ENH: Enable users to pass JSON filters to select subsets of data

fmriprep/cli/run.py

@@ -13,6 +13,7 @@
 import gc
 import uuid
 import warnings
+import json
 from argparse import ArgumentParser
 from argparse import ArgumentDefaultsHelpFormatter
 from multiprocessing import cpu_count
@@ -81,6 +82,8 @@ 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('-t', '--task-id', action='store',
                         help='select a specific task to be processed')
     g_bids.add_argument('--echo-idx', action='store', type=int,
@@ -522,6 +525,8 @@ def build_workflow(opts, retval):
     bids_dir = opts.bids_dir.resolve()
     output_dir = opts.output_dir.resolve()
     work_dir = opts.work_dir.resolve()
+    bids_filters = json.loads(opts.bids_filters.read_text()) \
+        if opts.bids_filters else None
 
     retval['return_code'] = 1
     retval['workflow'] = None
@@ -672,6 +677,7 @@ def build_workflow(opts, retval):
         use_bbr=opts.use_bbr,
         use_syn=opts.use_syn_sdc,
         work_dir=str(work_dir),
+        bids_filters=bids_filters,
     )
     retval['return_code'] = 0
 

fmriprep/workflows/base.py

@@ -69,6 +69,7 @@ def init_fmriprep_wf(
     use_bbr,
     use_syn,
     work_dir,
+    bids_filters,
 ):
     """
     This workflow organizes the execution of FMRIPREP, with a sub-workflow for
@@ -123,6 +124,7 @@ def init_fmriprep_wf(
             use_bbr=True,
             use_syn=True,
             work_dir='.',
+            bids_filters=None,
         )
 
 
@@ -257,6 +259,7 @@ def init_fmriprep_wf(
             use_aroma=use_aroma,
             use_bbr=use_bbr,
             use_syn=use_syn,
+            bids_filters=bids_filters,
         )
 
         single_subject_wf.config['execution']['crashdump_dir'] = (
@@ -308,6 +311,7 @@ def init_single_subject_wf(
     use_aroma,
     use_bbr,
     use_syn,
+    bids_filters,
 ):
     """
     This workflow organizes the preprocessing pipeline for a single subject.
@@ -363,6 +367,7 @@ def init_single_subject_wf(
             use_aroma=False,
             use_bbr=True,
             use_syn=True,
+            bids_filters=None,
         )
 
 
@@ -449,7 +454,8 @@ def init_single_subject_wf(
         use_syn : bool
             **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
 
     Inputs
 
@@ -465,7 +471,7 @@ def init_single_subject_wf(
             'bold': ['/completely/made/up/path/sub-01_task-nback_bold.nii.gz']
         }
     else:
-        subject_data = collect_data(layout, subject_id, task_id, echo_idx)[0]
+        subject_data = collect_data(layout, subject_id, task_id, echo_idx, bids_filters=bids_filters)[0]
 
     # Make sure we always go through these two checks
     if not anat_only and subject_data['bold'] == []: