Merge branch 'develop' into datetime-none

Author: sgiavasis

.github/Dockerfiles/AFNI.23.3.09-jammy.Dockerfile

@@ -14,151 +14,152 @@
 
 # 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:6.0.6.5-jammy as FSL
-FROM ghcr.io/fcp-indi/c-pac/ubuntu:jammy-non-free as AFNI
+FROM ghcr.io/fcp-indi/c-pac/fsl:6.0.6.5-jammy AS fsl
+FROM ghcr.io/fcp-indi/c-pac/ubuntu:jammy-non-free AS afni
 USER root
 ENV AFNI_VERSION="23.3.09"
 # To use the same Python environment to share common libraries
-COPY --from=FSL /usr/share/fsl/6.0 /usr/share/fsl/6.0
+COPY --from=fsl /usr/share/fsl/6.0 /usr/share/fsl/6.0
 ENV FSLDIR=/usr/share/fsl/6.0 \
-    PATH=/usr/share/fsl/6.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
-    LD_LIBRARY_PATH=/usr/share/fsl/6.0/lib:$LD_LIBRARY_PATH
+  PATH=/usr/share/fsl/6.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
+  LD_LIBRARY_PATH=/usr/share/fsl/6.0/lib:$LD_LIBRARY_PATH
 
 # install AFNI
 COPY dev/docker_data/required_afni_pkgs.txt /opt/required_afni_pkgs.txt
 COPY dev/docker_data/checksum/AFNI.${AFNI_VERSION}.sha384 /tmp/AFNI.${AFNI_VERSION}.sha384
 ENV PATH=/opt/afni:$PATH
 RUN apt-get update \
-    && apt-get install -y --no-install-recommends \
-      apt-transport-https \
-      bc \
-      bzip2 \
-      cmake \
-      curl \
-      dh-autoreconf \
-      eog \
-      evince \
-      firefox \
-      gedit \
-      git \
-      gnome-terminal \
-      gnome-tweaks \
-      gnupg \
-      gsl-bin \
-      libcanberra-gtk-module \
-      libcurl4-openssl-dev \
-      libexpat1-dev \
-      libgdal-dev \
-      libgfortran-11-dev \
-      libgiftiio-dev \
-      libgl1-mesa-dri \
-      libglib2.0-dev \
-      libglu1-mesa \
-      libglu1-mesa-dev \
-      libglw1-mesa \
-      libglw1-mesa-dev \
-      libgomp1 \
-      libgsl-dev \
-      libjpeg-progs \
-      libjpeg62 \
-      libmotif-dev \
-      libnode-dev \
-      libopenblas-dev \
-      libssl-dev \
-      libtool \
-      libudunits2-dev \
-      libx11-dev \
-      libxext-dev \
-      libxft-dev \
-      libxft2 \
-      libxi-dev \
-      libxm4 \
-      libxml2 \
-      libxml2-dev \
-      libxmu-dev \
-      libxmu-headers \
-      libxpm-dev \
-      libxslt1-dev \
-      m4 \
-      mesa-common-dev \
-      mesa-utils \
-      nautilus \
-      netpbm \
-      ninja-build \
-      openssh-client \
-      pkg-config \
-      r-base-dev \
-      rsync \
-      software-properties-common \
-      tcsh \
-      unzip \
-      vim \
-      wget \
-      x11proto-xext-dev \
-      xauth \
-      xfonts-100dpi \
-      xfonts-base \
-      xterm \
-      xutils-dev \
-      xvfb \
-      zlib1g-dev \
-    && curl -LOJ https://github.com/afni/afni/archive/AFNI_${AFNI_VERSION}.tar.gz \
-    && sha384sum --check /tmp/AFNI.${AFNI_VERSION}.sha384 \
-    && ln -svf /usr/lib/x86_64-linux-gnu/libgsl.so.27 /usr/lib/x86_64-linux-gnu/libgsl.so.19 \
-    && ln -svf /usr/lib/x86_64-linux-gnu/libgsl.so.27 /usr/lib/x86_64-linux-gnu/libgsl.so.0 \
-    && mkdir /opt/afni \
-    && tar -xvf afni-AFNI_${AFNI_VERSION}.tar.gz -C /opt/afni --strip-components 1 \
-    && rm -rf afni-AFNI_${AFNI_VERSION}.tar.gz \
-    # Fix GLwDrawA per https://github.com/afni/afni/blob/AFNI_23.1.10/src/other_builds/OS_notes.linux_fedora_25_64.txt
-    && cd /usr/include/GL \
-    && mv GLwDrawA.h GLwDrawA.h.orig \
-    && sed 's/GLAPI WidgetClass/extern GLAPI WidgetClass/' GLwDrawA.h.orig > GLwDrawA.h \
-    && cd /opt/afni/src \
-    && sed '/^INSTALLDIR =/c INSTALLDIR = /opt/afni' other_builds/Makefile.linux_ubuntu_22_64 > Makefile \
-    && make vastness && make cleanest \
-    && cd /opt/afni \
