From 045c65e4cf6ec7544869f3508264517cc3344809 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Tue, 7 Nov 2023 20:49:04 +0100
Subject: [PATCH 01/17] Add support for MNE-ICALabel

---
 mne_bids_pipeline/_config.py                  |  6 ++
 .../steps/preprocessing/_06a_run_ica.py       | 56 ++++++++++++++++---
 2 files changed, 54 insertions(+), 8 deletions(-)
 mode change 100644 => 100755 mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py

diff --git a/mne_bids_pipeline/_config.py b/mne_bids_pipeline/_config.py
index 32e0c9735..d5507b756 100644
--- a/mne_bids_pipeline/_config.py
+++ b/mne_bids_pipeline/_config.py
@@ -1367,6 +1367,12 @@
 false-alarm rate increases dramatically.
 """
 
+ica_use_icalabel = False
+"""
+Whether to use MNE-ICALabel to automatically label ICA components. Only available for
+EEG data.
+"""
+
 # Rejection based on peak-to-peak amplitude
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
diff --git a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
old mode 100644
new mode 100755
index efd8bec84..b827774dd
--- a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
+++ b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
@@ -17,6 +17,7 @@
 import pandas as pd
 import numpy as np
 import autoreject
+from mne_icalabel import label_components
 
 import mne
 from mne.report import Report
@@ -184,7 +185,7 @@ def make_eog_epochs(
     return eog_epochs
 
 
-def detect_bad_components(
+def detect_bad_components_mne(
     *,
     cfg,
     which: Literal["eog", "ecg"],
@@ -195,7 +196,7 @@ def detect_bad_components(
     session: Optional[str],
 ) -> Tuple[List[int], np.ndarray]:
     artifact = which.upper()
-    msg = f"Performing automated {artifact} artifact detection …"
+    msg = f"Performing automated {artifact} artifact detection (MNE) …"
     logger.info(**gen_log_kwargs(message=msg))
 
     if which == "eog":
@@ -395,7 +396,18 @@ 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)
 
     if cfg.ica_reject == "autoreject_local":
@@ -448,7 +460,7 @@ def run_ica(
 
     # ECG and EOG component detection
     if epochs_ecg:
-        ecg_ics, ecg_scores = detect_bad_components(
+        ecg_ics, ecg_scores = detect_bad_components_mne(
             cfg=cfg,
             which="ecg",
             epochs=epochs_ecg,
@@ -461,7 +473,7 @@ def run_ica(
         ecg_ics = ecg_scores = []
 
     if epochs_eog:
-        eog_ics, eog_scores = detect_bad_components(
+        eog_ics, eog_scores = detect_bad_components_mne(
             cfg=cfg,
             which="eog",
             epochs=epochs_eog,
@@ -473,11 +485,30 @@ def run_ica(
     else:
         eog_ics = eog_scores = []
 
+    # Run MNE-ICALabel if requested.
+    if cfg.ica_use_icalabel:
+        msg = "Performing automated artifact detection (MNE-ICALabel) …"
+        logger.info(**gen_log_kwargs(message=msg))
+
+        label_results = label_components(inst=epochs, ica=ica, method="iclabel")
+        icalabel_ics = []
+        icalabel_labels = []
+        for idx, label in enumerate(label_results["labels"]):
+            if label not in ["brain", "other"]:
+                icalabel_ics.append(idx)
+                icalabel_labels.append(label)
+
+        msg = f"Detected {len(icalabel_ics)} artifact-related ICs in {len(epochs)} epochs."
+        logger.info(**gen_log_kwargs(message=msg))
+
     # Save ICA to disk.
     # We also store the automatically identified ECG- and EOG-related ICs.
     msg = "Saving ICA solution and detected artifacts to disk."
     logger.info(**gen_log_kwargs(message=msg))
-    ica.exclude = sorted(set(ecg_ics + eog_ics))
+    if cfg.ica_use_icalabel:
+        ica.exclude = sorted(set(ecg_ics + eog_ics + icalabel_ics))
+    else:
+        ica.exclude = sorted(set(ecg_ics + eog_ics))
     ica.save(out_files["ica"], overwrite=True)
     _update_for_splits(out_files, "ica")
 
