Merge pull request #1788 from FCP-INDI/rbc-update

🔧 Base `rbc-options` on `fmriprep-options`' preproc

Author: sgiavasis

CHANGELOG.md

@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Moved default pipeline config into directory with other preconfigs
 - Added crash messages from during and before graph building to logs
 - Added data-config-specific hash string to C-PAC-generated config files
+- Updated `rbc-options` preconfig to use `fmriprep-options` preprocessing
 
 ### Fixed
 - Replaces ``DwellTime`` with ``EffectiveEchoSpacing`` for FSL usage of the term

CPAC/resources/configs/pipeline_config_rbc-options.yml

@@ -7,7 +7,7 @@
 #
 # Tip: This file can be edited manually with a text editor for quick modifications.
 
-FROM: fx-options
+FROM: fmriprep-options
 
 pipeline_setup:
   # Name for this pipeline configuration - useful for identification.
@@ -33,24 +33,12 @@ pipeline_setup:
     # This saves disk space, but any additional preprocessing or analysis will have to be completely re-run.
     remove_working_dir: On
 
-anatomical_preproc:
-  # N4 bias field correction via ANTs
-  n4_bias_field_correction:
-    # this is a fork option
-    run:
-      - On
-
 registration_workflows:
   anatomical_registration:
-    T1w_brain_template: /usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz
-    T1w_brain_template_mask: /usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
-    T1w_template: /usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
-
+    T1w_brain_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz
+    T1w_brain_template_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
+    T1w_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
   functional_registration:
-    coregistration:
-      func_input_prep:
-        input: [fmriprep_reference]
-
     func_registration_to_template:
       # these options modify the application (to the functional data), not the calculation, of the
       # T1-to-template and EPI-to-template transforms calculated earlier during registration
@@ -73,11 +61,10 @@ registration_workflows:
 
       target_template:
         T1_template:
-          T1w_brain_template_funcreg: /usr/share/fsl/5.0/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
-          T1w_brain_template_mask_funcreg: /usr/share/fsl/5.0/data/standard/MNI152_T1_${func_resolution}_brain_mask.nii.gz
-          T1w_template_for_resample: 
-          T1w_template_funcreg: /usr/share/fsl/5.0/data/standard/MNI152_T1_${func_resolution}.nii.gz
-
+          T1w_brain_template_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
+          T1w_brain_template_mask_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain_mask.nii.gz
+          T1w_template_for_resample: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
+          T1w_template_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}.nii.gz
 
 functional_preproc:
   truncation:
@@ -94,10 +81,6 @@ functional_preproc:
     run: 
       - On
 
-  motion_estimates_and_correction:
-    motion_correction:
-      using: [3dvolreg]
-
   distortion_correction:
     using:
        - PhaseDiff
@@ -186,7 +169,6 @@ nuisance_corrections:
         # CSF erosion default is using millimeter erosion method when use erosion for CSF.
         csf_mask_erosion_mm:
 
-
 timeseries_extraction:
   run: On
   connectivity_matrix: