♻️ Just turn off FreeSurfer for surface if also on for brain extraction

Author: shnizzedy

CPAC/pipeline/cpac_pipeline.py

@@ -857,12 +857,7 @@ def build_anat_preproc_stack(rpool, cfg, pipeline_blocks=None):
         pipeline_blocks += anat_blocks
 
         if not rpool.check_rpool('freesurfer-subject-dir'):
-            if freesurfer_preproc in pipeline_blocks:
-                pipeline_blocks[
-                    pipeline_blocks.index(freesurfer_preproc)
-                ] = freesurfer_abcd_preproc
-            else:
-                pipeline_blocks += [freesurfer_abcd_preproc]
+            pipeline_blocks += [freesurfer_abcd_preproc]
 
     # Anatomical T1 brain masking
     if not rpool.check_rpool('space-T1w_desc-brain_mask') or \

CPAC/surface/tests/test_config.py

@@ -1,15 +1,26 @@
 """
 Tests for surface configuration
+"""
+import os
+import pkg_resources as p
+import pytest
+import yaml
+
+from CPAC.pipeline.cpac_pipeline import run_workflow
+from CPAC.utils.configuration import Configuration
+
+
+@pytest.mark.timeout(60)
+def test_duplicate_freesurfer():
+    """The pipeline should build fast if freesurfer is not self-duplicating"""
+    c = Configuration(yaml.safe_load('FROM: abcd-options'))
+    sub_dict = yaml.safe_load(open(p.resource_filename(
+        "CPAC",
+        os.path.join(
+            "resources",
+            "configs",
+            "data_config_S3-BIDS-ABIDE.yml"
+        )
+    ), 'r'))[0]
 
-FROM: abcd-options
-pipeline_setup:
-  pipeline_name: ABCD-blip
-  output_directory:
-    quality_control:
-      generate_xcpqc_files: On
-functional_preproc:
-  distortion_correction:
-    using:
-      - PhaseDiff
-      - Blip
-"""
+    run_workflow(sub_dict, c, False, test_config=True)

CPAC/utils/configuration.py

@@ -117,6 +117,15 @@ def __init__(self, config_map=None):
                     regressor['Name'] = f'Regressor-{str(i + 1)}'
                 # replace spaces with hyphens in Regressor 'Name's
                 regressor['Name'] = regressor['Name'].replace(' ', '-')
+
+        # Don't double-run FreeSurfer
+        try:
+            if 'FreeSurfer-ABCD' in config_map['anatomical_preproc'][
+                    'brain_extraction']['using']:
+                config_map['surface_analysis']['freesurfer']['run'] = False
+        except TypeError:
+            pass
+
         config_map = schema(config_map)
 
         # remove 'FROM' before setting attributes now that it's imported

dev/circleci_data/requirements.txt

@@ -4,5 +4,6 @@ spython >= 0.0.81
 pytest
 pytest_bdd
 pytest_click
+pytest-timeout
 pyyaml
 yamlordereddictloader

dev/docker_data/default_pipeline.yml

@@ -170,6 +170,7 @@ surface_analysis:
   # select those 'Freesurfer-' labeled options further below in anatomical_preproc.
   freesurfer: 
 
+    # If anatomical_preproc['brain_extraction']['using'] includes FreeSurfer-ABCD and this switch is On, C-PAC will automatically turn this switch Off to avoid running FreeSurfer twice unnecessarily
     run: Off
 
     # Add extra arguments to recon-all command