C88N refactoring (#116)

* [REFAC] make C88N conform with the Pipeline class + PEP8 clean * [BUG] typo in dir names * [TEST] making paths consistent in pipeline test execution [skip ci] * Using the right contrast ids * Using the right contrast ids * [BUG] in ci script for pipeline changes * [BUG] correctly forming results download link * Allowing to tweak the number of processes the runner uses * [ENH] Allowing to run group and subject level independantly * [TEST] test the runner launching first level or second level only * [DOC] runner : allow to run levels separately * [BUG] inside unit_tests workflow * Pipeline refac after merge * Refac pipeline * [TEST] rewrite test file + bugs in pipeline file * Codespell * [REFAC] C88N [skip ci] * [REFAC] using narps_open.core for contrast files selection [TEST] updates [skip ci] * Issue with base directory [skip ci] * Back to the right order of contrasts [skip ci] * [REFAC] naming [skip ci] * Issue with groupComp [skip ci] * [BUG] subject ids in search patterns [skip ci] * Remove unwanted graphs[skip ci]
Inria-Empenn · Jan 4, 2024 · 94cf9cb · 94cf9cb
1 parent 27b567e
commit 94cf9cb
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Showing 5 changed files with 786 additions and 577 deletions.
diff --git a/narps_open/pipelines/__init__.py b/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,

diff --git a/narps_open/pipelines/team_2T6S.py b/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')