FIX: Storing --bids-filters within config file

fmriprep/cli/parser.py

@@ -48,7 +48,8 @@ def _drop_sub(value):
 
     def _filter_pybids_none_any(dct):
         import bids
-        return {k: bids.layout.Query.ANY if v == "*" else v
+        return {k: bids.layout.Query.NONE if v is None else
+                (bids.layout.Query.ANY if v == "*" else v)
                 for k, v in dct.items()}
 
     def _bids_filter(value):

fmriprep/config.py

@@ -410,6 +410,13 @@ def init(cls):
                 ignore=("code", "stimuli", "sourcedata", "models",
                         "derivatives", re.compile(r'^\.')))
         cls.layout = cls._layout
+        if cls.bids_filters:
+            from bids.layout import Query
+            # unserialize pybids Query enum values
+            for acq, filters in cls.bids_filters.items():
+                cls.bids_filters[acq] = {
+                    k: getattr(Query, v[7:-4]) if not isinstance(v, Query) and 'Query' in v else v
+                    for k, v in filters.items()}
 
 
 # These variables are not necessary anymore

fmriprep/data/tests/config.toml

@@ -61,3 +61,9 @@ stop_on_first_crash = false
 [nipype.plugin_args]
 maxtasksperchild = 1
 raise_insufficient = false
+
+[execution.bids_filters.t1w]
+reconstruction = "<Query.NONE: 1>"
+
+[execution.bids_filters.t2w]
+reconstruction = "<Query.NONE: 1>"