🐛 RBC updates: Switch to MNI2006 templates & CBIG's Schaefer; fix XCP-QC 'final' values (#1737)

Author: shnizzedy

.github/workflows/build_stages.yml

@@ -59,6 +59,13 @@ jobs:
         with:
           since_last_remote_commit: "true"
           files: .github/Dockerfiles/*
+      - name: Set tag
+        run: |
+          TAG=$(sed 's/\./:/' <(echo ${{ matrix.Dockerfile }}))
+          DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}/$TAG" | tr '[:upper:]' '[:lower:]')
+          echo DOCKER_TAG=$DOCKER_TAG >> $GITHUB_ENV
+          docker manifest inspect $DOCKER_TAG >/dev/null
+          echo "::set-output name=not_yet_exists::$?"
       - name: Set up Docker Buildx
         uses: docker/[email protected]
         if: contains(steps.changed-files-base.outputs.all_changed_files, matrix.Dockerfile) || contains(steps.changed-files.outputs.all_changed_files, matrix.Dockerfile)
@@ -69,11 +76,6 @@ jobs:
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
         if: contains(steps.changed-files-base.outputs.all_changed_files, matrix.Dockerfile) || contains(steps.changed-files.outputs.all_changed_files, matrix.Dockerfile)
-      - name: Set tag
-        run: |
-          TAG=$(sed 's/\./:/' <(echo ${{ matrix.Dockerfile }}))
-          echo DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}/$TAG" | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
-        if: contains(steps.changed-files-base.outputs.all_changed_files, matrix.Dockerfile) || contains(steps.changed-files.outputs.all_changed_files, matrix.Dockerfile)
       - name: Build and push Docker image
         uses: docker/[email protected]
         with:
@@ -149,7 +151,10 @@ jobs:
       - name: Set tag
         run: |
           TAG=$(sed 's/\./:/' <(echo ${{ matrix.Dockerfile }}))
-          echo DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}/$TAG" | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
+          DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}/$TAG" | tr '[:upper:]' '[:lower:]')
+          echo DOCKER_TAG=$DOCKER_TAG >> $GITHUB_ENV
+          docker manifest inspect $DOCKER_TAG >/dev/null
+          echo "::set-output name=not_yet_exists::$?"
         if: contains(steps.changed-files-base.outputs.all_changed_files, matrix.Dockerfile) || contains(steps.changed-files.outputs.all_changed_files, matrix.Dockerfile)
       - name: Prep Dockerfiles for forked repository
         if: github.repository_owner != 'FCP-INDI' && contains(steps.changed-files-base.outputs.all_changed_files, matrix.Dockerfile) || contains(steps.changed-files.outputs.all_changed_files, matrix.Dockerfile)
@@ -216,36 +221,39 @@ jobs:
         since_last_remote_commit: "true"
         files_from_source_file: |
           .github/stage_requirements/${{ matrix.variant }}.txt
+    - name: Set tag
+      run: |
+        TAG="stage-base:${{ matrix.variant }}-$(cat version)"
+        DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}/$TAG" | tr '[:upper:]' '[:lower:]')
+        echo DOCKER_TAG=$DOCKER_TAG >> $GITHUB_ENV
+        docker manifest inspect $DOCKER_TAG >/dev/null
+        echo "::set-output name=not_yet_exists::$?"
+      id: docker_tag
     - name: Clear up some space on runner
-      if: steps.changed-files-base.outputs.any_changed == 'true' || steps.changed-files.outputs.any_changed == 'true'
+      if: steps.changed-files-base.outputs.any_changed == 'true' || steps.changed-files.outputs.any_changed == 'true' || steps.docker_tag.not_yet_exists == 1
       run: |
         sudo rm -rf /usr/share/dotnet
         sudo rm -rf /opt/ghc
         sudo rm -rf "/usr/local/share/boost"
         sudo rm -rf "$AGENT_TOOLSDIRECTORY"
     - name: Set up Docker Buildx
       uses: docker/[email protected]
-      if: steps.changed-files-base.outputs.any_changed == 'true' || steps.changed-files.outputs.any_changed == 'true'
+      if: steps.changed-files-base.outputs.any_changed == 'true' || steps.changed-files.outputs.any_changed == 'true' || steps.docker_tag.not_yet_exists == 1
     - name: Log in to GitHub Container Registry
       uses: docker/login-action@v1
       with:
         registry: ghcr.io
         username: ${{ github.actor }}
         password: ${{ secrets.GITHUB_TOKEN }}
-      if: steps.changed-files-base.outputs.any_changed == 'true' || steps.changed-files.outputs.any_changed == 'true'
-    - name: Set tag
-      run: |
-        TAG="stage-base:${{ matrix.variant }}-$(cat version)"
-        echo DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}/$TAG" | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
-      if: steps.changed-files-base.outputs.any_changed == 'true' || steps.changed-files.outputs.any_changed == 'true'
+      if: steps.changed-files-base.outputs.any_changed == 'true' || steps.changed-files.outputs.any_changed == 'true' || steps.docker_tag.not_yet_exists == 1
     - name: Prep Dockerfiles for forked repository
-      if: steps.changed-files-base.outputs.any_changed == 'true' || steps.changed-files.outputs.any_changed == 'true'
+      if: steps.changed-files-base.outputs.any_changed == 'true' || steps.changed-files.outputs.any_changed == 'true' || steps.docker_tag.not_yet_exists == 1
       run: |
           .github/scripts/local_ghcr .github/Dockerfiles/base-${{ matrix.variant }}.Dockerfile ${{ github.repository_owner }} $DOCKER_TAG
           cat .github/Dockerfiles/base-${{ matrix.variant }}.Dockerfile
     - name: See Dockerfile
       run: cat .github/Dockerfiles/base-${{ matrix.variant }}.Dockerfile
-      if: steps.changed-files-base.outputs.any_changed == 'true' || steps.changed-files.outputs.any_changed == 'true'
+      if: steps.changed-files-base.outputs.any_changed == 'true' || steps.changed-files.outputs.any_changed == 'true' || steps.docker_tag.not_yet_exists == 1
     - name: Build and push base image
       uses: docker/[email protected]
       with:
@@ -256,7 +264,7 @@ jobs:
           ${{ env.DOCKER_TAG }}
         cache-from: type=gha
         cache-to: type=gha,mode=max
-      if: steps.changed-files-base.outputs.any_changed == 'true' || steps.changed-files.outputs.any_changed == 'true'
+      if: steps.changed-files-base.outputs.any_changed == 'true' || steps.changed-files.outputs.any_changed == 'true' || steps.docker_tag.not_yet_exists == 1
 
