Merge pull request #231 from chrisfilo/enh/task_id

[RTM] add an option to limit the analysis just to one task

fmriprep/run_workflow.py

@@ -41,6 +41,7 @@ def main():
     g_input = parser.add_argument_group('fMRIprep specific arguments')
     g_input.add_argument('-s', '--session-id', action='store', default='single_session')
     g_input.add_argument('-r', '--run-id', action='store', default='single_run')
+    g_input.add_argument('--task-id', help='limit the analysis only ot one task', action='store')
     g_input.add_argument('-d', '--data-type', action='store', choices=['anat', 'func'])
     g_input.add_argument('--debug', action='store_true', default=False,
                          help='run debug version of workflow')
@@ -150,7 +151,8 @@ def create_workflow(opts):
     logger.info('Subject list: %s', ', '.join(subject_list))
 
     # Build main workflow and run
-    preproc_wf = base_workflow_enumerator(subject_list, settings=settings)
+    preproc_wf = base_workflow_enumerator(subject_list, task_id=opts.task_id,
+                                          settings=settings)
     preproc_wf.base_dir = settings['work_dir']
     preproc_wf.run(**plugin_settings)
 

fmriprep/utils/misc.py

@@ -46,7 +46,7 @@ def is_fieldmap_file(string):
 }
 
 
-def collect_bids_data(dataset, subject, session=None, run=None):
+def collect_bids_data(dataset, subject, task=None, session=None, run=None):
     subject = str(subject)
     if subject.startswith('sub-'):
         subject = subject[4:]
@@ -74,6 +74,9 @@ def collect_bids_data(dataset, subject, session=None, run=None):
         't1w': {'type': 'T1w', 'ext': 'nii'}
     }
 
+    if task:
+        queries['epi']['task'] = task
+
     #  Add a subject key pair to each query we make so that we only deal with
     #  files related to this workflows specific subject. Could be made opt...
     for key in queries.keys():

fmriprep/workflows/base.py

@@ -22,20 +22,21 @@
     epi_mean_t1_registration, epi_mni_transformation)
 
 
-def base_workflow_enumerator(subject_list, settings):
+def base_workflow_enumerator(subject_list, task_id, settings):
     workflow = pe.Workflow(name='workflow_enumerator')
     generated_list = []
     for subject in subject_list:
-        generated_workflow = base_workflow_generator(subject, settings)
+        generated_workflow = base_workflow_generator(subject, task_id=task_id,
+                                                     settings=settings)
         if generated_workflow:
             generated_list.append(generated_workflow)
     workflow.add_nodes(generated_list)
 
     return workflow
 
 
-def base_workflow_generator(subject_id, settings):
-    subject_data = collect_bids_data(settings['bids_root'], subject_id)
+def base_workflow_generator(subject_id, task_id, settings):
+    subject_data = collect_bids_data(settings['bids_root'], subject_id, task_id)
 
     settings["biggest_epi_file_size_gb"] = get_biggest_epi_file_size_gb(subject_data['func'])