Fix the freesurfer build image (extract version from install_fs_pruned.sh)

Author: dkuegler

.github/actions/build-docker/action.yml

@@ -33,7 +33,7 @@ runs:
     - name: Set up Docker Buildx
       uses: docker/setup-buildx-action@v3
     - name: Recover freesurfer build image
-      if: ${{ startsWith( inputs.freesurfer-build-image, 'fastsurfer:') }}
+      if: ${{ contains( inputs.freesurfer-build-image, 'fastsurfer-build:freesurfer') }}
       uses: ./.github/actions/load-docker
       with:
         docker-image: ${{ inputs.freesurfer-build-image }}
@@ -46,18 +46,18 @@ runs:
       run: |
         echo "::group::Build FastSurfer Image"
         if [[ "${{ inputs.tag }}" != "auto" ]] ; then image_name="${{ inputs.tag }}" 
-        else v="$(bash $FASTSURFER_HOME/run_fastsurfer.sh --version)" ; image_name="fastsurfer:cpu-${v/+/_}" 
+        else v="$(bash "$FASTSURFER_HOME/run_fastsurfer.sh" --version)" ; image_name="fastsurfer:cpu-${v/+/_}" 
         fi
-        cmd="python $FASTSURFER_HOME/Docker/build.py --device cpu --tag $image_name --target ${{ inputs.target }}"
+        cmd=(python "$FASTSURFER_HOME/Docker/build.py" --device cpu --tag "$image_name" --target "${{ inputs.target }}")
         if [[ "${{ inputs.freesurfer-build-image }}" != "rebuild" ]] ; then 
-          cmd="$cmd --freesurfer_build_image ${{ inputs.freesurfer-build-image }}"
+          cmd+=(--freesurfer_build_image "${{ inputs.freesurfer-build-image }}")
         fi
-        $cmd
+        "${cmd[@]}"
         echo "::endgroup::"
         echo "::group::Save image as artifact"
         echo "IMAGE_NAME=$image_name" | tee /tmp/image_name.env >> $GITHUB_OUTPUT
         # Export image
-        docker save $image_name -o /tmp/docker-image.tar
+        docker save "$image_name" -o /tmp/docker-image.tar
     - name: Save docker image
       uses: actions/upload-artifact@v4
       with:

.github/workflows/quicktest.yaml

@@ -24,10 +24,12 @@ on:
   workflow_dispatch:
     inputs:
       docker-image:
-        name: 'Docker image to run with'
         description: 'Which docker image should be used to run this test (build-cached => build from git)'
         default: build-cached
         type: string
+      freesurfer_build_image:
+        description: 'FreeSurfer build image to build with'
+        type: string
 
 env:
   SUBJECTS_DIR: /tmp/subjects
@@ -99,13 +101,29 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+      - name: Get the FreeSurfer version
+        shell: bash
+        run: |
+          # get the FreeSurfer verson from install_fs_pruned.sh
+          {
+            eval "$(grep "^fslink=" ./Docker/install_fs_pruned.sh)"
+            fs_version="$(basename "$(dirname "$fslink")")"
+            fs_version_short="${fs_version//\./}"
+            echo "FS_VERSION=$fs_version"
+            echo "FS_VERSION_SHORT=$fs_version_short"
+            if [[ -n "${{ inputs.freesurfer_build_image }}" ]] ; then
+              echo "FS_BUILD_IMAGE=${{ inputs.freesurfer_build_image }}"
+            else
+              echo "FS_BUILD_IMAGE=deepmi/fastsurfer-build:freesurfer$fs_version_short"
+            fi
+          } > $GITHUB_ENV
       - uses: ./.github/actions/build-docker@dev
         # This action needs the "full" checkout (located at ${{ inputs.fastsurfer-home }})
         with:
           fastsurfer-home: .
           # currently, this image has to be updated and used to circumvent storage limitations in github actions
           # and it is also faster to use this prebuilt, reduced-size freesurfer distribution
-          freesurfer-build-image: dkuegler/fastsurfer:fs741-build-image
+          freesurfer-build-image: "${{ env.FS_BUILD_IMAGE }}"
   run-1mm:
     name: 'Run FastSurfer on the 1mm sample image'
     needs: build-docker-latest