⬆️ Upgrade dependencies for 1.8.6

.github/Dockerfiles/AFNI.23.0.07-bionic.Dockerfile

@@ -0,0 +1,58 @@
+FROM ghcr.io/fcp-indi/c-pac/ubuntu:python3.10-bionic-non-free as AFNI
+USER root
+
+# install AFNI
+COPY dev/docker_data/required_afni_pkgs.txt /opt/required_afni_pkgs.txt
+RUN if [ -f /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0]; then \
+        ln -svf /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0 /usr/lib/x86_64-linux-gnu/libGL.so.1; \
+    fi && \
+    libs_path=/usr/lib/x86_64-linux-gnu && \
+    if [ -f $libs_path/libgsl.so.23 ]; then \
+        ln -svf $libs_path/libgsl.so.23 $libs_path/libgsl.so.19 && \
+        ln -svf $libs_path/libgsl.so.23 $libs_path/libgsl.so.0; \
+    elif [ -f $libs_path/libgsl.so.23.0.0 ]; then \
+        ln -svf $libs_path/libgsl.so.23.0.0 $libs_path/libgsl.so.19 && \
+        ln -svf $libs_path/libgsl.so.23.0.0 $libs_path/libgsl.so.0; \
+    elif [ -f $libs_path/libgsl.so ]; then \
+        ln -svf $libs_path/libgsl.so $libs_path/libgsl.so.0; \
+    fi && \
+    LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH && \
+    export LD_LIBRARY_PATH && \
+    apt-get update && apt-get install -y libglw1-mesa-dev && \
+    AFNI_VERSION="23.0.07" && \
+    curl -LOJ https://github.com/afni/afni/archive/AFNI_${AFNI_VERSION}.tar.gz && \
+    mkdir /opt/afni && \
+    tar -xvf afni-AFNI_${AFNI_VERSION}.tar.gz -C /opt/afni --strip-components 1 && \
+    rm -rf afni-AFNI_${AFNI_VERSION}.tar.gz && \
+    cd /opt/afni/src && \
+    sed '/^INSTALLDIR =/c INSTALLDIR = /opt/afni' Makefile.linux_ubuntu_16_64 > Makefile && \
+    make vastness && make cleanest && \
+    cd /opt/afni && \
+    # filter down to required packages
+    ls > full_ls && \
+    sed 's/linux_openmp_64\///g' /opt/required_afni_pkgs.txt | sort > required_ls && \
+    comm -2 -3 full_ls required_ls | xargs rm -rf full_ls required_ls && \
+    apt-get remove -y libglw1-mesa-dev && \
+    ldconfig
+
+# set up AFNI
+ENV PATH=/opt/afni:$PATH
+
+ENTRYPOINT ["/bin/bash"]
+
+# Link libraries for Singularity images
+RUN ldconfig
+
+RUN apt-get clean && \
+    apt-get autoremove -y && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+FROM scratch
+LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
+AFNI 21.1.00 (Domitian) stage"
+LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
+COPY --from=AFNI /lib/x86_64-linux-gnu/ld* /lib/x86_64-linux-gnu/
+COPY --from=AFNI /lib/x86_64-linux-gnu/lib*so* /lib/x86_64-linux-gnu/
+COPY --from=AFNI /lib64/ld* /lib64/
+COPY --from=AFNI /opt/afni/ /opt/afni/
+COPY --from=AFNI /usr/lib/x86_64-linux-gnu/lib*so* /usr/lib/x86_64-linux-gnu/

.github/Dockerfiles/ANTs.2.4.3.Python3.10-bionic.Dockerfile

@@ -0,0 +1,21 @@
+FROM ghcr.io/fcp-indi/c-pac/ubuntu:python3.10-bionic-non-free as ANTs
+
+USER root
+RUN curl -sL https://github.com/ANTsX/ANTs/releases/download/v2.4.3/ants-2.4.3-ubuntu-18.04-X64-gcc.zip -o /tmp/ANTs.zip \
+  && unzip /tmp/ANTs.zip -d /tmp \
+  && mkdir /usr/lib/ants \
+  && mv /tmp/ants-2.4.3/* /usr/lib/ants \
+  && curl -fsSL --retry 5 https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz \
+    | tar -xz -C /usr/lib/ants --strip-components 1 \
+  && mkdir /ants_template \
+  && curl -sL https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/3133832/Oasis.zip -o /tmp/Oasis.zip \
+  && unzip /tmp/Oasis.zip -d /tmp \
+  && mv /tmp/MICCAI2012-Multi-Atlas-Challenge-Data /ants_template/oasis
+
+# Only keep what we need
+FROM scratch
+LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
+ANTs 2.4.3 stage"
+LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
+COPY --from=ANTs /usr/lib/ants/ /usr/lib/ants/
+COPY --from=ANTs /ants_template/ /ants_template/

.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.5
+FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.6.dev
 LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [ABCD-HCP BIDS fMRI Pipeline](https://github.com/DCAN-Labs/abcd-hcp-pipeline/blob/e480a8f99534f1b05f37bf44c64827384b69b383/Dockerfile)"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root

.github/Dockerfiles/C-PAC.develop-bionic.Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.5
+FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.6.dev
 LABEL org.opencontainers.image.description "Full C-PAC image"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root

.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.5
+FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.6.dev
 LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [fMRIPrep LTS](https://reproducibility.stanford.edu/fmriprep-lts#long-term-support-lts)"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root

.github/Dockerfiles/C-PAC.develop-lite-bionic.Dockerfile

@@ -1,12 +1,24 @@
-FROM ghcr.io/fcp-indi/c-pac:latest-bionic
+FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.6.dev
 LABEL org.opencontainers.image.description "Full C-PAC image without FreeSurfer"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root
+
+# install C-PAC
+COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml
+COPY . /code
+RUN pip install -e /code
+# set up runscript
+COPY dev/docker_data /code/docker_data
+RUN rm -Rf /code/docker_data/Dockerfiles && \
+    mv /code/docker_data/* /code && \
+    rm -Rf /code/docker_data && \
+    chmod +x /code/run.py && \
+    rm -Rf /code/run-with-freesurfer.sh
 ENTRYPOINT ["/code/run.py"]
 
-# remove FreeSurfer, link libraries & clean up
-RUN rm -rf /usr/lib/freesurfer/ /code/run-with-freesurfer.sh /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
-    ln -svf /usr/lib/x86_64-linux-gnu/libgsl.so.23 /usr/lib/x86_64-linux-gnu/libgsl.so.0 && ldconfig && \
+# link libraries & clean up
+RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
+    ldconfig && \
     chmod 777 $(ls / | grep -v sys | grep -v proc)
 
 # set user

.github/Dockerfiles/FSL.5.0.10-bionic.Dockerfile

@@ -1,4 +1,20 @@
-FROM ghcr.io/shnizzedy/c-pac/fsl:neurodebian-bionic as FSL-Neurodebian
+# Copyright (C) 2021-2023  C-PAC Developers
+
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+FROM ghcr.io/fcp-indi/c-pac/fsl:data as data
 FROM ghcr.io/fcp-indi/c-pac/ubuntu:bionic-non-free AS FSL
 
 USER root
@@ -14,7 +30,6 @@ ENV FSLDIR=/usr/share/fsl/5.0 \
     PATH=/usr/lib/fsl/5.0:$PATH \
     TZ=America/New_York
 
-
 # Installing and setting up FSL
 RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && \
      echo $TZ > /etc/timezone && \
@@ -45,4 +60,5 @@ COPY --from=FSL /usr/bin/wish /usr/bin/wish
 COPY --from=FSL /usr/share/fsl/ /usr/share/fsl/
 COPY --from=FSL /usr/lib/ /usr/lib/
 COPY --from=FSL /lib/x86_64-linux-gnu/lib*so* /lib/x86_64-linux-gnu/
-COPY --from=FSL-Neurodebian /usr/share/fsl/5.0/data/standard/tissuepriors/*mm /usr/share/fsl/5.0/data/standard/tissuepriors/
+# install C-PAC resources into FSL
+COPY --from=data /fsl_data/standard /usr/share/fsl/5.0/data/standard

.github/Dockerfiles/FSL.5.0.9-5.neurodebian-xenial.Dockerfile

@@ -1,3 +1,20 @@
+# Copyright (C) 2021-2023  C-PAC Developers
+
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+FROM ghcr.io/fcp-indi/c-pac/fsl:data as data
 FROM ghcr.io/fcp-indi/c-pac/ubuntu:xenial-20200114 as FSL
 USER root
 
@@ -24,17 +41,6 @@ ENV FSLDIR=/usr/share/fsl/5.0 \
     AFNI_PLUGINPATH="/usr/lib/afni/plugins" \
     PATH=/usr/lib/fsl/5.0:$PATH
 
