Add wFSL

.github/workflows/wfsl-apptainer-image.yml

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+name: Apptainer Build wFSL
+
+on:
+  workflow_dispatch:
+    inputs:
+      IMAGE_NAME:
+        description: 'Name of the image to build'
+        default: 'infant-freesurfer-wfsl'
+        required: false
+      IMAGE_TAG:
+        description: 'Tag of the image to build'
+        default: 'latest'
+        required: false
+
+defaults:
+  run:
+    shell: bash
+
+env:
+  APPTAINER_VERSION: 1.2.5
+  ORAS_VERSION: 1.1.0
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    name: Build Apptainer image
+    permissions:
+      contents: write
+      packages: write
+
+    steps:
+      - name: Clear up space
+        run: |
+          set -eux -o pipefail
+          sudo rm -rf /opt/hostedtoolcache /usr/share/dotnet /usr/local/lib/android /usr/share/swift /usr/local/lib/android
+      - name: Download Apptainer
+        run: |
+          set -eux -o pipefail
+          curl -o "apptainer-${APPTAINER_VERSION}.deb" -L https://github.com/apptainer/apptainer/releases/download/v${APPTAINER_VERSION}/apptainer_${APPTAINER_VERSION}_amd64.deb
+          export DEBIAN_FRONTEND=noninteractive
+          sudo apt-get update -yq  || echo "Couldn't update apt packages. Will attempt installation without update" >&2
+          sudo dpkg --install --force-depends "apptainer-${APPTAINER_VERSION}.deb" && sudo apt-get install --fix-broken --yes --quiet
+          apptainer >&2 --version && echo >&2 "Apptainer installed successfully!"
+          apptainer remote login -u ${{ github.actor }} -p ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io && echo "Logged in to remote registry successfully" >&2
+
+      - name: Install ORAS
+        run: |
+          set -eux -o pipefail
+          curl -o "oras_${ORAS_VERSION}.tar.gz" -L "https://github.com/oras-project/oras/releases/download/v${ORAS_VERSION}/oras_${ORAS_VERSION}_linux_amd64.tar.gz"
+
+          # Install the executable:
+          tar -xvf oras_${ORAS_VERSION}.tar.gz && chmod +x oras && sudo mv oras /usr/local/bin/oras
+          sudo mv "${DOWNLOAD_PATH}" /usr/local/bin/oras && sudo chmod +x /usr/local/bin/oras & oras >&2 version && echo >&2 "oras installed successfully!"
+          oras login -u ${{ github.actor }} -p ${{ secrets.GITHUB_TOKEN }} ghcr.io && echo "Logged in to remote registry successfully" >&2
+
+      - name: Check out code for the container build
+        uses: actions/checkout@v4
+
+      - name: Build Container
+        run: |
+          set -eux -o pipefail
+          IMAGE_NAME=${{ inputs.IMAGE_NAME }}
+          IMAGE_TAG=${{ inputs.IMAGE_TAG }}
+          IMAGE_PATH="${GITHUB_WORKSPACE}/${IMAGE_NAME}".sif
+
+          echo "IMAGE_NAME=${IMAGE_NAME}" >> $GITHUB_ENV
+          echo "IMAGE_TAG=${IMAGE_TAG}" >> $GITHUB_ENV
+          echo "IMAGE_PATH=${IMAGE_PATH}" >> $GITHUB_ENV
+
+          echo "IMAGE_NAME=${IMAGE_NAME}" >&2
+          echo "IMAGE_TAG=${IMAGE_TAG}" >&2
+          echo "IMAGE_PATH=${IMAGE_PATH}" >&2
+
+          apptainer build --fix-perms --disable-cache --force "${IMAGE_PATH}" SingularitywFSL
+
+          echo "Container built successfully" >&2
+
+          echo "Container size:" >&2
+          du -h "${IMAGE_PATH}" >&2
+
+          echo "Container labels:" >&2
+          apptainer inspect "${IMAGE_PATH}" >&2
+
+      - name: Push Container
+        run: |
+          set -eux -o pipefail
+
+          # Log in:
+          apptainer remote login -u ${{ github.actor }} -p ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
+
+          # Push the image:
+          apptainer push -U "${IMAGE_PATH}" oras://ghcr.io/${{ github.repository }}/${IMAGE_NAME}:${IMAGE_TAG}
+          echo "Done" >&2

SingularitywFSL

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+Bootstrap: oras
+From: ghcr.io/uw-psych/infantfreesurfer-singularity/infantfreesurfer:latest
+
+%environment
+	export PATH="/opt/niftyreg-master/bin:$PATH"
+	export LD_LIBRARY_PATH="/opt/niftyreg-master/lib:$LD_LIBRARY_PATH"
+	export FSLDIR="/opt/fsl-6.0.2"
+	export PATH="/opt/fsl-6.0.2/bin:$PATH"
+	export FSLOUTPUTTYPE="NIFTI_GZ"
+	export FSLMULTIFILEQUIT="TRUE"
+	export FSLTCLSH="/opt/fsl-6.0.2/bin/fsltclsh"
+	export FSLWISH="/opt/fsl-6.0.2/bin/fslwish"
+	export FSLLOCKDIR=""
+	export FSLMACHINELIST=""
+	export FSLREMOTECALL=""
+	export FSLGECUDAQ="cuda.q"
+
+%post
+	yum install -y -q \
+		ca-certificates \
+		cmake \
+		gcc-c++ \
+		git \
+		make
+	yum clean all
+	rm -rf /var/cache/yum/*
+	mkdir -p /tmp/niftyreg/build
+	git clone https://github.com/KCL-BMEIS/niftyreg /tmp/niftyreg/source
+	cd /tmp/niftyreg/build
+	cmake -DCMAKE_INSTALL_PREFIX=/opt/niftyreg-master -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF /tmp/niftyreg/source
+	make -j1
+	make install
+	ldconfig
+	rm -rf /tmp/niftyreg
+
+	yum install -y -q \
+		bc \
+		curl \
+		file \
+		libGL \
+		libGLU \
+		libICE \
+		libSM \
+		libX11 \
+		libXcursor \
+		libXext \
+		libXft \
+		libXinerama \
+		libXrandr \
+		libXt \
+		libgomp \
+		libjpeg \
+		libmng \
+		libpng12 \
+		nano \
+		openblas-serial \
+		sudo \
+		wget
+	yum clean all
+	rm -rf /var/cache/yum/*
+	echo "Downloading FSL ..."
+	mkdir -p /opt/fsl-6.0.2
+	curl -fL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.2-centos6_64.tar.gz | tar -xz -C /opt/fsl-6.0.2 --strip-components 1
+	echo "Installing FSL conda environment ..."
+	bash /opt/fsl-6.0.2/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.2
+