@@ -495,12 +526,20 @@ def run_ica(
     for component in ecg_ics:
         row_idx = tsv_data["component"] == component
         tsv_data.loc[row_idx, "status"] = "bad"
-        tsv_data.loc[row_idx, "status_description"] = "Auto-detected ECG artifact"
+        tsv_data.loc[row_idx, "status_description"] = "Auto-detected ECG artifact (MNE)"
 
     for component in eog_ics:
         row_idx = tsv_data["component"] == component
         tsv_data.loc[row_idx, "status"] = "bad"
-        tsv_data.loc[row_idx, "status_description"] = "Auto-detected EOG artifact"
+        tsv_data.loc[row_idx, "status_description"] = "Auto-detected EOG artifact (MNE)"
+
+    if cfg.ica_use_icalabel:
+        for component, label in zip(icalabel_ics, icalabel_labels):
+            row_idx = tsv_data["component"] == component
+            tsv_data.loc[row_idx, "status"] = "bad"
+            tsv_data.loc[
+                row_idx, "status_description"
+            ] = f"Auto-detected {label} (MNE-ICALabel)"
 
     tsv_data.to_csv(out_files["components"], sep="\t", index=False)
 
@@ -588,6 +627,7 @@ def get_config(
         ica_reject=config.ica_reject,
         ica_eog_threshold=config.ica_eog_threshold,
         ica_ctps_ecg_threshold=config.ica_ctps_ecg_threshold,
+        ica_use_icalabel=config.ica_use_icalabel,
         autoreject_n_interpolate=config.autoreject_n_interpolate,
         random_state=config.random_state,
         ch_types=config.ch_types,

From 307b9c08aa82b702bc7beb171b4c285e337d3912 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Tue, 7 Nov 2023 20:59:55 +0100
Subject: [PATCH 02/17] Refactor

---
 .../steps/preprocessing/_06a_run_ica.py       | 95 ++++++++++---------
 1 file changed, 52 insertions(+), 43 deletions(-)

diff --git a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
index b827774dd..56af5fbc9 100755
--- a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
+++ b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
@@ -458,33 +458,6 @@ def run_ica(
     if cfg.task is not None:
         title += f", task-{cfg.task}"
 
-    # ECG and EOG component detection
-    if epochs_ecg:
-        ecg_ics, ecg_scores = detect_bad_components_mne(
-            cfg=cfg,
-            which="ecg",
-            epochs=epochs_ecg,
-            ica=ica,
-            ch_names=None,  # we currently don't allow for custom channels
-            subject=subject,
-            session=session,
-        )
-    else:
-        ecg_ics = ecg_scores = []
-
-    if epochs_eog:
-        eog_ics, eog_scores = detect_bad_components_mne(
-            cfg=cfg,
-            which="eog",
-            epochs=epochs_eog,
-            ica=ica,
-            ch_names=cfg.eog_channels,
-            subject=subject,
-            session=session,
-        )
-    else:
-        eog_ics = eog_scores = []
-
     # Run MNE-ICALabel if requested.
     if cfg.ica_use_icalabel:
         msg = "Performing automated artifact detection (MNE-ICALabel) …"
@@ -500,15 +473,41 @@ def run_ica(
 
