adding specific switch for correct_restore_brain_intensity_abcd nodeblock

Author: birajstha

CHANGELOG.md

@@ -43,6 +43,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - Renamed `desc-ref_bold` created in this workflow to `desc-unifized_bold`.
   - `coregistration_prep_fmriprep` nodeblock now checks if `desc-unifized_bold` exists in the Resource Pool, if not it runs the `FSL-AFNI subworkflow` to create it.
 - Input `desc-brain_bold` to `desc-preproc_bold` for `sbref` generation nodeblock `coregistration_prep_vol`.
+- Introduced specific switch for `correct_restore_brain_intensity_abcd` nodeblock, enabling it by default only in `abcd-options` pre-config.
 
 ### Fixed
 

CPAC/anat_preproc/anat_preproc.py

@@ -3161,9 +3161,8 @@ def fast_bias_field_correction(config=None, wf_name="fast_bias_field_correction"
 
 @nodeblock(
     name="correct_restore_brain_intensity_abcd",
-    config=["anatomical_preproc", "brain_extraction"],
-    option_key="using",
-    option_val="FreeSurfer-ABCD",
+    config=["anatomical_preproc", "brain_extraction", "FreeSurfer-ABCD"],
+    switch=["correct_restore_brain_intensity_abcd"],
     inputs=[
         (
             "desc-preproc_T1w",

CPAC/pipeline/schema.py

@@ -638,6 +638,9 @@ def sanitize(filename):
                     "regmask_path": Maybe(str),
                 },
                 "FreeSurfer-BET": {"T1w_brain_template_mask_ccs": Maybe(str)},
+                "FreeSurfer-ABCD": {
+                    "correct_restore_brain_intensity_abcd": bool1_1,
+                },
             },
         },
         "segmentation": {

CPAC/resources/configs/pipeline_config_abcd-options.yml

@@ -80,6 +80,9 @@ anatomical_preproc:
     # this is a fork option
     using: [FreeSurfer-ABCD]
 
+    FreeSurfer-ABCD:
+      correct_restore_brain_intensity_abcd: On
+
   # Non-local means filtering via ANTs DenoiseImage
   non_local_means_filtering:
 

CPAC/resources/configs/pipeline_config_blank.yml

@@ -419,6 +419,9 @@ anatomical_preproc:
       # niworkflows-ants registration mask (can be optional)
       regmask_path: /ants_template/oasis/T_template0_BrainCerebellumRegistrationMask.nii.gz
 
+    FreeSurfer-ABCD:
+      correct_restore_brain_intensity_abcd: Off
+
   run_t2: Off
 
   # Bias field correction based on square root of T1w * T2w

CPAC/resources/configs/pipeline_config_default.yml

@@ -484,6 +484,9 @@ anatomical_preproc:
       # Template to be used for FreeSurfer-BET brain extraction in CCS-options pipeline
       T1w_brain_template_mask_ccs: /ccs_template/MNI152_T1_1mm_first_brain_mask.nii.gz
 
+    FreeSurfer-ABCD:
+      correct_restore_brain_intensity_abcd: Off
+
 
 segmentation: