Update BIDS data grabbing to grab only anatomical and PET data (no functional)

Author: mnoergaard

niworkflows/interfaces/bids.py

@@ -260,7 +260,7 @@ class BIDSDataGrabber(SimpleInterface):
 
     input_spec = _BIDSDataGrabberInputSpec
     output_spec = _BIDSDataGrabberOutputSpec
-    _require_funcs = True
+    _require_funcs = False
 
     def __init__(self, *args, **kwargs):
         anat_only = kwargs.pop('anat_only', None)
@@ -282,12 +282,7 @@ def _run_interface(self, runtime):
                 f'No T1w images found for subject sub-{self.inputs.subject_id}'
             )
 
-        if self._require_funcs and not bids_dict['bold']:
-            raise FileNotFoundError(
-                f'No functional images found for subject sub-{self.inputs.subject_id}'
-            )
-
-        for imtype in ['bold', 't2w', 'flair', 'fmap', 'sbref', 'roi', 'pet', 'asl']:
+        for imtype in ['t2w', 'flair', 'fmap', 'sbref', 'roi', 'pet', 'asl']:
             if not bids_dict[imtype]:
                 LOGGER.info('No "%s" images found for sub-%s', imtype, self.inputs.subject_id)
 

niworkflows/utils/bids.py

@@ -39,7 +39,7 @@
     'pet': {'suffix': 'pet'},
     'roi': {'datatype': 'anat', 'suffix': 'roi'},
     'sbref': {'datatype': 'func', 'suffix': 'sbref', 'part': ['mag', None]},
-    't1w': {'datatype': 'anat', 'suffix': 'T1w', 'part': ['mag', None]},
+    't1w': {'suffix': 'T1w'},
     't2w': {'datatype': 'anat', 'suffix': 'T2w', 'part': ['mag', None]},
     'asl': {'datatype': 'perf', 'suffix': 'asl'},
 }
@@ -236,8 +236,9 @@ def collect_data(
         'return_type': 'file',
         'subject': participant_label,
         'extension': ['.nii', '.nii.gz'],
-        'session': session_id or Query.OPTIONAL,
     }
+    if session_id is not None:
+        layout_get_kwargs['session'] = session_id
 
     queries = queries or DEFAULT_BIDS_QUERIES
     bids_filters = bids_filters or {}
@@ -248,20 +249,10 @@ def collect_data(
                 # avoid clobbering layout.get
                 del layout_get_kwargs[entity]
 
-    if task:
-        queries['bold']['task'] = task
-
-    if echo:
-        queries['bold']['echo'] = echo
-
     subj_data = {
         dtype: sorted(layout.get(**layout_get_kwargs, **query)) for dtype, query in queries.items()
     }
 
-    # Special case: multi-echo BOLD, grouping echos
-    if group_echos and 'bold' in subj_data and any('_echo-' in bold for bold in subj_data['bold']):
-        subj_data['bold'] = group_multiecho(subj_data['bold'])
-
     return subj_data, layout