Add FreeSurfer 8.2.0 support (bids/freesurfer:8)

.circleci/config.yml

@@ -190,8 +190,10 @@ jobs:
             FS_MAJOR_VERSION=<< parameters.version >>
             if [[ FS_MAJOR_VERSION -eq 6 ]]; then
               FS_VERSION=6.0.1
-            else
+            elif [[ FS_MAJOR_VERSION -eq 7 ]]; then
               FS_VERSION=7.4.1
+            else
+              FS_VERSION=8.2.0
             fi
 
             : "Pushing unstable versions for ${FS_MAJOR_VERSION} to DockerHub"
@@ -227,7 +229,7 @@ jobs:
 
           else
               : "No DOCKER_TOKEN, skipping push to DockerHub"
-              exit 1
+              exit 0
           fi
 
 workflows:
@@ -252,6 +254,20 @@ workflows:
           branches:
             only: /.*/
 
+    # fs8 has no precomputed group2 fixture (test job compares against
+    # ds114_test<N>_freesurfer_precomp_v6.0.0), so it's built/deployed here
+    # without going through the test job/matrix, unlike 6/7.
+    - build:
+        name: build_<< matrix.version >>
+        matrix:
+          parameters:
+            version: ['8']
+        filters:
+          tags:
+            only: /.*/
+          branches:
+            only: /.*/
+
     - test:
         name: test_<< matrix.version >>_<< matrix.test >>
         matrix:
@@ -281,3 +297,19 @@ workflows:
             only: /.*/
           tags:
             only: /.*/
+
+    # No test_8_* jobs (see build_8 above), so this only requires build_8.
+    - deploy:
+        name: deploy_<< matrix.version >>
+        matrix:
+          parameters:
+            version: ['8']
+        context:
+        - dockerhub
+        requires:
+        - build_<< matrix.version >>
+        filters:
+          branches:
+            only: /.*/
+          tags:
+            only: /.*/

