adding changes suggested

Author: birajstha

CHANGELOG.md

@@ -24,7 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Required positional parameter "wf" in input and output of `ingress_pipeconfig_paths` function, where a node to reorient templates is added to the `wf`.
 - Required positional parameter "orientation" to `resolve_resolution`.
 - Optional positional argument "cfg" to `create_lesion_preproc`.
-- New switch `mask_sbref` under `func_input_prep` in functional registration.
+- New switch `mask_sbref` under `func_input_prep` in functional registration and set to default `on`.
 - New resource `desc-head_bold` as non skull-stripped bold from nodeblock `bold_masking`.
 
 ### Changed
@@ -57,7 +57,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - as output from FNIRT registration.
   - as inputs from Nodeblocks requesting it and, replaced with `space-template_desc-brain_mask`.
   - from outputs tsv.
-
+- Inputs `[desc-motion_bold, bold]` from `coregistration_prep_vol` nodeblock.
+- `input` field from `coregistration` in blank and default config.
+- `reg_with_skull` swtich from `func_input_prep` in blank and default config.
 
 ## [1.8.7] - 2024-05-03
 

CPAC/pipeline/cpac_pipeline.py

@@ -1288,8 +1288,8 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None):
                 coregistration_prep_vol,
                 coregistration_prep_mean,
                 coregistration_prep_fmriprep,
-                mask_sbref,
             ],
+            mask_sbref,
         ]
 
         # Distortion/Susceptibility Correction

CPAC/pipeline/schema.py

@@ -725,12 +725,10 @@ def sanitize(filename):
                     "reference": In({"brain", "restore-brain"}),
                     "interpolation": In({"trilinear", "sinc", "spline"}),
                     "using": str,
-                    "input": str,
                     "cost": str,
                     "dof": int,
                     "arguments": Maybe(str),
                     "func_input_prep": {
-                        "reg_with_skull": bool1_1,
                         "input": [
                             In(
                                 {

CPAC/registration/registration.py

@@ -3167,7 +3167,7 @@ def mask_sbref(wf, cfg, strat_pool, pipe_num, opt=None):
         "input",
     ],
     option_val="Selected_Functional_Volume",
-    inputs=[("desc-preproc_bold", ["desc-head_bold", "bold"], "sbref")],
+    inputs=[("desc-preproc_bold", "sbref")],
     outputs=["sbref"],
 )
 def coregistration_prep_vol(wf, cfg, strat_pool, pipe_num, opt=None):
@@ -3182,14 +3182,7 @@ def coregistration_prep_vol(wf, cfg, strat_pool, pipe_num, opt=None):
         outputtype="NIFTI_GZ",
     )
 
-    if not cfg.registration_workflows["functional_registration"]["coregistration"][
-        "func_input_prep"
-    ]["reg_with_skull"]:
-        node, out = strat_pool.get_data("desc-preproc_bold")
-    else:
-        # TODO check which file is functional_skull_leaf
-        # TODO add a function to choose brain or skull?
-        node, out = strat_pool.get_data(["desc-head_bold", "bold"])
+    node, out = strat_pool.get_data("desc-preproc_bold")
 
     wf.connect(node, out, get_func_volume, "in_file_a")
 

CPAC/resources/configs/pipeline_config_abcd-options.yml

@@ -199,9 +199,6 @@ registration_workflows:
       run: On
       func_input_prep:
 
-        # Choose whether to use functional brain or skull as the input to functional-to-anatomical registration
-        reg_with_skull: On
-
         # Choose whether to use the mean of the functional/EPI as the input to functional-to-anatomical registration or one of the volumes from the functional 4D timeseries that you choose.
         # input: ['Mean_Functional', 'Selected_Functional_Volume', 'fmriprep_reference']
         input: [Selected_Functional_Volume]

CPAC/resources/configs/pipeline_config_blank.yml

@@ -706,9 +706,6 @@ registration_workflows:
       run: Off
       func_input_prep:
 
-        # Choose whether to use functional brain or skull as the input to functional-to-anatomical registration
-        reg_with_skull: Off
-
         # Choose whether to use the mean of the functional/EPI as the input to functional-to-anatomical registration or one of the volumes from the functional 4D timeseries that you choose.
         # input: ['Mean_Functional', 'Selected_Functional_Volume', 'fmriprep_reference']
         input: [Mean_Functional]
@@ -724,8 +721,8 @@ registration_workflows:
           #Input the index of which volume from the functional 4D timeseries input file you wish to use as the input for functional-to-anatomical registration.
           func_reg_input_volume: 0
 
-        # Independent of the above `reg_with_skull` option
-        mask_sbref: Off
+        # Mask the sbref created by coregistration input prep nodeblocks above before registration
+        mask_sbref: On
 
       boundary_based_registration:
 
@@ -755,8 +752,7 @@ registration_workflows:
       # Choose FSL or ABCD as coregistration method
       using: FSL
 
-      # Choose brain or whole-head as coregistration input
-      input: brain
+      #TODO Add input field here to choose between whole head or brain
 
       # Choose coregistration interpolation
       interpolation: trilinear

CPAC/resources/configs/pipeline_config_default.yml

@@ -766,8 +766,7 @@ registration_workflows:
       # Choose FSL or ABCD as coregistration method
       using: FSL
 
-      # Choose brain or whole-head as coregistration input
-      input: brain
+      #TODO Add input field here to choose between whole head or brain
 
       # Choose coregistration interpolation
       interpolation: trilinear
@@ -783,9 +782,6 @@ registration_workflows:
 
       func_input_prep:
 
-        # Choose whether to use functional brain or skull as the input to functional-to-anatomical registration
-        reg_with_skull: Off
-
         # Choose whether to use the mean of the functional/EPI as the input to functional-to-anatomical registration or one of the volumes from the functional 4D timeseries that you choose.
         # input: ['Mean_Functional', 'Selected_Functional_Volume', 'fmriprep_reference']
         input: ['Mean_Functional']
@@ -802,6 +798,9 @@ registration_workflows:
           #Input the index of which volume from the functional 4D timeseries input file you wish to use as the input for functional-to-anatomical registration.
           func_reg_input_volume: 0
 
+        # Mask the sbref created by coregistration input prep nodeblocks above before registration
+        mask_sbref: On
+
       boundary_based_registration:
         # this is a fork point
         #   run: [On, Off] - this will run both and fork the pipeline