Merge pull request #1654 from FCP-INDI/fix/double-recon-all

🐛 Don't run `recon-all` twice

Author: sgiavasis

CPAC/anat_preproc/anat_preproc.py

@@ -3188,7 +3188,7 @@ def correct_restore_brain_intensity_abcd(wf, cfg, strat_pool, pipe_num, opt=None
     wf.connect(node, out, merge_t1_acpc_to_list, 'in3')
 
     merge_t1_acpc = pe.Node(interface=fslMerge(),
-                            name='merge_t1_acpc')
+                            name=f'merge_t1_acpc_{pipe_num}')
 
     merge_t1_acpc.inputs.dimension = 't'
 

CPAC/surface/tests/test_config.py

@@ -0,0 +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]
+
+    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