-# install CPAC resources into FSL
-RUN curl -sL http://fcon_1000.projects.nitrc.org/indi/cpac_resources.tar.gz -o /tmp/cpac_resources.tar.gz && \
-    tar xfz /tmp/cpac_resources.tar.gz -C /tmp && \
-    cp -n /tmp/cpac_image_resources/MNI_3mm/* $FSLDIR/data/standard && \
-    cp -n /tmp/cpac_image_resources/MNI_4mm/* $FSLDIR/data/standard && \
-    cp -n /tmp/cpac_image_resources/symmetric/* $FSLDIR/data/standard && \
-    cp -n /tmp/cpac_image_resources/HarvardOxford-lateral-ventricles-thr25-2mm.nii.gz $FSLDIR/data/atlases/HarvardOxford && \
-    cp -nr /tmp/cpac_image_resources/tissuepriors/2mm $FSLDIR/data/standard/tissuepriors && \
-    cp -nr /tmp/cpac_image_resources/tissuepriors/3mm $FSLDIR/data/standard/tissuepriors && \
-    chmod -R ugo+r $FSLDIR/data/standard
-
 ENTRYPOINT ["/bin/bash"]
 
 # Link libraries for Singularity images
@@ -59,3 +65,5 @@ COPY --from=FSL /usr/share/man/man1/fsl.1.gz /usr/share/man/man1/
 COPY --from=FSL /usr/share/data/fsl-mni152-templates /usr/share/data/fsl-mni152-templates
 COPY --from=FSL /usr/share/doc/fsl-mni152-templates /usr/share/doc/fsl-mni152-templates
 COPY --from=FSL /usr/share/fsl /usr/share/fsl
+# install C-PAC resources into FSL
+COPY --from=data /fsl_data/standard /usr/share/fsl/5.0/data/standard

.github/Dockerfiles/FSL.6.0.6.4-Python3.10-bionic.Dockerfile

@@ -0,0 +1,77 @@
+# Copyright (C) 2023  C-PAC Developers
+
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+FROM ghcr.io/fcp-indi/c-pac/fsl:data as data
+FROM ghcr.io/fcp-indi/c-pac/ubuntu:bionic-non-free AS FSL
+
+USER root
+
+# set up FSL environment
+ENV FSLDIR=/usr/share/fsl/6.0 \
+    FSLOUTPUTTYPE=NIFTI_GZ \
+    FSLMULTIFILEQUIT=TRUE \
+    POSSUMDIR=/usr/share/fsl/6.0 \
+    LD_LIBRARY_PATH=/usr/share/fsl/6.0:$LD_LIBRARY_PATH \
+    FSLTCLSH=/usr/bin/tclsh \
+    FSLWISH=/usr/bin/wish \
+    PATH=/usr/share/fsl/6.0/bin:$PATH \
+    TZ=America/New_York
+
+# Installing and setting up FSL
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \
+    &&  echo $TZ > /etc/timezone \
+    && apt-get update \
+    && apt-get install -y tclsh wish \
+    && echo "Downloading FSL ..." \
+    && mkdir -p /usr/share/fsl/6.0 \
+    && curl -sSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.4-centos6_64.tar.gz \
+    | tar zx -C /usr/share/fsl/6.0 --strip-components=1 \
+    --exclude=fsl/bin/mist \
+    --exclude=fsl/bin/possum \
+    --exclude=fsl/data/possum \
+    --exclude=fsl/data/mist \
+    --exclude=fsl/data/first \
+    && ln -s /usr/share/fsl/6.0 /usr/share/fsl/5.0 \
+    && if [ -f /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0]; then \
+        ln -svf /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0 /usr/lib/x86_64-linux-gnu/libGL.so.1; \
+    fi \
+    && ldconfig \
+    && curl -sL http://fcon_1000.projects.nitrc.org/indi/cpac_resources.tar.gz -o /tmp/cpac_resources.tar.gz \
+    && tar xfz /tmp/cpac_resources.tar.gz -C /tmp \
+    && cp -n /tmp/cpac_image_resources/MNI_3mm/* $FSLDIR/data/standard \
+    && cp -n /tmp/cpac_image_resources/MNI_4mm/* $FSLDIR/data/standard \
+    && cp -n /tmp/cpac_image_resources/symmetric/* $FSLDIR/data/standard \
+    && cp -n /tmp/cpac_image_resources/HarvardOxford-lateral-ventricles-thr25-2mm.nii.gz $FSLDIR/data/atlases/HarvardOxford \
+    && cp -nr /tmp/cpac_image_resources/tissuepriors/2mm $FSLDIR/data/standard/tissuepriors \
+    && cp -nr /tmp/cpac_image_resources/tissuepriors/3mm $FSLDIR/data/standard/tissuepriors \
+    && chmod -R ugo+r $FSLDIR/data/standard
+
+ENTRYPOINT ["/bin/bash"]
+
+# set user
+USER c-pac_user
+
+# Only keep what we need
+FROM scratch
+LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
+FSL 6.0.4 stage"
+LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
+COPY --from=FSL /usr/bin/tclsh /usr/bin/tclsh
+COPY --from=FSL /usr/bin/wish /usr/bin/wish
+COPY --from=FSL /usr/share/fsl /usr/share/fsl
+COPY --from=FSL /lib/x86_64-linux-gnu/lib*so* /lib/x86_64-linux-gnu/
+# install C-PAC resources into FSL
+COPY --from=data /fsl_data/standard /usr/share/fsl/6.0/data/standard