Dockerfile_fs6

@@ -64,43 +64,7 @@ RUN apt-get update -qq \
          --exclude='subjects/fsaverage6' \
          --exclude='subjects/fsaverage_sym' \
          --exclude='trctrain'
-ENV CONDA_DIR="/opt/miniconda-latest" \
-    PATH="/opt/miniconda-latest/bin:$PATH"
-RUN apt-get update -qq \
-    && apt-get install -y -q --no-install-recommends \
-           bzip2 \
-           ca-certificates \
-           curl \
-    && rm -rf /var/lib/apt/lists/* \
-    # Install dependencies.
-    && export PATH="/opt/miniconda-latest/bin:$PATH" \
-    && echo "Downloading Miniconda installer ..." \
-    && conda_installer="/tmp/miniconda.sh" \
-    && curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
-    && bash "$conda_installer" -b -p /opt/miniconda-latest \
-    && rm -f "$conda_installer" \
-    && conda update -yq -nbase conda \
-    && conda install -yq -nbase conda-libmamba-solver \
-    && conda config --set solver libmamba \
-    # Prefer packages in conda-forge
-    && conda config --system --prepend channels conda-forge \
-    # Packages in lower-priority channels not considered if a package with the same
-    # name exists in a higher priority channel. Can dramatically speed up installations.
-    # Conda recommends this as a default
-    # https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html
-    && conda config --set channel_priority strict \
-    && conda config --system --set auto_update_conda false \
-    && conda config --system --set show_channel_urls true \
-    # Enable `conda activate`
-    && conda init bash \
-    && conda install -y  --name base \
-           "pandas=1.5.3" \
-    && bash -c "source activate base \
-    &&   python -m pip install --no-cache-dir  \
-             "nibabel"" \
-    # Clean up
-    && sync && conda clean --all --yes && sync \
-    && rm -rf ~/.cache/pip/*
+RUN bash -c 'apt-get update -qq && apt-get install -y -q --no-install-recommends bzip2 ca-certificates curl && rm -rf /var/lib/apt/lists/* && export PATH="/opt/miniconda-latest/bin:$PATH" && echo "Downloading Miniconda installer ..." && conda_installer="/tmp/miniconda.sh" && curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash "$conda_installer" -b -p /opt/miniconda-latest && rm -f "$conda_installer" && conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main && conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r && conda update -yq -nbase conda && conda install -yq -nbase conda-libmamba-solver && conda config --set solver libmamba && conda config --system --prepend channels conda-forge && conda config --set channel_priority strict && conda config --system --set auto_update_conda false && conda config --system --set show_channel_urls true && conda init bash && conda install -y --name base pandas && bash -c "source activate base && python -m pip install --no-cache-dir nibabel" && sync && conda clean --all --yes && sync && rm -rf ~/.cache/pip/*'
 RUN bash -c 'curl -sL https://deb.nodesource.com/setup_18.x | bash -'
 RUN apt-get update -qq \
            && apt-get install -y -q --no-install-recommends \
@@ -114,6 +78,7 @@ ENV FSLDIR="/usr/share/fsl/5.0" \
     LD_LIBRARY_PATH="/usr/lib/fsl/5.0:" \
     FSLTCLSH="/usr/bin/tclsh" \
     FSLWISH="/usr/bin/wish"
+ENV FS_VERSION="6.0.1"
 ENV OS="Linux" \
     FS_OVERRIDE="0" \
     FIX_VERTEX_AREA="" \
@@ -122,11 +87,13 @@ ENV OS="Linux" \
     MNI_DIR="/opt/freesurfer/mni" \
     LOCAL_DIR="/opt/freesurfer/local" \
     FREESURFER_HOME="/opt/freesurfer" \
+    FREESURFER="/opt/freesurfer" \
     FSFAST_HOME="/opt/freesurfer/fsfast" \
     MINC_BIN_DIR="/opt/freesurfer/mni/bin" \
     MINC_LIB_DIR="/opt/freesurfer/mni/lib" \
     MNI_DATAPATH="/opt/freesurfer/mni/data" \
     FMRI_ANALYSIS_DIR="/opt/freesurfer/fsfast" \
+    FUNCTIONALS_DIR="/opt/freesurfer/sessions" \
     PERL5LIB="/opt/freesurfer/mni/share/perl5" \
     MNI_PERL5LIB="/opt/freesurfer/mni/share/perl5/" \
     PATH="/opt/miniconda-latest/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin" \
@@ -211,17 +178,10 @@ RUN printf '{ \
         "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    bc \\\\\\n    ca-certificates \\\\\\n    curl \\\\\\n    libgomp1 \\\\\\n    libxmu6 \\\\\\n    libxt6 \\\\\\n    perl \\\\\\n    tcsh\\nrm -rf /var/lib/apt/lists/*\\necho \\"Downloading FreeSurfer ...\\"\\nmkdir -p /opt/freesurfer\\ncurl -fL ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz \\\\\\n| tar -xz -C /opt/freesurfer --owner root --group root --no-same-owner --strip-components 1 \\\\\\n  --exclude='"'"'average/mult-comp-cor'"'"' \\\\\\n  --exclude='"'"'lib/cuda'"'"' \\\\\\n  --exclude='"'"'lib/qt'"'"' \\\\\\n  --exclude='"'"'subjects/V1_average'"'"' \\\\\\n  --exclude='"'"'subjects/bert'"'"' \\\\\\n  --exclude='"'"'subjects/cvs_avg35'"'"' \\\\\\n  --exclude='"'"'subjects/cvs_avg35_inMNI152'"'"' \\\\\\n  --exclude='"'"'subjects/fsaverage3'"'"' \\\\\\n  --exclude='"'"'subjects/fsaverage4'"'"' \\\\\\n  --exclude='"'"'subjects/fsaverage5'"'"' \\\\\\n  --exclude='"'"'subjects/fsaverage6'"'"' \\\\\\n  --exclude='"'"'subjects/fsaverage_sym'"'"' \\\\\\n  --exclude='"'"'trctrain'"'"'" \
       } \
     }, \
-    { \
-      "name": "env", \
-      "kwds": { \
-        "CONDA_DIR": "/opt/miniconda-latest", \
-        "PATH": "/opt/miniconda-latest/bin:$PATH" \
-      } \
-    }, \
     { \
       "name": "run", \
       "kwds": { \
-        "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    bzip2 \\\\\\n    ca-certificates \\\\\\n    curl\\nrm -rf /var/lib/apt/lists/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-latest/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-latest\\nrm -f \\"$conda_installer\\"\\nconda update -yq -nbase conda\\nconda install -yq -nbase conda-libmamba-solver\\nconda config --set solver libmamba\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda install -y  --name base \\\\\\n    \\"pandas=1.5.3\\"\\nbash -c \\"source activate base\\n  python -m pip install --no-cache-dir  \\\\\\n      \\"nibabel\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
+        "command": "bash -c '"'"'apt-get update -qq && apt-get install -y -q --no-install-recommends bzip2 ca-certificates curl && rm -rf /var/lib/apt/lists/* && export PATH=\\"/opt/miniconda-latest/bin:$PATH\\" && echo \\"Downloading Miniconda installer ...\\" && conda_installer=\\"/tmp/miniconda.sh\\" && curl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash \\"$conda_installer\\" -b -p /opt/miniconda-latest && rm -f \\"$conda_installer\\" && conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main && conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r && conda update -yq -nbase conda && conda install -yq -nbase conda-libmamba-solver && conda config --set solver libmamba && conda config --system --prepend channels conda-forge && conda config --set channel_priority strict && conda config --system --set auto_update_conda false && conda config --system --set show_channel_urls true && conda init bash && conda install -y --name base pandas && bash -c \\"source activate base && python -m pip install --no-cache-dir nibabel\\" && sync && conda clean --all --yes && sync && rm -rf ~/.cache/pip/*'"'"'" \
       } \
     }, \
     { \
@@ -263,6 +223,12 @@ RUN printf '{ \
         "FSLWISH": "/usr/bin/wish" \
       } \
     }, \
+    { \
+      "name": "env", \
+      "kwds": { \
+        "FS_VERSION": "6.0.1" \
+      } \
+    }, \
     { \
       "name": "env", \
       "kwds": { \
@@ -274,11 +240,13 @@ RUN printf '{ \
         "MNI_DIR": "/opt/freesurfer/mni", \
         "LOCAL_DIR": "/opt/freesurfer/local", \
         "FREESURFER_HOME": "/opt/freesurfer", \
+        "FREESURFER": "/opt/freesurfer", \
         "FSFAST_HOME": "/opt/freesurfer/fsfast", \
         "MINC_BIN_DIR": "/opt/freesurfer/mni/bin", \
         "MINC_LIB_DIR": "/opt/freesurfer/mni/lib", \
         "MNI_DATAPATH": "/opt/freesurfer/mni/data", \
         "FMRI_ANALYSIS_DIR": "/opt/freesurfer/fsfast", \
+        "FUNCTIONALS_DIR": "/opt/freesurfer/sessions", \
         "PERL5LIB": "/opt/freesurfer/mni/share/perl5", \
         "MNI_PERL5LIB": "/opt/freesurfer/mni/share/perl5/", \
         "PATH": "/opt/miniconda-latest/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin", \