docs, fixes

Author: bpinsard

fmriprep/cli/run.py

@@ -83,8 +83,11 @@ def get_parser():
     # Re-enable when option is actually implemented
     # g_bids.add_argument('-r', '--run-id', action='store', default='single_run',
     #                     help='select a specific run to be processed')
-    g_bids.add_argument('--bids-filters', action='store', type=Path,
-                        help='the path to a JSON file describing custom BIDS input filter')
+    g_bids.add_argument(
+        '--bids-filters', action='store', type=Path,
+        help='the path to a JSON file describing custom BIDS input filter'
+             ' using pybids {<suffix>:{<entity>:<filter>,...},...} '
+             '(https://github.com/bids-standard/pybids/blob/master/bids/layout/config/bids.json)')
     g_bids.add_argument('-t', '--task-id', action='store',
                         help='select a specific task to be processed')
     g_bids.add_argument('--echo-idx', action='store', type=int,

fmriprep/workflows/base.py

@@ -208,6 +208,9 @@ def init_fmriprep_wf(
             If fieldmaps are present and enabled, this is not run, by default.
         work_dir : str
             Directory in which to store workflow execution state and temporary files
+        bids_filters : dict
+            Provides finer specification of the pipeline input files using pybids entities filters.
+            A dict with the following structure {<suffix>:{<entity>:<filter>,...},...}
 
     """
     fmriprep_wf = Workflow(name='fmriprep_wf')
@@ -455,7 +458,8 @@ def init_single_subject_wf(
             **Experimental**: Enable ANTs SyN-based susceptibility distortion correction (SDC).
             If fieldmaps are present and enabled, this is not run, by default.
         bids_filters : dict
-            For BIDSDataGrabber output_query
+            Provides finer specification of the pipeline input files using pybids entities filters.
+            A dict with the following structure {<suffix>:{<entity>:<filter>,...},...}
 
     Inputs