C88N refactoring

narps_open/pipelines/__init__.py

@@ -43,7 +43,7 @@
     'B23O': None,
     'B5I6': None,
     'C22U': None,
-    'C88N': None,
+    'C88N': 'PipelineTeamC88N',
     'DC61': None,
     'E3B6': None,
     'E6R3': None,

narps_open/pipelines/team_2T6S.py

@@ -502,6 +502,7 @@ def get_group_level_analysis_sub_workflow(self, method):
             height_threshold = 0.001, height_threshold_type = 'p-value',
             force_activation = True),
             name = 'threshold', iterfield = ['stat_image', 'contrast_index'])
+        threshold.synchronize = True
 
         l2_analysis = Workflow(
             base_dir = self.directories.working_dir,
@@ -512,7 +513,8 @@ def get_group_level_analysis_sub_workflow(self, method):
             (selectfiles_groupanalysis, sub_contrasts, [
                 ('contrast', 'file_list'),
                 ('participants', 'participants_file')]),
-            (estimate_model, estimate_contrast, [('spm_mat_file', 'spm_mat_file'),
+            (estimate_model, estimate_contrast, [
+                ('spm_mat_file', 'spm_mat_file'),
                 ('residual_image', 'residual_image'),
                 ('beta_images', 'beta_images')]),
             (estimate_contrast, threshold, [('spm_mat_file', 'spm_mat_file'),
@@ -528,11 +530,9 @@ def get_group_level_analysis_sub_workflow(self, method):
 
         if method in ('equalRange', 'equalIndifference'):
             contrasts = [('Group', 'T', ['mean'], [1]), ('Group', 'T', ['mean'], [-1])]
-
             threshold.inputs.contrast_index = [1, 2]
-            threshold.synchronize = True
 
-            ## Specify design matrix
+            # Specify design matrix
             one_sample_t_test_design = Node(OneSampleTTestDesign(),
                 name = 'one_sample_t_test_design')
 
@@ -543,11 +543,9 @@ def get_group_level_analysis_sub_workflow(self, method):
         elif method == 'groupComp':
             contrasts = [
                 ('Eq range vs Eq indiff in loss', 'T', ['Group_{1}', 'Group_{2}'], [-1, 1])]
-
             threshold.inputs.contrast_index = [1]
-            threshold.synchronize = True
 
-            # Node for the design matrix
+            # Specify design matrix
             two_sample_t_test_design = Node(TwoSampleTTestDesign(),
                 name = 'two_sample_t_test_design')