Use unique_labels.

fmriprep/cli/run.py

@@ -220,16 +220,10 @@ def main():
 
         from fmriprep.reports.core import generate_reports
 
-        # Generate reports phase
-        session_list = (
-            config.execution.get().get('bids_filters', {}).get('bold', {}).get('session')
-        )
-
         failed_reports = generate_reports(
-            config.execution.participant_label,
+            config.execution.unique_labels,
             config.execution.fmriprep_dir,
             config.execution.run_uuid,
-            session_list=session_list,
         )
         write_derivative_description(
             config.execution.bids_dir,

fmriprep/cli/workflow.py

@@ -77,25 +77,17 @@ def build_workflow(config_file, retval):
         desc_content = dset_desc_path.read_bytes()
         config.execution.bids_description_hash = sha256(desc_content).hexdigest()
 
-    # First check that bids_dir looks like a BIDS folder
-    subject_list = collect_participants(
-        config.execution.layout, participant_label=config.execution.participant_label
-    )
-
     # Called with reports only
     if config.execution.reports_only:
-        build_log.log(25, 'Running --reports-only on participants %s', ', '.join(subject_list))
-        session_list = (
-            config.execution.bids_filters.get('bold', {}).get('session')
-            if config.execution.bids_filters
-            else None
+        build_log.log(
+            25,
+            'Running --reports-only on participants %s',
+            ', '.join(config.execution.unique_labels),
         )
-
         failed_reports = generate_reports(
-            config.execution.participant_label,
+            config.execution.unique_labels,
             config.execution.fmriprep_dir,
             config.execution.run_uuid,
-            session_list=session_list,
         )
         if failed_reports:
             config.loggers.cli.error(
@@ -110,7 +102,7 @@ def build_workflow(config_file, retval):
     init_msg = [
         "Building fMRIPrep's workflow:",
         f'BIDS dataset path: {config.execution.bids_dir}.',
-        f'Participant list: {subject_list}.',
+        f'Participant list: {config.execution.unique_labels}.',
         f'Run identifier: {config.execution.run_uuid}.',
         f'Output spaces: {config.execution.output_spaces}.',
     ]
@@ -123,7 +115,7 @@ def build_workflow(config_file, retval):
 
     build_log.log(25, f"\n{' ' * 11}* ".join(init_msg))
 
-    retval['workflow'] = init_fmriprep_wf()
+    retval['workflow'] = init_fmriprep_wf(config.execution.unique_labels)
 
     # Check for FS license after building the workflow
     if not check_valid_fs_license():

fmriprep/config.py

@@ -441,6 +441,8 @@ class execution(_Config):
     """Select a particular task from all available in the dataset."""
     templateflow_home = _templateflow_home
     """The root folder of the TemplateFlow client."""
+    unique_labels = None
+    """Combinations of subject + session identifiers to be preprocessed."""
     work_dir = Path('work').absolute()
     """Path to a working directory where intermediate results will be available."""
     write_graph = False
@@ -468,6 +470,12 @@ class execution(_Config):
     @classmethod
     def init(cls):
         """Create a new BIDS Layout accessible with :attr:`~execution.layout`."""
+        # Convert string literal None to NoneType
+        if cls.unique_labels:
+            cls.unique_labels = [
+                [sub, ses] if ses != 'None' else [sub, None] for sub, ses in cls.unique_labels
+            ]
+
         if cls.fs_license_file and Path(cls.fs_license_file).is_file():
             os.environ['FS_LICENSE'] = str(cls.fs_license_file)