         msg = f"Detected {len(icalabel_ics)} artifact-related ICs in {len(epochs)} epochs."
         logger.info(**gen_log_kwargs(message=msg))
+        ica.exclude = sorted(icalabel_ics)
+    else:
+        # Run MNE's built-in ECG and EOG component detection
+        if epochs_ecg:
+            ecg_ics, ecg_scores = detect_bad_components_mne(
+                cfg=cfg,
+                which="ecg",
+                epochs=epochs_ecg,
+                ica=ica,
+                ch_names=None,  # we currently don't allow for custom channels
+                subject=subject,
+                session=session,
+            )
+        else:
+            ecg_ics = ecg_scores = []
+
+        if epochs_eog:
+            eog_ics, eog_scores = detect_bad_components_mne(
+                cfg=cfg,
+                which="eog",
+                epochs=epochs_eog,
+                ica=ica,
+                ch_names=cfg.eog_channels,
+                subject=subject,
+                session=session,
+            )
+        else:
+            eog_ics = eog_scores = []
+
+        ica.exclude = sorted(set(ecg_ics + eog_ics))
 
     # Save ICA to disk.
     # We also store the automatically identified ECG- and EOG-related ICs.
     msg = "Saving ICA solution and detected artifacts to disk."
     logger.info(**gen_log_kwargs(message=msg))
-    if cfg.ica_use_icalabel:
-        ica.exclude = sorted(set(ecg_ics + eog_ics + icalabel_ics))
-    else:
-        ica.exclude = sorted(set(ecg_ics + eog_ics))
     ica.save(out_files["ica"], overwrite=True)
     _update_for_splits(out_files, "ica")
 
@@ -523,16 +522,6 @@ def run_ica(
         )
     )
 
-    for component in ecg_ics:
-        row_idx = tsv_data["component"] == component
-        tsv_data.loc[row_idx, "status"] = "bad"
-        tsv_data.loc[row_idx, "status_description"] = "Auto-detected ECG artifact (MNE)"
-
-    for component in eog_ics:
-        row_idx = tsv_data["component"] == component
-        tsv_data.loc[row_idx, "status"] = "bad"
-        tsv_data.loc[row_idx, "status_description"] = "Auto-detected EOG artifact (MNE)"
-
     if cfg.ica_use_icalabel:
         for component, label in zip(icalabel_ics, icalabel_labels):
             row_idx = tsv_data["component"] == component
@@ -540,6 +529,20 @@ def run_ica(
             tsv_data.loc[
                 row_idx, "status_description"
             ] = f"Auto-detected {label} (MNE-ICALabel)"
+    else:
+        for component in ecg_ics:
+            row_idx = tsv_data["component"] == component
+            tsv_data.loc[row_idx, "status"] = "bad"
+            tsv_data.loc[
+                row_idx, "status_description"
+            ] = "Auto-detected ECG artifact (MNE)"
+
+        for component in eog_ics:
+            row_idx = tsv_data["component"] == component
+            tsv_data.loc[row_idx, "status"] = "bad"
+            tsv_data.loc[
+                row_idx, "status_description"
+            ] = "Auto-detected EOG artifact (MNE)"
 
     tsv_data.to_csv(out_files["components"], sep="\t", index=False)
 
@@ -549,10 +552,16 @@ def run_ica(
     logger.info(**gen_log_kwargs(message=msg))
 
     report = Report(info_fname=epochs, title=title, verbose=False)
+
     ecg_evoked = None if epochs_ecg is None else epochs_ecg.average()
     eog_evoked = None if epochs_eog is None else epochs_eog.average()
-    ecg_scores = None if len(ecg_scores) == 0 else ecg_scores
-    eog_scores = None if len(eog_scores) == 0 else eog_scores
+
+    if cfg.ica_use_icalabel:
+        # We didn't run MNE's scoring
+        ecg_scores = eog_scores = None
+    else:
+        ecg_scores = None if len(ecg_scores) == 0 else ecg_scores
+        eog_scores = None if len(eog_scores) == 0 else eog_scores
 
     with _agg_backend():
         if cfg.ica_reject == "autoreject_local":

From fbfa83e902163261030f62701120f7a16ae8f7cd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Tue, 7 Nov 2023 21:02:22 +0100
Subject: [PATCH 03/17] Add dependency

