⏪ Revert pipeline configs to develop

Author: shnizzedy

CPAC/resources/configs/pipeline_config_abcd-options.yml

@@ -6,13 +6,14 @@
 # http://fcp-indi.github.io for more info.
 #
 # Tip: This file can be edited manually with a text editor for quick modifications.
+
 FROM: fmriprep-options
 
-pipeline_setup:
 
+pipeline_setup: 
   # Name for this pipeline configuration - useful for identification.
-  # This string will be sanitized and used in filepaths
   pipeline_name: cpac_fx-options
+
   output_directory:
 
     # Quality control outputs
@@ -21,41 +22,62 @@ pipeline_setup:
       # Generate eXtensible Connectivity Pipeline-style quality control files
       generate_xcpqc_files: On
 
-nuisance_corrections:
-  2-nuisance_regression:
-
+nuisance_corrections: 
+  2-nuisance_regression: 
     # this is a fork point
     #   run: [On, Off] - this will run both and fork the pipeline
     run: [On]
 
+    # switch to Off if nuisance regression is off and you don't want to write out the regressors
+    create_regressors: On
+
     # Select which nuisance signal corrections to apply
     Regressors:
       - Name: Regressor-1
         Bandpass:
           bottom_frequency: 0.01
           top_frequency: 0.08
         CerebrospinalFluid:
-          erode_mask: Off
+          erode_mask: false
           extraction_resolution: 2
-          include_delayed: On
-          include_delayed_squared: On
-          include_squared: On
+          include_delayed: true
+          include_delayed_squared: true
+          include_squared: true
           summary: Mean
         GlobalSignal:
-          include_delayed: On
-          include_delayed_squared: On
-          include_squared: On
+          include_delayed: true
+          include_delayed_squared: true
+          include_squared: true
           summary: Mean
         Motion:
-          include_delayed: On
-          include_delayed_squared: On
-          include_squared: On
+          include_delayed: true
+          include_delayed_squared: true
+          include_squared: true
         WhiteMatter:
-          erode_mask: Off
+          erode_mask: false
           extraction_resolution: 2
-          include_delayed: On
-          include_delayed_squared: On
-          include_squared: On
+          include_delayed: true
+          include_delayed_squared: true
+          include_squared: true
           summary: Mean
-        PolyOrt:
+        PolyOrt: 
           degree: 2
+
+    # Standard Lateral Ventricles Binary Mask
+    # used in CSF mask refinement for CSF signal-related regressions
+    lateral_ventricles_mask: 
+    # Process and refine masks used to produce regressors and time series for
+    # regression.
+    regressor_masks: 
+      erode_anatomical_brain_mask: 
+        # Erode binarized anatomical brain mask. If choosing True, please also set seg_csf_use_erosion: True; regOption: niworkflows-ants.
+        run: On
+
+      erode_csf: 
+        # Erode binarized csf tissue mask.
+        run: On
+
+      erode_wm: 
+        # Erode WM binarized tissue mask.
+        run: On
+