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FIX: Ignore sourcedata and derivatives when fetching data #1788

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merged 1 commit into from
Sep 26, 2019
+4 −1
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FIX: Ignore sourcedata and derivatives when fetching data #1788

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5 changes: 4 additions & 1 deletion fmriprep/cli/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
"""

import os
import re
from pathlib import Path
import logging
import sys
Expand Down Expand Up @@ -544,7 +545,9 @@ def build_workflow(opts, retval):
retval['run_uuid'] = run_uuid

# First check that bids_dir looks like a BIDS folder
layout = BIDSLayout(str(bids_dir), validate=False)
layout = BIDSLayout(str(bids_dir), validate=False,
ignore=("code", "stimuli", "sourcedata", "models",
"derivatives", re.compile(r'^\.')))
subject_list = collect_participants(
layout, participant_label=opts.participant_label)
retval['subject_list'] = subject_list
Expand Down