Fix handling of analyze_channels for EEG data, where some steps (like ERP calculation) would previously fail

docs/source/v1.7.md.inc

@@ -16,7 +16,9 @@
 
 [//]: # (- Whatever (#000 by @whoever))
 
-[//]: # (### :bug: Bug fixes)
+### :bug: Bug fixes
+
+- Fixed an error when using [`analyze_channels`][mne_bids_pipeline._config.analyze_channels] with EEG data, where e.g. ERP creation didn't work. (#883 by @hoechenberger)
 
 [//]: # (- Whatever (#000 by @whoever))
 

mne_bids_pipeline/_config.py

@@ -3,7 +3,7 @@
 from collections.abc import Sequence
 from typing import Annotated, Any, Callable, Literal, Optional, Union
 
-from annotated_types import Ge, Interval, Len
+from annotated_types import Ge, Interval, Len, MinLen
 from mne import Covariance
 from mne_bids import BIDSPath
 
@@ -382,7 +382,9 @@
     ```
 """
 
-analyze_channels: Union[Literal["all", "ch_types"], Sequence["str"]] = "ch_types"
+analyze_channels: Union[
+    Literal["all", "ch_types"], Annotated[Sequence["str"], MinLen(1)]
+] = "ch_types"
 """
 The names of the channels to analyze during ERP/ERF and time-frequency analysis
 steps. For certain paradigms, e.g. EEG ERP research, it is common to constrain

mne_bids_pipeline/_config_utils.py

@@ -423,22 +423,21 @@ def get_mf_ctc_fname(
 def _restrict_analyze_channels(
     inst: RawEpochsEvokedT, cfg: SimpleNamespace
 ) -> RawEpochsEvokedT:
-    if cfg.analyze_channels:
-        analyze_channels = cfg.analyze_channels
-        if cfg.analyze_channels == "ch_types":
-            analyze_channels = cfg.ch_types
-            inst.apply_proj()
-        # We special-case the average reference here to work around a situation
-        # where e.g. `analyze_channels` might contain only a single channel:
-        # `concatenate_epochs` below will then fail when trying to create /
-        # apply the projection. We can avoid this by removing an existing
-        # average reference projection here, and applying the average reference
-        # directly – without going through a projector.
-        elif "eeg" in cfg.ch_types and cfg.eeg_reference == "average":
-            inst.set_eeg_reference("average")
-        else:
-            inst.apply_proj()
-        inst.pick(analyze_channels)
+    analyze_channels = cfg.analyze_channels
+    if cfg.analyze_channels == "ch_types":
+        analyze_channels = cfg.ch_types
+        inst.apply_proj()
+    # We special-case the average reference here to work around a situation
+    # where e.g. `analyze_channels` might contain only a single channel:
+    # `concatenate_epochs` below will then fail when trying to create /
+    # apply the projection. We can avoid this by removing an existing
+    # average reference projection here, and applying the average reference
+    # directly – without going through a projector.
+    elif "eeg" in cfg.ch_types and cfg.eeg_reference == "average":
+        inst.set_eeg_reference("average")
+    else:
+        inst.apply_proj()
+    inst.pick(analyze_channels)
     return inst
 
 

mne_bids_pipeline/steps/sensor/_01_make_evoked.py

@@ -11,6 +11,7 @@
     _pl,
     _restrict_analyze_channels,
     get_all_contrasts,
+    get_eeg_reference,
     get_sessions,
     get_subjects,
 )
@@ -172,6 +173,7 @@ def get_config(
         contrasts=get_all_contrasts(config),
         noise_cov=_sanitize_callable(config.noise_cov),
         analyze_channels=config.analyze_channels,
+        eeg_reference=get_eeg_reference(config),
         ch_types=config.ch_types,
         report_evoked_n_time_points=config.report_evoked_n_time_points,
         **_bids_kwargs(config=config),

mne_bids_pipeline/steps/sensor/_06_make_cov.py

@@ -13,6 +13,7 @@
 from ..._config_utils import (
     _bids_kwargs,
     _restrict_analyze_channels,
+    get_eeg_reference,
     get_noise_cov_bids_path,
     get_sessions,
     get_subjects,
@@ -292,6 +293,7 @@ def get_config(
         conditions=config.conditions,
         contrasts=config.contrasts,
         analyze_channels=config.analyze_channels,
+        eeg_reference=get_eeg_reference(config),
         noise_cov_method=config.noise_cov_method,
         **_bids_kwargs(config=config),
     )

mne_bids_pipeline/tests/configs/config_ERP_CORE.py

@@ -212,6 +212,41 @@
     }
 
     eeg_reference = ["P9", "P10"]
+    # Analyze all EEG channels -- we only specify the channels here for the purpose of
+    # demonstration
+    analyze_channels = [
+        "FP1",
+        "F3",
+        "F7",
+        "FC3",
+        "C3",
+        "C5",
+        "P3",
+        "P7",
+        "P9",
+        "PO7",
+        "PO3",
+        "O1",
+        "Oz",
+        "Pz",
+        "CPz",
+        "FP2",
+        "Fz",
+        "F4",
+        "F8",
+        "FC4",
+        "FCz",
+        "Cz",
+        "C4",
+        "C6",
+        "P4",
+        "P8",
+        "P10",
+        "PO8",
+        "PO4",
+        "O2",
+    ]
+
     epochs_tmin = -0.2
     epochs_tmax = 0.8
     baseline = (None, 0)
@@ -224,6 +259,41 @@
     }
 
     eeg_reference = "average"
+    # Analyze all EEG channels -- we only specify the channels here for the purpose of
+    # demonstration
+    analyze_channels = [
+        "FP1",
+        "F3",
+        "F7",
+        "FC3",
+        "C3",
+        "C5",
+        "P3",
+        "P7",
+        "P9",
+        "PO7",
+        "PO3",
+        "O1",
+        "Oz",
+        "Pz",
+        "CPz",
+        "FP2",
+        "Fz",
+        "F4",
+        "F8",
+        "FC4",
+        "FCz",
+        "Cz",
+        "C4",
+        "C6",
+        "P4",
+        "P8",
+        "P10",
+        "PO8",
+        "PO4",
+        "O2",
+    ]
+
     ica_n_components = 30 - 1
     for i in range(1, 180 + 1):
         orig_name = f"stimulus/{i}"