Merge pull request #1931 from FCP-INDI/rm/monkey-ABCD

🔥 Remove `monkey-ABCD` tests for 1.8.5

Author: sgiavasis

.github/workflows/smoke_test_participant.yml

@@ -122,14 +122,6 @@ jobs:
           - ''
         participant:
           - 032102 032106 032164 032167 032130 032128 2215 2312 032191 032195
-        include:
-          # requires T2w
-          - preconfig: monkey-ABCD
-            variant: ''
-            participant: 032102 032106 032130 032128 032191 032195
-          - preconfig: monkey-ABCD
-            variant: ABCD-HCP
-            participant: 032102 032106 032130 032128 032191 032195
     steps:
       - name: Get C-PAC
         run: |

CPAC/pipeline/__init__.py

@@ -25,7 +25,8 @@
                         x in ALL_PIPELINE_CONFIGS if 'pipeline_config' in x]
 ALL_PIPELINE_CONFIGS.sort()
 AVAILABLE_PIPELINE_CONFIGS = [preconfig for preconfig in ALL_PIPELINE_CONFIGS
-                              if preconfig != 'benchmark-ANTS' and
+                              if preconfig not in
+                              ['benchmark-ANTS', 'monkey-ABCD'] and
                               not preconfig.startswith('regtest-')]
 
 

CPAC/resources/configs/pipeline_config_abcd-options.yml

@@ -32,12 +32,11 @@ surface_analysis:
   # If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
   # select those 'Freesurfer-' labeled options further below in anatomical_preproc.
   freesurfer:
+    run_reconall: On
 
     # Ingress freesurfer recon-all folder
     ingress_reconall: On
 
-    run_reconall: On
-
   # Run ABCD-HCP post FreeSurfer and fMRISurface pipeline
   post_freesurfer:
     run: On

CPAC/resources/configs/pipeline_config_anat-only.yml

@@ -203,15 +203,3 @@ network_centrality:
     # Sparsity value for Sparsity Threshold
     # Pearson's r value for Correlation Threshold
     correlation_threshold: 0.001
-
-# PREPROCESSING
-# -------------
-surface_analysis:
-
-  # Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
-  # If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
-  # select those 'Freesurfer-' labeled options further below in anatomical_preproc.
-  freesurfer:
-
-    # Ingress freesurfer recon-all folder
-    ingress_reconall: Off

CPAC/resources/configs/pipeline_config_benchmark-ANTS.yml

@@ -358,15 +358,3 @@ seed_based_correlation_analysis:
   #   /path/to/atlas.nii.gz: Avg, DualReg, MultReg
   sca_roi_paths:
     s3://fcp-indi/resources/cpac/resources/rois_2mm.nii.gz: Avg, MultReg
-
-# PREPROCESSING
-# -------------
-surface_analysis:
-
-  # Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
-  # If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
-  # select those 'Freesurfer-' labeled options further below in anatomical_preproc.
-  freesurfer:
-
-    # Ingress freesurfer recon-all folder
-    ingress_reconall: Off

CPAC/resources/configs/pipeline_config_benchmark-FNIRT.yml

@@ -382,15 +382,3 @@ seed_based_correlation_analysis:
   #   /path/to/atlas.nii.gz: Avg, DualReg, MultReg
   sca_roi_paths:
     s3://fcp-indi/resources/cpac/resources/rois_2mm.nii.gz: Avg, MultReg
-
-# PREPROCESSING
-# -------------
-surface_analysis:
-
-  # Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
-  # If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
-  # select those 'Freesurfer-' labeled options further below in anatomical_preproc.
-  freesurfer:
-
-    # Ingress freesurfer recon-all folder
-    ingress_reconall: Off

CPAC/resources/configs/pipeline_config_default-deprecated.yml

@@ -208,15 +208,3 @@ network_centrality:
 
   # Calculate Degree, Eigenvector Centrality, or Functional Connectivity Density.
   run: On
-
-# PREPROCESSING
-# -------------
-surface_analysis:
-
-  # Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
-  # If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
-  # select those 'Freesurfer-' labeled options further below in anatomical_preproc.
-  freesurfer:
-
-    # Ingress freesurfer recon-all folder
-    ingress_reconall: Off

CPAC/resources/configs/pipeline_config_fmriprep-options.yml

@@ -585,15 +585,3 @@ PyPEER:
 
   # Template-space eye mask
   eye_mask_path:
-
-# PREPROCESSING
-# -------------
-surface_analysis:
-
-  # Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
-  # If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
-  # select those 'Freesurfer-' labeled options further below in anatomical_preproc.
-  freesurfer:
-
-    # Ingress freesurfer recon-all folder
-    ingress_reconall: Off

CPAC/resources/configs/pipeline_config_fx-options.yml

@@ -59,15 +59,3 @@ nuisance_corrections:
           summary: Mean
         PolyOrt:
           degree: 2
-
-# PREPROCESSING
-# -------------
-surface_analysis:
-
-  # Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
-  # If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
-  # select those 'Freesurfer-' labeled options further below in anatomical_preproc.
-  freesurfer:
-
-    # Ingress freesurfer recon-all folder
-    ingress_reconall: Off

CPAC/resources/configs/pipeline_config_monkey-ABCD.yml

@@ -555,15 +555,3 @@ seed_based_correlation_analysis:
     /Template/DMN-Ghahremani2016/thr_bin_hjin/HRzstat_DMN_3_thr4.nii.gz: Avg
     s3://fcp-indi/resources/cpac/resources/parcellation/Markov91_L_0.5mm.nii.gz: Avg
     s3://fcp-indi/resources/cpac/resources/parcellation/Markov91_R_0.5mm.nii.gz: Avg
-
-# PREPROCESSING
-# -------------
-surface_analysis:
-
-  # Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
-  # If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
-  # select those 'Freesurfer-' labeled options further below in anatomical_preproc.
-  freesurfer:
-
-    # Ingress freesurfer recon-all folder
-    ingress_reconall: Off