Merge pull request #229 from chrisfilo/fix/manual_workflow_type

[RTM] manual workflow type and missing T1ws error

fmriprep/run_workflow.py

@@ -52,10 +52,9 @@ def main():
                          help='nipype plugin configuration file')
     g_input.add_argument('-w', '--work-dir', action='store',
                          default=op.join(os.getcwd(), 'work'))
-    g_input.add_argument('-t', '--workflow-type', default='ds005', required=False,
-                         action='store', choices=['ds005', 'ds054', 'HPC', 'spiral'],
-                         help='''workflow type, a monkeypatch while it is not 
-                         automatically identified''')
+    g_input.add_argument('-t', '--workflow-type', default='auto', required=False,
+                         action='store', choices=['auto', 'ds005', 'ds054'],
+                         help='specify workflow type manually')
 
     # ANTs options
     g_ants = parser.add_argument_group('specific settings for ANTs registrations')
@@ -88,7 +87,8 @@ def create_workflow(opts):
         'ants_nthreads': opts.ants_nthreads,
         'skull_strip_ants': opts.skull_strip_ants,
         'output_dir': op.abspath(opts.output_dir),
-        'work_dir': op.abspath(opts.work_dir)
+        'work_dir': op.abspath(opts.work_dir),
+        'workflow_type': opts.workflow_type
     }
 
     # set up logger

fmriprep/workflows/base.py

@@ -39,11 +39,16 @@ def base_workflow_generator(subject_id, settings):
 
     settings["biggest_epi_file_size_gb"] = get_biggest_epi_file_size_gb(subject_data['func'])
 
-    if subject_data['t1w'] != [] and subject_data['sbref'] != []:
+    if subject_data['t1w'] == []:
+        raise Exception("No T1w images found for participant %s. All workflows require T1w images."%subject_id)
+
+    if subject_data['sbref'] != [] or settings['workflow_type'] == "ds054":
         return wf_ds054_type(subject_data, settings, name=subject_id)
-    if subject_data['t1w'] != [] and subject_data['sbref'] == []:
+    elif subject_data['sbref'] == [] or settings['workflow_type'] == "ds005":
         return wf_ds005_type(subject_data, settings, name=subject_id)
-    return None
+    else:
+        raise Exception("Could not figure out what kind of workflow to run for this dataset.")
+
 
 
 def wf_ds054_type(subject_data, settings, name='fMRI_prep'):