DOCKER: Revert convert3d to tarball installation

Dockerfile

@@ -88,6 +88,15 @@ 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 \
+    --exclude "c3d-1.4.0-Linux-x86_64/lib" \
+    --exclude "c3d-1.4.0-Linux-x86_64/share" \
+    --exclude "c3d-1.4.0-Linux-x86_64/bin/c3d_gui"
+
 # Micromamba
 FROM downloader as micromamba
 WORKDIR /
@@ -168,6 +177,7 @@ RUN apt-get update -qq \
 COPY --from=freesurfer /opt/freesurfer /opt/freesurfer
 COPY --from=afni /opt/afni-latest /opt/afni-latest
 COPY --from=workbench /opt/workbench /opt/workbench
+COPY --from=c3d /opt/convert3d /opt/convert3d
 
 # Simulate SetUpFreeSurfer.sh
 ENV OS="Linux" \

env.yml

@@ -23,9 +23,6 @@ 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)