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 5d217e36d..9f9fb55aa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -44,6 +44,7 @@ dependencies = [
     "autoreject",
     "mne[hdf5] >=1.2",
     "mne-bids[full]",
+    "mna-icalabel",
     "filelock",
     "setuptools >=65",
 ]

From a04dac10a975bc941615539c74b6c52248cbeeb2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Tue, 7 Nov 2023 21:08:47 +0100
Subject: [PATCH 04/17] Sanity check

---
 mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
index 56af5fbc9..66c906380 100755
--- a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
+++ b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
@@ -79,6 +79,10 @@ def fit_ica(
         algorithm = "infomax"
         fit_params = dict(extended=True)
 
+    if cfg.ica_use_icalabel:
+        # The ICALabel network was trained on extended-Infomax ICA decompositions
+        assert algorithm in ["picard-extended_infomax", "extended_infomax"]
+
     ica = ICA(
         method=algorithm,
         random_state=cfg.random_state,

From 86ba18d6e671d8b7c074af5e3b1eeb61bc04ec54 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Tue, 7 Nov 2023 22:30:20 +0100
Subject: [PATCH 05/17] Update pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9f9fb55aa..9993a034e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -44,7 +44,7 @@ dependencies = [
     "autoreject",
     "mne[hdf5] >=1.2",
     "mne-bids[full]",
-    "mna-icalabel",
+    "mne-icalabel",
     "filelock",
     "setuptools >=65",
 ]

From 2e629c00bfcc2bed2a3c4f5bcf79c7eff0a67808 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Wed, 8 Nov 2023 11:26:17 +0100
Subject: [PATCH 06/17] Add validation and fix docs

---
 docs/source/settings/preprocessing/ssp_ica.md      |  1 +
 mne_bids_pipeline/_config.py                       |  8 ++++++++
 mne_bids_pipeline/_config_import.py                | 14 ++++++++++++++
 .../steps/preprocessing/_06a_run_ica.py            | 12 ++++++++----
 4 files changed, 31 insertions(+), 4 deletions(-)

diff --git a/docs/source/settings/preprocessing/ssp_ica.md b/docs/source/settings/preprocessing/ssp_ica.md
index b132ef4bf..23f510796 100644
--- a/docs/source/settings/preprocessing/ssp_ica.md
+++ b/docs/source/settings/preprocessing/ssp_ica.md
@@ -24,6 +24,7 @@ tags:
         - ssp_ecg_channel
         - ica_reject
         - ica_algorithm
+        - ica_use_icalabel
         - ica_l_freq
         - ica_max_iterations
         - ica_n_components
diff --git a/mne_bids_pipeline/_config.py b/mne_bids_pipeline/_config.py
index d5507b756..7582b7d54 100644
--- a/mne_bids_pipeline/_config.py
+++ b/mne_bids_pipeline/_config.py
@@ -1371,6 +1371,14 @@
 """
 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
+    ```
 """
 
 # Rejection based on peak-to-peak amplitude
diff --git a/mne_bids_pipeline/_config_import.py b/mne_bids_pipeline/_config_import.py
index 14a55df2e..81a492d41 100644
--- a/mne_bids_pipeline/_config_import.py
+++ b/mne_bids_pipeline/_config_import.py
@@ -345,6 +345,20 @@ def _check_config(config: SimpleNamespace, config_path: Optional[PathLike]) -> N
                 f"but got shape {destination.shape}"
             )
 
+    # 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, val):
     # convert a default to a default factory if needed, having an explicit
diff --git a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
index 66c906380..3c388ab77 100755
--- a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
+++ b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
@@ -79,10 +79,6 @@ def fit_ica(
         algorithm = "infomax"
         fit_params = dict(extended=True)
 
-    if cfg.ica_use_icalabel:
-        # The ICALabel network was trained on extended-Infomax ICA decompositions
-        assert algorithm in ["picard-extended_infomax", "extended_infomax"]
-
     ica = ICA(
         method=algorithm,
         random_state=cfg.random_state,
@@ -276,6 +272,14 @@ def run_ica(
     in_files: dict,
 ) -> dict:
     """Run ICA."""
+    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.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]
     bids_basename = raw_fnames[0].copy().update(processing=None, split=None, run=None)
     out_files = dict()

From ef07ed4d2aa5b2493602d88705b0b452331c17a9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Wed, 8 Nov 2023 11:30:27 +0100
Subject: [PATCH 07/17] Update changelog

---
 docs/source/v1.5.md.inc | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/docs/source/v1.5.md.inc b/docs/source/v1.5.md.inc
index 5522271b1..40a86d747 100644
--- a/docs/source/v1.5.md.inc
+++ b/docs/source/v1.5.md.inc
@@ -3,6 +3,10 @@
 This release contains a number of very important bug fixes that address problems related to decoding, time-frequency analysis, and inverse modeling.
 All users are encouraged to update.
 
+We also improved logging during parallel processing, added support for finding and repairing bad epochs via
+[`autoreject`](https://autoreject.github.io), and included support for automatic labeling of ICA artifacts
+via [MNE-ICALabel][https://mne.tools/mne-icalabel].
+
 ### :new: New features & enhancements
 
 - Added `deriv_root` argument to CLI (#773 by @vferat)
@@ -22,6 +26,7 @@ All users are encouraged to update.
 - Added support for "local" [`autoreject`](https://autoreject.github.io) to find (and repair) bad channels on a per-epoch
   basis before submitting them to ICA fitting. This can be enabled by setting [`ica_reject`][mne_bids_pipeline._config.ica_reject]
   to `"autoreject_local"`. (#810 by @hoechenberger)
+- Added support for automated labeling of ICA components via [MNE-ICALabel][https://mne.tools/mne-icalabel] (#812 by @hoechenberger)
 - Website documentation tables can now be sorted (e.g., to find examples that use a specific feature) (#808 by @larsoner)
 
 [//]: # (### :warning: Behavior changes)

From 85dcc8a552ef5d8cac10f9f66e45c430b0d58ec4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Wed, 8 Nov 2023 11:39:55 +0100
Subject: [PATCH 08/17] Fix check and add test case

---
 mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py | 2 +-
 mne_bids_pipeline/tests/configs/config_ERP_CORE.py    | 7 ++++++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
index 3c388ab77..98390d3e6 100755
--- a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
