BUG: Fix bug with Maxwell step when find_noise_channels_meg=False (#847)

mne-tools · Feb 7, 2024 · fe56c01 · fe56c01
1 parent 92be603
commit fe56c01
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Showing 4 changed files with 9 additions and 5 deletions.
diff --git a/docs/source/v1.6.md.inc b/docs/source/v1.6.md.inc
@@ -23,6 +23,7 @@
 - Fix bug where EEG `reject` params were not used for `ch_types = ["meg", "eeg"]` (#839 by @larsoner)
 - Fix bug where implicit `mf_reference_run` could change across invocations of `mne_bids_pipeline`, breaking caching (#839 by @larsoner)
 - Fix bug where `--no-cache` had no effect (#839 by @larsoner)
+- Fix bug where the Maxwell filtering step would fail if [`find_noisy_channels_meg = False`][mne_bids_pipeline._config.find_noisy_channels_meg]` was used (#847 by @larsoner)
 - Fix bug where raw, empty-room, and custom noise covariances were errantly calculated on data without ICA or SSP applied (#840 by @larsoner)
 
 ### :medical_symbol: Code health

diff --git a/mne_bids_pipeline/_import_data.py b/mne_bids_pipeline/_import_data.py
@@ -683,10 +683,11 @@ def _get_run_rest_noise_path(
 
 
 def _get_mf_reference_run_path(
+    *,
     cfg: SimpleNamespace,
     subject: str,
     session: Optional[str],
-    add_bads: bool,
+    add_bads: Optional[bool] = None,
 ) -> dict:
     return _get_run_path(
         cfg=cfg,

diff --git a/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py b/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py
@@ -64,7 +64,7 @@ def get_input_fnames_esss(
         mf_reference_run=cfg.mf_reference_run,
         **kwargs,
     )
-    in_files.update(_get_mf_reference_run_path(add_bads=True, **kwargs))
+    in_files.update(_get_mf_reference_run_path(**kwargs))
     return in_files
 
 
@@ -241,7 +241,8 @@ def get_input_fnames_maxwell_filter(
         )
 
     # reference run (used for `destination` and also bad channels for noise)
-    in_files.update(_get_mf_reference_run_path(add_bads=True, **kwargs))
+    # use add_bads=None here to mean "add if autobad is turned on"
+    in_files.update(_get_mf_reference_run_path(**kwargs))
 
     is_rest_noise = run is None and task in ("noise", "rest")
     if is_rest_noise:

diff --git a/mne_bids_pipeline/tests/configs/config_ds003392.py b/mne_bids_pipeline/tests/configs/config_ds003392.py
@@ -6,8 +6,9 @@
 subjects = ["01"]
 
 task = "localizer"
-find_flat_channels_meg = True
-find_noisy_channels_meg = True
+# usually a good idea to use True, but we know no bads are detected for this dataset
+find_flat_channels_meg = False
+find_noisy_channels_meg = False
 use_maxwell_filter = True
 ch_types = ["meg"]