.github/Dockerfiles/FSL.data.Dockerfile

@@ -0,0 +1,22 @@
+FROM ghcr.io/fcp-indi/c-pac/ubuntu:bionic-non-free AS FSL
+
+USER root
+
+# install CPAC resources into FSL
+RUN mkdir -p /fsl_data/atlases/HarvordOxford fsl_data/standard/tissuepriors \
+    && curl -sL http://fcon_1000.projects.nitrc.org/indi/cpac_resources.tar.gz -o /tmp/cpac_resources.tar.gz \
+    && tar xfz /tmp/cpac_resources.tar.gz -C /tmp \
+    && cp -n /tmp/cpac_image_resources/MNI_3mm/* /fsl_data/standard \
+    && cp -n /tmp/cpac_image_resources/MNI_4mm/* /fsl_data/standard \
+    && cp -n /tmp/cpac_image_resources/symmetric/* /fsl_data/standard \
+    && cp -n /tmp/cpac_image_resources/HarvardOxford-lateral-ventricles-thr25-2mm.nii.gz /fsl_data/atlases/HarvardOxford \
+    && cp -nr /tmp/cpac_image_resources/tissuepriors/2mm /fsl_data/standard/tissuepriors \
+    && cp -nr /tmp/cpac_image_resources/tissuepriors/3mm /fsl_data/standard/tissuepriors \
+    && chmod -R ugo+r /fsl_data/standard
+
+FROM scratch
+LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
+FSL data"
+LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
+
+COPY --from=FSL /fsl_data/standard fsl_data/standard

.github/Dockerfiles/FreeSurfer.7.3.2-Python3.10-bionic.Dockerfile

@@ -0,0 +1,15 @@
+FROM ghcr.io/fcp-indi/c-pac/ubuntu:python3.10-bionic-non-free as FreeSurfer
+
+USER root
+
+ENV FREESURFER_HOME=/opt/freesurfer \
+    NO_FSFAST=1
+RUN mkdir -p /opt/freesurfer \
+  && curl -fsSL --retry 5 https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-ubuntu18_amd64-7.3.2.tar.gz \
+  | tar -xz -C /opt/freesurfer --strip-components 1
+
+# Only keep what we need
+FROM scratch
+LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
+FreeSurfer 7.3.2 stage"
+COPY --from=FreeSurfer /opt/freesurfer/ /opt/freesurfer

.github/Dockerfiles/ICA-AROMA.0.4.4-beta-bionic.Dockerfile

@@ -0,0 +1,26 @@
+FROM ghcr.io/fcp-indi/c-pac/ubuntu:bionic-non-free AS ICA-AROMA
+USER root
+
+# install ICA-AROMA
+RUN mkdir -p /opt/ICA-AROMA
+RUN curl -sL https://github.com/rhr-pruim/ICA-AROMA/archive/v0.4.4-beta.tar.gz | tar -xzC /opt/ICA-AROMA --strip-components 1
+RUN chmod +x /opt/ICA-AROMA/ICA_AROMA.py
+ENV PATH=/opt/ICA-AROMA:$PATH
+
+ENTRYPOINT ["/bin/bash"]
+
+# Link libraries for Singularity images
+RUN ldconfig
+
+RUN apt-get clean && \
+    apt-get autoremove -y && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# set user
+USER c-pac_user
+
+# Only keep what we need
+FROM scratch
+LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
+ICA-AROMA 0.4.4-beta stage"
+COPY --from=ICA-AROMA /opt/ICA-AROMA/ /opt/ICA-AROMA/