+++ b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
@@ -275,7 +275,7 @@ def run_ica(
     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.algorithm in ["picard-extended_infomax", "extended_infomax"]
+        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"
diff --git a/mne_bids_pipeline/tests/configs/config_ERP_CORE.py b/mne_bids_pipeline/tests/configs/config_ERP_CORE.py
index 47fcb5846..ad625fae4 100644
--- a/mne_bids_pipeline/tests/configs/config_ERP_CORE.py
+++ b/mne_bids_pipeline/tests/configs/config_ERP_CORE.py
@@ -71,12 +71,17 @@
 t_break_annot_start_after_previous_event = 3.0
 t_break_annot_stop_before_next_event = 1.5
 
+# Settings for autoreject and ICA
 if task == "N400":  # test autoreject local without ICA
     spatial_filter = None
     reject = "autoreject_local"
     autoreject_n_interpolate = [2, 4]
-elif task == "N170":  # test autoreject local before ICA
+elif task == "N170":  # test autoreject local before ICA, and MNE-ICALabel
     spatial_filter = "ica"
+    ica_algorithm = "picard-extended_infomax"
+    ica_use_icalabel = True
+    ica_l_freq = 1
+    h_freq = 100
     ica_reject = "autoreject_local"
     reject = "autoreject_global"
     autoreject_n_interpolate = [2, 4]

From e86f179bb9093beb9801a9540045a1444fa0b871 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Wed, 8 Nov 2023 12:21:30 +0100
Subject: [PATCH 09/17] Add cfg.h_freq

---
 mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
index 98390d3e6..89492da04 100755
--- a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
+++ b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
@@ -649,6 +649,7 @@ def get_config(
         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,

From cd405c26f874915fd9763ade98b4dbbb929a75e7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Wed, 8 Nov 2023 13:11:27 +0100
Subject: [PATCH 10/17] Add onnxruntime dependency

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 9993a034e..344f0dc8b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -45,6 +45,7 @@ dependencies = [
     "mne[hdf5] >=1.2",
     "mne-bids[full]",
     "mne-icalabel",
+    "onnxruntime",  # for mne-icalabel
     "filelock",
     "setuptools >=65",
 ]

From 4a85e5130446b8f2ccb5b4d3a89d16896e07fa1c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Wed, 8 Nov 2023 13:30:34 +0100
Subject: [PATCH 11/17] Better logging

---
 mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
index 89492da04..0622cee4f 100755
--- a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
+++ b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
@@ -225,7 +225,7 @@ def detect_bad_components_mne(
         logger.warning(**gen_log_kwargs(message=warn))
     else:
         msg = (
-            f"Detected {len(inds)} {artifact}-related ICs in "
+            f"Detected {len(inds)} {artifact}-related independent component(s) in "
             f"{len(epochs)} {artifact} epochs."
         )
         logger.info(**gen_log_kwargs(message=msg))
@@ -479,7 +479,10 @@ def run_ica(
                 icalabel_ics.append(idx)
                 icalabel_labels.append(label)
 
-        msg = f"Detected {len(icalabel_ics)} artifact-related ICs in {len(epochs)} epochs."
+        msg = (
+            f"Detected {len(icalabel_ics)} artifact-related independent component(s) "
+            f"in {len(epochs)} epochs."
+        )
         logger.info(**gen_log_kwargs(message=msg))
         ica.exclude = sorted(icalabel_ics)
     else:

From 2d63230164ccccf7de9f0f46cbeb4f1cbdc90328 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Wed, 8 Nov 2023 13:49:16 +0100
Subject: [PATCH 12/17] Adjust test config

---
 mne_bids_pipeline/tests/configs/config_ERP_CORE.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/mne_bids_pipeline/tests/configs/config_ERP_CORE.py b/mne_bids_pipeline/tests/configs/config_ERP_CORE.py
index ad625fae4..f9c94699a 100644
--- a/mne_bids_pipeline/tests/configs/config_ERP_CORE.py
+++ b/mne_bids_pipeline/tests/configs/config_ERP_CORE.py
@@ -84,7 +84,7 @@
     h_freq = 100
     ica_reject = "autoreject_local"
     reject = "autoreject_global"
-    autoreject_n_interpolate = [2, 4]
+    autoreject_n_interpolate = [5, 10]  # Only for testing!
 else:
     spatial_filter = "ica"
     ica_reject = dict(eeg=350e-6, eog=500e-6)
