From a37c90d2c3ec3efde454091433b9dd831354d984 Mon Sep 17 00:00:00 2001 From: Mathias Goncalves Date: Fri, 2 Sep 2022 15:54:36 -0400 Subject: [PATCH] Merge pull request #2843 from mgxd/fix/sbref-filtering FIX: Filter sbrefs by BIDS filters if available --- fmriprep/workflows/bold/base.py | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py index 2d2ac4740..005b18f5c 100644 --- a/fmriprep/workflows/bold/base.py +++ b/fmriprep/workflows/bold/base.py @@ -231,9 +231,14 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False): ) # Find associated sbref, if possible - entities["suffix"] = "sbref" - entities["extension"] = [".nii", ".nii.gz"] # Overwrite extensions - sbref_files = layout.get(return_type="file", **entities) + overrides = { + "suffix": "sbref", + "extension": [".nii", ".nii.gz"], + } + if config.execution.bids_filters: + overrides.update(config.execution.bids_filters.get('sbref', {})) + sb_ents = {**entities, **overrides} + sbref_files = layout.get(return_type="file", **sb_ents) sbref_msg = f"No single-band-reference found for {os.path.basename(ref_file)}." if sbref_files and "sbref" in config.workflow.ignore: