fix: participant_labels is None error / better location for config file

Author: oesteban

fmriprep/cli/parser.py

@@ -389,8 +389,12 @@ def parse_args(args=None, namespace=None):
 
     # First check that bids_dir looks like a BIDS folder
     config.init_layout()
+    all_subjects = config.execution.layout.get_subjects()
+    if config.execution.participant_label is None:
+        config.execution.participant_label = all_subjects
+
     participant_label = set(config.execution.participant_label)
-    missing_subjects = participant_label - set(config.execution.layout.get_subjects())
+    missing_subjects = participant_label - set(all_subjects)
     if missing_subjects:
         config.loggers.cli.error(
             "One or more participant labels were not found in the BIDS directory: "

fmriprep/cli/workflow.py

@@ -27,13 +27,14 @@ def build_workflow(config_file, retval):
     retval['return_code'] = 1
     retval['workflow'] = None
 
-    # warn if older results exist
+    # warn if older results exist: check for dataset_description.json in output folder
     msg = check_pipeline_version(
         version, output_dir / 'fmriprep' / 'dataset_description.json'
     )
     if msg is not None:
         build_log.warning(msg)
 
+    # Please note this is the input folder's dataset_description.json
     dset_desc_path = config.execution.bids_dir / 'dataset_description.json'
     if dset_desc_path.exists():
         from hashlib import sha256

fmriprep/workflows/base.py

@@ -86,6 +86,12 @@ def init_fmriprep_wf():
         else:
             fmriprep_wf.add_nodes([single_subject_wf])
 
+        # Dump a copy of the config file into the log directory
+        log_dir = config.execution.output_dir / 'fmriprep' / 'sub-{}'.format(subject_id) \
+            / 'log' / config.execution.run_uuid
+        log_dir.mkdir(exist_ok=True, parents=True)
+        config.to_filename(log_dir / 'fmriprep.toml')
+
     return fmriprep_wf
 
 
@@ -294,19 +300,11 @@ def init_single_subject_wf(subject_id):
               ('outputnode.t1w2fsnative_xfm', 'inputnode.t1w2fsnative_xfm'),
               ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm')]),
         ])
-
-    # Dump a copy of the config file into the log directory
-    log_dir = config.execution.output_dir / 'fmriprep' / 'sub-{}'.format(subject_id) \
-        / 'log' / config.execution.run_uuid
-    log_dir.mkdir(exist_ok=True, parents=True)
-    config.to_filename(log_dir / 'fmriprep.toml')
     return workflow
 
 
 def _prefix(subid):
-    if subid.startswith('sub-'):
-        return subid
-    return '-'.join(('sub', subid))
+    return '-'.join(('sub', subid.lstrip('sub-')))
 
 
 def _pop(inlist):