Merge branch 'main' into documentation

narps_open/core/common.py

@@ -63,3 +63,24 @@ def list_intersection(list_1: list, list_2: list) -> list:
     - list, the intersection of list_1 and list_2
     """
     return [e for e in list_1 if e in list_2]
+
+def list_to_file(input_list: list, file_name: str = 'elements.tsv') -> str:
+    """
+    Create a tsv file containing elements of the input list.
+    This function is meant to be used in a Nipype Function Node.
+
+    Parameters :
+    - input_list: list
+
+    Returns:
+    - output_file: path to the created file
+    """
+    from os.path import abspath
+    output_file = abspath(file_name)
+
+    # Write un element per line
+    with open(output_file, 'w') as writer:
+        for element in input_list:
+            writer.write(f'{element}\n')
+
+    return output_file

narps_open/data/participants.py

@@ -51,9 +51,9 @@ def get_participants_subset(nb_participants: int = 108) -> list:
     return get_all_participants()[0:nb_participants]
 
 def get_group(group_name: str) -> list:
-    """ Return a list containing all the participants inside the group_name group
+    """ Return a list containing all the participants inside the group_name group """
 
-        Warning : the subject ids are return as written in the participants file (i.e.: 'sub-*')
-    """
     participants = get_participants_information()
-    return participants.loc[participants['group'] == group_name]['participant_id'].values.tolist()
+    group = participants.loc[participants['group'] == group_name]['participant_id'].values.tolist()
+
+    return [p.replace('sub-', '') for p in group]

narps_open/pipelines/__init__.py

@@ -8,7 +8,7 @@
 
 # List all the available pipelines and the corresponding class for each
 implemented_pipelines = {
-    '08MQ': None,
+    '08MQ': 'PipelineTeam08MQ',
     '0C7Q': None,
     '0ED6': None,
     '0H5E': None,
@@ -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')