   trigger-next-workflow:
     needs: build-base

CHANGELOG.md

@@ -44,6 +44,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fixed [bug](https://github.com/FCP-INDI/C-PAC/issues/1702) that was causing `single_step_resampling` to crash with `3dVolReg`
 - Fixed [bug](https://github.com/FCP-INDI/C-PAC/issues/1686) that was causing datasets containing phase-difference field maps to crash.
 - Fixed merge error preventing QC files and surface derivatives copying to output directory and renaming connectome → connectivity matrix files
+- Fixed some incorrect connections in XCP-QC file generation
 - Fixed a bug where subsequent subjects' logs were being appended to prior subjects' logs
 - Fixed templates used for rodent pipeline and added outputs that were missing
 - Fixed [bug](https://github.com/FCP-INDI/C-PAC/issues/1556) in which ITK header imprecision was causing N4 bias correction to crash

CPAC/func_preproc/func_preproc.py

@@ -1577,7 +1577,8 @@ def bold_mask_fsl_afni(wf, cfg, strat_pool, pipe_num, opt=None):
      "option_key": ["func_masking", "using"],
      "option_val": "FSL_AFNI",
      "inputs": [["desc-motion_bold", "desc-preproc_bold", "bold"],
-                 "motion-basefile"],
+                "motion-basefile", "FSL-AFNI-bold-ref", "FSL-AFNI-brain-mask",
+                "FSL-AFNI-brain-probseg"],
      "outputs": ["space-bold_desc-brain_mask",
                  "desc-ref_bold"]}
     '''
@@ -1598,12 +1599,11 @@ def bold_mask_fsl_afni(wf, cfg, strat_pool, pipe_num, opt=None):
         name=f"init_aff_{pipe_num}",
         n_procs=cfg.pipeline_setup['system_config']['num_OMP_threads'],
     )
+    node, out = strat_pool.get_data('FSL-AFNI-bold-ref')
+    wf.connect(node, out, init_aff, 'fixed_image')
 
