Fix/restore brain intensity abcd

CHANGELOG.md

@@ -44,6 +44,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - `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`.
 - Turned `generate_xcpqc_files` on for all preconfigurations except `blank`.
+- Introduced specific switch `restore_t1w_intensity` 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", "restore_t1w_intensity"],
+    switch=["run"],
     inputs=[
         (
             "desc-preproc_T1w",

CPAC/pipeline/schema.py

@@ -639,6 +639,9 @@ def sanitize(filename):
                 },
                 "FreeSurfer-BET": {"T1w_brain_template_mask_ccs": Maybe(str)},
             },
+            "restore_t1w_intensity": {
+                "run": bool1_1,
+            },
         },
         "segmentation": {
             "run": bool1_1,

CPAC/resources/configs/pipeline_config_abcd-options.yml

@@ -84,6 +84,9 @@ anatomical_preproc:
     # this is a fork option
     using: [FreeSurfer-ABCD]
 
+  restore_t1w_intensity:
+    run: 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
 
+  restore_t1w_intensity:
+    run: 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
 
+  restore_t1w_intensity:
+    run: Off
+
 
 segmentation: