXext \
+        libtiff \
+        libpng15 \
+        tcsh \
+        bc \
+        ncurses-compat-libs \
+        unzip && \
+    dnf clean all
+
+COPY --from=build-fsl /bin/micromamba /bin/micromamba
+COPY --from=build-fsl /opt/conda/envs/fsl /opt/conda/envs/fsl
+COPY --from=build_freesurfer /usr/local/freesurfer/8.2.0* /opt/freesurfer
+
+# Set environment variables for FreeSurfer and FSL
+ENV MAMBA_ROOT_PREFIX="/opt/conda" \
+    PATH="${PATH}:/opt/conda/envs/fsl/bin" \
+    CPATH="/opt/conda/envs/fsl/include:${CPATH}" \
+    LD_LIBRARY_PATH="/opt/conda/envs/fsl/lib:${LD_LIBRARY_PATH}" \
+    CONDA_PYTHON="/opt/conda/envs/fsl/bin/python"
+ENV LANG="C.UTF-8" \
+    LC_ALL="C.UTF-8" \
+    PYTHONNOUSERSITE=1 \
+    FSLDIR="/opt/conda/envs/fsl" \
+    FSLOUTPUTTYPE="NIFTI_GZ" \
+    FSLMULTIFILEQUIT="TRUE" \
+    FSLLOCKDIR="" \
+    FSLMACHINELIST="" \
+    FSLREMOTECALL="" \
+    FSLGECUDAQ="cuda.q"
+ENV FREESURFER_HOME="/opt/freesurfer"
+ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
+    FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
+    MNI_DIR="$FREESURFER_HOME/mni" \
+    LOCAL_DIR="$FREESURFER_HOME/local" \
+    MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
+    MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
+    MNI_DATAPATH="$FREESURFER_HOME/mni/data" \
+    FSL_DIR=${FSLDIR} \
+    FREESURFER="/opt/freesurfer"
+ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
+    MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
+    PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
+ENV USER=freesurfer \ 
+    LOGNAME=freesurfer