-    init_aff.inputs.fixed_image = cfg.functional_preproc[
-        'func_masking']['FSL_AFNI']['bold_ref']
-
-    init_aff.inputs.fixed_image_mask = cfg.functional_preproc[
-        'func_masking']['FSL_AFNI']['brain_mask']
+    node, out = strat_pool.get_data('FSL-AFNI-brain-mask')
+    wf.connect(node, out, init_aff, 'fixed_image_mask')
 
     init_aff.inputs.search_grid = (40, (0, 40, 40))
 
@@ -1633,8 +1633,8 @@ def bold_mask_fsl_afni(wf, cfg, strat_pool, pipe_num, opt=None):
         n_procs=cfg.pipeline_setup['system_config']['num_OMP_threads'],
     )
 
-    norm.inputs.fixed_image = cfg.functional_preproc[
-        'func_masking']['FSL_AFNI']['bold_ref']
+    node, out = strat_pool.get_data('FSL-AFNI-bold-ref')
+    wf.connect(node, out, norm, 'fixed_image')
 
     map_brainmask = pe.Node(
         ants.ApplyTransforms(
@@ -1643,10 +1643,10 @@ def bold_mask_fsl_afni(wf, cfg, strat_pool, pipe_num, opt=None):
         ),
         name=f"map_brainmask_{pipe_num}",
     )
-    
+
     # Use the higher resolution and probseg for numerical stability in rounding
-    map_brainmask.inputs.input_image = cfg.functional_preproc[
-        'func_masking']['FSL_AFNI']['brain_probseg']
+    node, out = strat_pool.get_data('FSL-AFNI-brain-probseg')
+    wf.connect(node, out, map_brainmask, 'input_image')
 
     binarize_mask = pe.Node(interface=fsl.maths.MathsCommand(),
                             name=f'binarize_mask_{pipe_num}')

CPAC/pipeline/cpac_pipeline.py

@@ -273,7 +273,8 @@ def run_workflow(sub_dict, c, run, pipeline_timing_info=None, p_name=None,
     set_up_logger(f'{subject_id}_expectedOutputs',
                   filename=f'{bidsier_prefix(c["subject_id"])}_'
                            'expectedOutputs.yml',
-                  level='info', log_dir=log_dir, mock=True)
+                  level='info', log_dir=log_dir, mock=True,
+                  overwrite_existing=True)
     if c.pipeline_setup['Debugging']['verbose']:
         set_up_logger('engine', level='debug', log_dir=log_dir, mock=True)
 

CPAC/pipeline/schema.py

@@ -866,7 +866,7 @@ def _changes_1_8_0_to_1_8_1(config_dict):
             # functional_mean_boolean must be True if one of the mutually-
             # exclusive options are
             # see mutex definition for more definition
-            'FSL-BET': Any(*(
+            'FSL-BET': Maybe(Any(*(
                 # exactly one mutually exclusive option on
                 [{k: d[k] for d in r for k in d} for r in [[
                     {
@@ -881,15 +881,15 @@ def _changes_1_8_0_to_1_8_1(config_dict):
                     **mutex['FSL-BET']['rem'],
                     'functional_mean_boolean': bool,
                     **{k: False for k in mutex['FSL-BET']['mutex']}
-                }])
+                }]))
             ),
             'FSL_AFNI': {
                 'bold_ref': Maybe(str),
                 'brain_mask': Maybe(str),
                 'brain_probseg': Maybe(str),
             },
             'Anatomical_Refined': {
-                'anatomical_mask_dilation': bool,
+                'anatomical_mask_dilation': Maybe(bool),
             },
             'apply_func_mask_in_native_space': bool,
         },