Don't perform ICA cleaning on raw data by default when epochs are pre…

…sent

Fixes mne-tools#925

docs/source/v1.9.md.inc

@@ -2,15 +2,22 @@
 
 ### :new: New features & enhancements
 
-- Added number of subject to `sub-average` report (#902, #910 by @SophieHerbst)
+- Added number of subjects to `sub-average` report (#902, #910 by @SophieHerbst)
 - The type annotations in the default configuration file are now easier to read: We
   replaced `Union[X, Y]` with `X | Y` and `Optional[X]` with `X | None`. (#908, #911 by @hoechenberger)
+- Added a new configuration option [`spatial_filter_raw`][mne_bids_pipeline._config.spatial_filter_raw]
+  to control whether to create cleaned raw data via ICA or SSP. Previously, we'd only clean epochs.
+  (#840, #926 by @larsoner and @hoechenberger)
 
 ### :warning: Behavior changes
 
 - All ICA HTML reports have been consolidated in the standard subject `*_report.html`
   file instead of producing separate files (#899 by @larsoner).
-- Changed default for `source_info_path_update` to `None`.  In `_04_make_forward.py`
+- When using ICA or SSP with resting-state data, we now automatically produce cleaned raw data files. This
+  behavior can be controlled via the new [`spatial_filter_raw`][mne_bids_pipeline._config.spatial_filter_raw]
+  configuration option. (#840, #926 by @larsoner and @hoechenberger)
+- Changed default for [`source_info_path_update`][mne_bids_pipeline._config.source_info_path_update]
+  to `None`.  In `_04_make_forward.py`
   and `_05_make_inverse.py`, we retrieve the info from the file from which
   the `noise_cov` is computed (#919 by @SophieHerbst)
 - The [`depth`][mne_bids_pipeline._config.depth] parameter doesn't accept `None`

mne_bids_pipeline/_config.py

@@ -1138,6 +1138,13 @@
     ICA fitting – this file will need to be updated!
 """
 
+spatial_filter_raw: bool | None = None
+"""
+Whether to clean the raw data with the spatial filter. If `True`, creates cleaned data
+from both, epochs and raw. If `False`, only creates cleaned epochs. If `None`, creates
+cleaned epochs and raw for resting-state data, and only cleaned epochs otherwise.
+"""
+
 min_ecg_epochs: Annotated[int, Ge(1)] = 5
 """
 Minimal number of ECG epochs needed to compute SSP projectors.

mne_bids_pipeline/steps/preprocessing/_08a_apply_ica.py

@@ -196,7 +196,12 @@ def apply_ica_raw(
     run: str,
     task: str | None,
     in_files: dict,
-) -> dict:
+) -> dict | None:
+    if cfg.spatial_filter_raw is None and not (cfg.task == "rest" or cfg.task_is_rest):
+        return
+    elif cfg.spatial_filter_raw is False:
+        return
+
     ica = _read_ica_and_exclude(in_files)
     in_key = list(in_files)[0]
     assert in_key.startswith("raw"), in_key
@@ -240,6 +245,8 @@ def get_config(
     cfg = SimpleNamespace(
         baseline=config.baseline,
         ica_reject=config.ica_reject,
+        spatial_filter_raw=config.spatial_filter_raw,
+        task_is_rest=config.task_is_rest,
         processing="filt" if config.regress_artifact is None else "regress",
         _epochs_split_size=config._epochs_split_size,
         **_import_data_kwargs(config=config, subject=subject),