Use cleaned epochs for sensor-space decoding, time-frequency analysis, and covariance calculation

docs/source/v1.5.md.inc

@@ -1,5 +1,8 @@
 ## v1.5.0 (unreleased)
 
+This release contains a number of very important bug fixes that address problems related to decoding, time-frequency analysis, and even inverse modeling.
+All users are encouraged to update.
+
 ### :new: New features & enhancements
 
 - Added `deriv_root` argument to CLI (#773 by @vferat)
@@ -30,3 +33,4 @@
 - Fixed bug with parallelization across runs for Maxwell filtering (#761 by @larsoner)
 - Fixed bug where head position files were not written with a proper suffix and extension (#761 by @larsoner)
 - Fixed bug where default values for `decoding_csp_times` and `decoding_csp_freqs` were not set dynamically based on the config parameters (#779 by @larsoner)
+- A number of processing steps errorneously always operated on un-cleaned epochs (`sensor/decoding_full_epochs`, `sensor/decoding_time_by_time`, `sensor/decoding_csp`), or operated on un-cleaned epochs (without PTP rejection) if not ICA or SSP was requested (`sensor/ime_frequency`, `sensor/make_cov`). The bug in `sensor/make_cov` could propagate to the source level as the covariance matrix is used for inverse modeling. (#796 by @hoechenberger)

mne_bids_pipeline/steps/sensor/_02_decoding_full_epochs.py

@@ -60,6 +60,7 @@ def get_input_fnames_epochs_decoding(
         run=None,
         recording=cfg.rec,
         space=cfg.space,
+        processing="clean",
         suffix="epo",
         extension=".fif",
         datatype=cfg.datatype,

mne_bids_pipeline/steps/sensor/_03_decoding_time_by_time.py

@@ -65,6 +65,7 @@ def get_input_fnames_time_decoding(
         run=None,
         recording=cfg.rec,
         space=cfg.space,
+        processing="clean",
         suffix="epo",
         extension=".fif",
         datatype=cfg.datatype,

mne_bids_pipeline/steps/sensor/_04_time_frequency.py

@@ -33,9 +33,6 @@ def get_input_fnames_time_frequency(
     subject: str,
     session: Optional[str],
 ) -> dict:
-    processing = None
-    if cfg.spatial_filter is not None:
-        processing = "clean"
     fname_epochs = BIDSPath(
         subject=subject,
         session=session,
@@ -46,7 +43,7 @@ def get_input_fnames_time_frequency(
         space=cfg.space,
         datatype=cfg.datatype,
         root=cfg.deriv_root,
-        processing=processing,
+        processing="clean",
         suffix="epo",
         extension=".fif",
         check=False,

mne_bids_pipeline/steps/sensor/_05_decoding_csp.py

@@ -124,6 +124,7 @@ def get_input_fnames_csp(
         run=None,
         recording=cfg.rec,
         space=cfg.space,
+        processing="clean",
         suffix="epo",
         extension=".fif",
         datatype=cfg.datatype,

mne_bids_pipeline/steps/sensor/_06_make_cov.py

@@ -37,7 +37,6 @@ def get_input_fnames_cov(
 ) -> dict:
     cov_type = _get_cov_type(cfg)
     in_files = dict()
-    processing = "clean" if cfg.spatial_filter is not None else None
     fname_epochs = BIDSPath(
         subject=subject,
         session=session,
@@ -48,7 +47,7 @@ def get_input_fnames_cov(
         space=cfg.space,
         extension=".fif",
         suffix="epo",
-        processing=processing,
+        processing="clean",
         datatype=cfg.datatype,
         root=cfg.deriv_root,
         check=False,