-    && VERSION_STRING=$(afni --version) \
-    && VERSION_NAME=$(echo $VERSION_STRING | awk -F"'" '{print $2}') \
-    # filter down to required packages
-    && ls > full_ls \
-    && sed 's/linux_openmp_64\///g' /opt/required_afni_pkgs.txt | sort > required_ls \
-    && comm -2 -3 full_ls required_ls | xargs rm -rf full_ls required_ls \
-    # get rid of stuff we just needed for building
-    && apt-get remove -y \
-      bzip2 \
-      cmake \
-      curl \
-      dh-autoreconf \
-      evince \
-      firefox \
-      gedit \
-      git \
-      gnome-terminal \
-      gnome-tweaks \
-      libglw1-mesa-dev \
-      m4 \
-      ninja-build \
-      openssh-client \
-      unzip \
-      wget \
-      xterm \
-    && ldconfig \
-    && rm -rf /opt/afni/src
+  && apt-get install -y --no-install-recommends \
+  apt-transport-https \
+  bc \
+  bzip2 \
+  cmake \
+  curl \
+  dh-autoreconf \
+  eog \
+  evince \
+  firefox \
+  gedit \
+  git \
+  gnome-terminal \
+  gnome-tweaks \
+  gnupg \
+  gsl-bin \
+  libcanberra-gtk-module \
+  libcurl4-openssl-dev \
+  libexpat1-dev \
+  libgdal-dev \
+  libgfortran-11-dev \
+  libgiftiio-dev \
+  libgl1-mesa-dri \
+  libglib2.0-dev \
+  libglu1-mesa \
+  libglu1-mesa-dev \
+  libglw1-mesa \
+  libglw1-mesa-dev \
+  libgomp1 \
+  libgsl-dev \
+  libjpeg-progs \
+  libjpeg62 \
+  libmotif-dev \
+  libnode-dev \
+  libopenblas-dev \
+  libssl-dev \
+  libtool \
+  libudunits2-dev \
+  libx11-dev \
+  libxext-dev \
+  libxft-dev \
+  libxft2 \
+  libxi-dev \
+  libxm4 \
+  libxml2 \
+  libxml2-dev \
+  libxmu-dev \
+  libxmu-headers \
+  libxpm-dev \
+  libxslt1-dev \
+  m4 \
+  mesa-common-dev \
+  mesa-utils \
+  nautilus \
+  netpbm \
+  ninja-build \
+  openssh-client \
+  pkg-config \
+  r-base-dev \
+  rsync \
+  software-properties-common \
+  tcsh \
+  unzip \
+  vim \
+  wget \
+  x11proto-xext-dev \
+  xauth \
+  xfonts-100dpi \
+  xfonts-base \
+  xterm \
+  xutils-dev \
+  xvfb \
+  zlib1g-dev \
+  && curl -LOJ https://github.com/afni/afni/archive/AFNI_${AFNI_VERSION}.tar.gz \
+  #&& sha384sum --check /tmp/AFNI.${AFNI_VERSION}.sha384 \
+  && ln -svf /usr/lib/x86_64-linux-gnu/libgsl.so.27 /usr/lib/x86_64-linux-gnu/libgsl.so.19 \
+  && ln -svf /usr/lib/x86_64-linux-gnu/libgsl.so.27 /usr/lib/x86_64-linux-gnu/libgsl.so.0 \
+  && mkdir /opt/afni \
+  && tar -xvf afni-AFNI_${AFNI_VERSION}.tar.gz -C /opt/afni --strip-components 1 \
+  && rm -rf afni-AFNI_${AFNI_VERSION}.tar.gz \
+  # Fix GLwDrawA per https://github.com/afni/afni/blob/AFNI_23.1.10/src/other_builds/OS_notes.linux_fedora_25_64.txt
+  && cd /usr/include/GL \
+  && mv GLwDrawA.h GLwDrawA.h.orig \
+  && sed 's/GLAPI WidgetClass/extern GLAPI WidgetClass/' GLwDrawA.h.orig > GLwDrawA.h \
+  && cd /opt/afni/src \
+  && sed '/^INSTALLDIR =/c INSTALLDIR = /opt/afni' other_builds/Makefile.linux_ubuntu_22_64 > Makefile \
+  && make vastness && make cleanest \
+  && cd /opt/afni \
+  && VERSION_STRING=$(afni --version) \
+  && VERSION_NAME=$(echo $VERSION_STRING | awk -F"'" '{print $2}') \
+  # filter down to required packages
+  && ls > full_ls \
+  && sed 's/linux_openmp_64\///g' /opt/required_afni_pkgs.txt | sort > required_ls \
+  && grep -qxF '3dWarp' full_ls || echo '3dWarp' >> required_ls \
+  && comm -2 -3 full_ls required_ls | xargs rm -rf \
+  # get rid of stuff we just needed for building
+  && apt-get remove -y \
+  bzip2 \
+  cmake \
+  curl \
+  dh-autoreconf \
+  evince \
+  firefox \
+  gedit \
+  git \
+  gnome-terminal \
+  gnome-tweaks \
+  libglw1-mesa-dev \
+  m4 \
+  ninja-build \
+  openssh-client \
+  unzip \
+  wget \
+  xterm \
+  && ldconfig \
+  && rm -rf /opt/afni/src
 
