Merge remote-tracking branch 'upstream/master' into enh/gradunwarp

Author: cneuromod_bot

.circleci/config.yml

@@ -4,7 +4,7 @@ _machine_defaults: &machine_defaults
     TZ: "/usr/share/zoneinfo/America/Los_Angeles"
     SCRATCH: "/scratch"
   machine:
-    image: ubuntu-2204:current
+    image: ubuntu-2204:2023.04.2
     docker_layer_caching: true
   working_directory: /tmp/src/fmriprep
   resource_class: large
@@ -192,6 +192,8 @@ jobs:
                 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
                 --build-arg VCS_REF=`git rev-parse --short HEAD` \
                 --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" .
+      - run:
+          command: docker images
       - run:
           name: Check Docker image
           command: |

Dockerfile

@@ -41,6 +41,8 @@ RUN python -m build /src/fmriprep
 
 # Utilities for downloading packages
 FROM ${BASE_IMAGE} as downloader
+# Bump the date to current to refresh curl/certificates/etc
+RUN echo "2023.07.20"
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
                     binutils \
@@ -59,7 +61,7 @@ RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/frees
 # AFNI
 FROM downloader as afni
 # Bump the date to current to update AFNI
-RUN echo "2023.04.04"
+RUN echo "2023.07.20"
 RUN mkdir -p /opt/afni-latest \
     && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
     | tar -xz -C /opt/afni-latest --strip-components 1 \
@@ -77,13 +79,6 @@ RUN mkdir -p /opt/afni-latest \
         -name "3dAutomask" -or \
         -name "3dvolreg" \) -delete
 
-# ANTs 2.4.4
-FROM downloader as ants
-RUN mkdir -p /opt && \
-    curl -sSLO "https://github.com/ANTsX/ANTs/releases/download/v2.4.4/ants-2.4.4-ubuntu-22.04-X64-gcc.zip" && \
-    unzip ants-2.4.4-ubuntu-22.04-X64-gcc.zip -d /opt && \
-    rm ants-2.4.4-ubuntu-22.04-X64-gcc.zip
-
 # Connectome Workbench 1.5.0
 FROM downloader as workbench
 RUN mkdir /opt/workbench && \
@@ -93,6 +88,12 @@ RUN mkdir /opt/workbench && \
     rm -rf /opt/workbench/libs_linux64_software_opengl /opt/workbench/plugins_linux64 && \
     strip --remove-section=.note.ABI-tag /opt/workbench/libs_linux64/libQt5Core.so.5
 
+# Convert3d 1.4.0
+FROM downloader as c3d
+RUN mkdir /opt/convert3d && \
+    curl -fsSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/Experimental/c3d-1.4.0-Linux-gcc64.tar.gz/download \
+    | tar -xz -C /opt/convert3d --strip-components 1
+
 # Micromamba
 FROM downloader as micromamba
 WORKDIR /
@@ -172,8 +173,8 @@ RUN apt-get update -qq \
 # Install files from stages
 COPY --from=freesurfer /opt/freesurfer /opt/freesurfer
 COPY --from=afni /opt/afni-latest /opt/afni-latest
-COPY --from=ants /opt/ants-2.4.4 /opt/ants
 COPY --from=workbench /opt/workbench /opt/workbench
+COPY --from=c3d /opt/convert3d/bin/c3d_affine_tool /usr/bin/c3d_affine_tool
 
 # Simulate SetUpFreeSurfer.sh
 ENV OS="Linux" \
@@ -197,11 +198,6 @@ ENV PATH="/opt/afni-latest:$PATH" \
     AFNI_IMSAVE_WARNINGS="NO" \
     AFNI_PLUGINPATH="/opt/afni-latest"
 
-# ANTs config
-ENV ANTSPATH="/opt/ants" \
-    PATH="/opt/ants/bin:$PATH" \
-    LD_LIBRARY_PATH="/opt/ants/lib:$LD_LIBRARY_PATH"
-
 # Workbench config
 ENV PATH="/opt/workbench/bin_linux64:$PATH" \
     LD_LIBRARY_PATH="/opt/workbench/lib_linux64:$LD_LIBRARY_PATH"

env.yml

@@ -23,9 +23,8 @@ dependencies:
   # Utilities
   - graphviz=6.0
   - pandoc=3.1
-  # Workflow dependencies: Convert3D
-  - convert3d=1.3.0
-  - libitk=5.2  # 5.3 fails with c3d
+  # Workflow dependencies: ANTs
+  - ants=2.4.4
   # Workflow dependencies: FSL (versions pinned in 6.0.6.2)
   - fsl-bet2=2111.0
   - fsl-flirt=2111.0