Add the code from PR "Add support for MNE-ICALabel #812"

mne_bids_pipeline/_config.py

@@ -1376,19 +1376,63 @@
 `1` or `None` to not perform any decimation.
 """
 
+ica_use_ecg_detection: bool = True
+"""
+Whether to use the MNE ECG detection on the ICA components.
+"""
+
 ica_ecg_threshold: float = 0.1
 """
 The cross-trial phase statistics (CTPS) threshold parameter used for detecting
 ECG-related ICs.
 """
 
+ica_use_eog_detection: bool = True
+"""
+Whether to use the MNE EOG detection on the ICA components.
+"""
+
 ica_eog_threshold: float = 3.0
 """
 The threshold to use during automated EOG classification. Lower values mean
 that more ICs will be identified as EOG-related. If too low, the
 false-alarm rate increases dramatically.
 """
 
+
+# From: https://github.com/mne-tools/mne-bids-pipeline/pull/812
+ica_use_icalabel: bool = False
+"""
+Whether to use MNE-ICALabel to automatically label ICA components. Only available for
+EEG data.
+!!! info
+    Using MNE-ICALabel mandates that you also set:
+    ```python
+    eeg_reference = "average"
+    ica_l_freq = 1
+    h_freq = 100
+    ```
+"""
+
+icalabel_include: Annotated[
+    Sequence[
+        Literal[
+            "brain",
+            "muscle artifact",
+            "eye blink",
+            "heart beat",
+            "line noise",
+            "channel noise",
+            "other",
+        ]
+    ],
+    Len(1, 7),
+] = ["brain", "other"]
+"""
+Which independent components (ICs) to keep based on the labels given by ICLabel.
+Possible labels are "brain", "muscle artifact", "eye blink", "heart beat", "line noise", "channel noise", "other".
+"""
+
 # ### Amplitude-based artifact rejection
 #
 # ???+ info "Good Practice / Advice"

mne_bids_pipeline/_config_import.py

@@ -341,6 +341,21 @@ def _check_config(config: SimpleNamespace, config_path: PathLike | None) -> None
                 f"but got shape {destination.shape}"
             )
 
+    # From: https://github.com/mne-tools/mne-bids-pipeline/pull/812
+    # MNE-ICALabel
+    if config.ica_use_icalabel:
+        if config.ica_l_freq != 1.0 or config.h_freq != 100.0:
+            raise ValueError(
+                f"When using MNE-ICALabel, you must set ica_l_freq=1 and h_freq=100, "
+                f"but got: ica_l_freq={config.ica_l_freq} and h_freq={config.h_freq}"
+            )
+
+        if config.eeg_reference != "average":
+            raise ValueError(
+                f'When using MNE-ICALabel, you must set eeg_reference="average", but '
+                f"got: eeg_reference={config.eeg_reference}"
+            )
+
 
 def _default_factory(key: str, val: Any) -> Any:
     # convert a default to a default factory if needed, having an explicit
@@ -350,6 +365,8 @@ def _default_factory(key: str, val: Any) -> Any:
         {"custom": (8, 24.0, 40)},  # decoding_csp_freqs
         ["evoked"],  # inverse_targets
         [4, 8, 16],  # autoreject_n_interpolate
+        # ["brain", "muscle artifact", "eye blink", "heart beat", "line noise", "channel noise", "other"], # icalabel_include
+        ["brain", "other"],
     ]
 
     def default_factory() -> Any:

mne_bids_pipeline/steps/preprocessing/_06a1_fit_ica.py

@@ -79,6 +79,14 @@ def run_ica(
     """Run ICA."""
     import matplotlib.pyplot as plt
 
+    if cfg.ica_use_icalabel:
+        # The ICALabel network was trained on extended-Infomax ICA decompositions fit
+        # on data flltered between 1 and 100 Hz.
+        assert cfg.ica_algorithm in ["picard-extended_infomax", "extended_infomax"]
+        assert cfg.ica_l_freq == 1.0
+        assert cfg.h_freq == 100.0
+        assert cfg.eeg_reference == "average"
+
     raw_fnames = [in_files.pop(f"raw_run-{run}") for run in cfg.runs]
     out_files = dict()
     bids_basename = raw_fnames[0].copy().update(processing=None, split=None, run=None)
@@ -164,7 +172,18 @@ def run_ica(
 
     # Set an EEG reference
     if "eeg" in cfg.ch_types:
-        projection = True if cfg.eeg_reference == "average" else False
+        if cfg.ica_use_icalabel:
+            assert cfg.eeg_reference == "average"
+            projection = False  # Avg. ref. needs to be applied for MNE-ICALabel
+        elif cfg.eeg_reference == "average":
+            projection = True
+        else:
+            projection = False
+
+        if not projection:
+            msg = "Applying average reference to EEG epochs used for ICA fitting."
+            logger.info(**gen_log_kwargs(message=msg))
+
         epochs.set_eeg_reference(cfg.eeg_reference, projection=projection)
 
     ar_reject_log = ar_n_interpolate_ = None
@@ -338,10 +357,12 @@ def get_config(
         ica_max_iterations=config.ica_max_iterations,
         ica_decim=config.ica_decim,
         ica_reject=config.ica_reject,
+        ica_use_icalabel=config.ica_use_icalabel,
         autoreject_n_interpolate=config.autoreject_n_interpolate,
         random_state=config.random_state,
         ch_types=config.ch_types,
         l_freq=config.l_freq,
+        h_freq=config.h_freq,
         epochs_decim=config.epochs_decim,
         raw_resample_sfreq=config.raw_resample_sfreq,
         event_repeated=config.event_repeated,