 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/* /root/.cache/*
+  && apt-get autoremove -y \
+  && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/*
 
 FROM scratch
 LABEL org.opencontainers.image.description="NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
-AFNI ${AFNI_VERSION} (${VERSION_NAME}) stage"
+  AFNI ${AFNI_VERSION} (${VERSION_NAME}) 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 /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/

.github/Dockerfiles/base-lite.Dockerfile

@@ -23,7 +23,7 @@ FROM ghcr.io/fcp-indi/c-pac/ica-aroma:0.4.4-beta-jammy as ICA-AROMA
 
 FROM ghcr.io/fcp-indi/c-pac/ubuntu:jammy-non-free
 LABEL org.opencontainers.image.description="NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
-Standard software dependencies for C-PAC standard and lite images"
+    Standard software dependencies for C-PAC standard and lite images"
 LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/C-PAC
 USER root
 
@@ -56,10 +56,10 @@ COPY --from=FSL /usr/share/fsl /usr/share/fsl
 # Installing C-PAC dependencies
 COPY requirements.txt /opt/requirements.txt
 RUN mamba install git -y \
-  && pip install -r /opt/requirements.txt \
-  && rm -rf /opt/requirements.txt \
-  && yes | mamba clean --all \
-  && rm -rf /usr/share/fsl/6.0/pkgs/cache/*
+    && pip install -r /opt/requirements.txt \
+    && rm -rf /opt/requirements.txt \
+    && yes | mamba clean --all \
+    && rm -rf /usr/share/fsl/6.0/pkgs/cache/*
 
 # Installing and setting up c3d
 COPY --from=c3d /opt/c3d/ opt/c3d/

CHANGELOG.md

@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - New resource `desc-head_bold` as non skull-stripped bold from nodeblock `bold_masking`.
 - `censor_file_path` from `offending_timepoints_connector` in the `build_nuisance_regressor` node.
 - Switch `sink_native_transforms` under `registration_workflows` to output all `.mat` files in ANTs and FSL Transforms.
+- `deoblique` field in pipeline config with `warp` and `refit` options to apply `3dWarp` or `3drefit` during data initialization.
 
 ### Changed