Merge branch 'master' of https://github.com/MICA-MNI/micapipe

.dockerignore

@@ -0,0 +1 @@
+./docs

.github/workflows/build_publish_container.yml

@@ -0,0 +1,54 @@
+name: Build and Publish Container
+
+on:
+  # run it on push to the default repository branch
+  push:
+    branches: [master]
+  # run it during pull request
+  pull_request:
+
+jobs:
+  # define job to build and publish docker image
+  build-and-push-docker-image:
+    name: Build Docker image and push to repositories
+    # run only when code is compiling and tests are passing
+    runs-on: ubuntu-latest
+
+    # steps to perform in job
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      # setup Docker buld action
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Login to Github Packages
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build image and push to Docker Hub and GitHub Container Registry
+        uses: docker/build-push-action@v2
+        with:
+          # relative path to the place where source code with Dockerfile is located
+          context: ./
+          # Note: tags has to be all lower-case
+          tags: |
+            micalab/micapipe:latest 
+            ghcr.io/mica-mni/micapipe:latest
+          # build on feature branches, push only on master branch
+          push: ${{ github.ref == 'refs/heads/master' }}
+
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}
+

Dockerfile

@@ -72,12 +72,12 @@ RUN apt-get update -qq \
     && make install \
     && rm -rf /tmp/dcm2niix
 
-ENV FSLDIR="/opt/fsl-6.0.3" \
-    PATH="/opt/fsl-6.0.3/bin:$PATH" \
+ENV FSLDIR="/opt/fsl-6.0.2" \
+    PATH="/opt/fsl-6.0.2/bin:$PATH" \
     FSLOUTPUTTYPE="NIFTI_GZ" \
     FSLMULTIFILEQUIT="TRUE" \
-    FSLTCLSH="/opt/fsl-6.0.3/bin/fsltclsh" \
-    FSLWISH="/opt/fsl-6.0.3/bin/fslwish" \
+    FSLTCLSH="/opt/fsl-6.0.2/bin/fsltclsh" \
+    FSLWISH="/opt/fsl-6.0.2/bin/fslwish" \
     FSLLOCKDIR="" \
     FSLMACHINELIST="" \
     FSLREMOTECALL="" \
@@ -105,15 +105,15 @@ RUN apt-get update -qq \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* \
     && echo "Downloading FSL ..." \
-    && mkdir -p /opt/fsl-6.0.3 \
-    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.3-centos6_64.tar.gz \
-    | tar -xz -C /opt/fsl-6.0.3 --strip-components 1 \
+    && mkdir -p /opt/fsl-6.0.2 \
+    && curl -fsSL --retry 5 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 \
     && sed -i '$iecho Some packages in this Docker container are non-free' $ND_ENTRYPOINT \
     && sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT \
     && sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT \
     && sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT
 
-RUN bash -c 'bash /opt/fsl-6.0.3/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.3'
+RUN bash -c 'bash /opt/fsl-6.0.2/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.2'
 
 ENV FREESURFER_HOME="/opt/freesurfer-6.0.0" \
     PATH="/opt/freesurfer-6.0.0/bin:$PATH"
@@ -271,12 +271,12 @@ RUN set -uex;            LD_LIBRARY_PATH=/lib64/:$PATH;            apt install -
 RUN bash -c 'wget https://www.dropbox.com/s/47lu1nojrderls1/install_R_env.sh?dl=0 -O /opt/install_R_env.sh && \
                     bash /opt/install_R_env.sh && cd /opt/afni-latest && rPkgsInstall -pkgs ALL'
 
-COPY [".", "/opt/micapipe"]
 
-RUN bash -c 'cd /opt/micapipe && mv fix_settings.sh /opt/fix1.068/settings.sh && mv fsl_conf/* /opt/fsl-6.0.3/etc/flirtsch/'
+COPY . /opt/micapipe/
 
+RUN bash -c 'cd /opt/micapipe && mv fix_settings.sh /opt/fix1.068/settings.sh && mv fsl_conf/* /opt/fsl-6.0.2/etc/flirtsch/'
 
-RUN bash -c 'mv /opt/micapipe/surfaces/fsaverage5 /opt/freesurfer-6.0.0/subjects'
+RUN bash -c 'cp -r /opt/micapipe/surfaces/fsaverage5 /opt/freesurfer-6.0.0/subjects'
 
 WORKDIR /home/mica
 
@@ -286,4 +286,4 @@ RUN sed -i '$isource /opt/freesurfer-6.0.0/SetUpFreeSurfer.sh' $ND_ENTRYPOINT
 
 RUN sed -i '$iexport FIXPATH=/opt/fix && export PATH="${FIXPATH}:${PATH}"' $ND_ENTRYPOINT
 
-ENTRYPOINT ["/neurodocker/startup.sh", "/opt/micapipe/mica-pipe"]
+ENTRYPOINT ["/neurodocker/startup.sh", "/opt/micapipe/micapipe"]

generate_micapipe_images.sh

@@ -2,19 +2,19 @@
 
 set -e
 
-# Generate Dockerfile.
+# Generate Dockerfile using neurodocker 0.7.0
 generate() {
   docker run --rm neurodocker:local generate "$1" \
     --base=ubuntu:bionic-20201119 \
     --pkg-manager=apt \
     --install "gcc g++ lsb-core bsdtar jq libopenblas-dev tree openjdk-8-jdk libstdc++6" \
     --dcm2niix version=v1.0.20190902 method=source\
-    --fsl version=6.0.3 \
+    --fsl version=6.0.2 \
     --run-bash 'bash /opt/fsl-6.0.3/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.3' \
     --freesurfer version=6.0.0 \
     --matlabmcr version=2017b\
     --afni version=latest\
-    --ants version=2.3.4 \
+    --ants version=2.3.1 \    # change manually the Dockefile to 2.3.4
     --run-bash "apt-get update && apt-get install -y gnupg2 && wget -O- http://neuro.debian.net/lists/xenial.de-fzj.full | tee /etc/apt/sources.list.d/neurodebian.sources.list && apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9 && apt-get update && apt-get install -y connectome-workbench=1.3.2-2~nd16.04+1" \
     --run-bash "cd /opt/ && wget http://www.fmrib.ox.ac.uk/~steve/ftp/fix1.068.tar.gz && tar xvfz fix1.068.tar.gz && rm fix1.068.tar.gz" \
     --user=mica \