@@ -254,6 +254,7 @@
     baseline = (None, 0)
     conditions = ["stimulus/face/normal", "stimulus/car/normal"]
     contrasts = [("stimulus/face/normal", "stimulus/car/normal")]
+    cluster_forming_t_threshold = 1.5  # Only for testing!
 elif task == "P3":
     rename_events = {
         "response/201": "response/correct",

From acc2acdc6f6fcce7c30cc1c69adc747ac28eba4c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Wed, 8 Nov 2023 13:49:20 +0100
Subject: [PATCH 13/17] Better doc

---
 mne_bids_pipeline/_config.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/mne_bids_pipeline/_config.py b/mne_bids_pipeline/_config.py
index 7582b7d54..e72f5e222 100644
--- a/mne_bids_pipeline/_config.py
+++ b/mne_bids_pipeline/_config.py
@@ -1457,7 +1457,8 @@
 
 !!! info
     This setting only takes effect if [`reject`][mne_bids_pipeline._config.reject] has
-    been set to `"autoreject_local"`.
+    been set to `"autoreject_local"`. It is not applied when using
+    `"autoreject_global"`.
 
 !!! info
     Channels marked as globally bad in the BIDS dataset (in `*_channels.tsv)`) will not

From 3032dd18a33d8a9a82295e5a3adc19c96aed2ac0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Wed, 8 Nov 2023 14:17:07 +0100
Subject: [PATCH 14/17] Change test config

---
 mne_bids_pipeline/tests/configs/config_ERP_CORE.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mne_bids_pipeline/tests/configs/config_ERP_CORE.py b/mne_bids_pipeline/tests/configs/config_ERP_CORE.py
index f9c94699a..d645adda5 100644
--- a/mne_bids_pipeline/tests/configs/config_ERP_CORE.py
+++ b/mne_bids_pipeline/tests/configs/config_ERP_CORE.py
@@ -84,7 +84,7 @@
     h_freq = 100
     ica_reject = "autoreject_local"
     reject = "autoreject_global"
-    autoreject_n_interpolate = [5, 10]  # Only for testing!
+    autoreject_n_interpolate = [12]  # Only for testing!
 else:
     spatial_filter = "ica"
     ica_reject = dict(eeg=350e-6, eog=500e-6)
@@ -254,7 +254,7 @@
     baseline = (None, 0)
     conditions = ["stimulus/face/normal", "stimulus/car/normal"]
     contrasts = [("stimulus/face/normal", "stimulus/car/normal")]
-    cluster_forming_t_threshold = 1.5  # Only for testing!
+    cluster_forming_t_threshold = 1.25  # Only for testing!
 elif task == "P3":
     rename_events = {
         "response/201": "response/correct",

From 03a3da9b70857ceb947e43671426cee3d108dafa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Wed, 8 Nov 2023 14:51:19 +0100
Subject: [PATCH 15/17] Try running both MNE and ICALabel artifact detection

---
 .../steps/preprocessing/_06a_run_ica.py       | 67 ++++++++++---------
 1 file changed, 35 insertions(+), 32 deletions(-)

diff --git a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
index 0622cee4f..b748a016d 100755
--- a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
+++ b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
@@ -136,7 +136,7 @@ def make_ecg_epochs(
         del raw  # Free memory
 
         if len(ecg_epochs) == 0:
-            msg = "No ECG events could be found. Not running ECG artifact " "detection."
+            msg = "No ECG events could be found. Not running ECG artifact detection."
             logger.info(**gen_log_kwargs(message=msg))
             ecg_epochs = None
     else:
@@ -174,7 +174,7 @@ def make_eog_epochs(
         eog_epochs = create_eog_epochs(raw, ch_name=ch_names, baseline=(None, -0.2))
 
         if len(eog_epochs) == 0:
-            msg = "No EOG events could be found. Not running EOG artifact " "detection."
+            msg = "No EOG events could be found. Not running EOG artifact detection."
             logger.warning(**gen_log_kwargs(message=msg))
             eog_epochs = None
     else:
@@ -466,14 +466,42 @@ def run_ica(
     if cfg.task is not None:
         title += f", task-{cfg.task}"
 
+    # Run MNE's built-in ECG and EOG component detection
+    if epochs_ecg:
+        ecg_ics, ecg_scores = detect_bad_components_mne(
+            cfg=cfg,
+            which="ecg",
+            epochs=epochs_ecg,
+            ica=ica,
+            ch_names=None,  # we currently don't allow for custom channels
+            subject=subject,
+            session=session,
+        )
+    else:
+        ecg_ics = ecg_scores = []
+
+    if epochs_eog:
+        eog_ics, eog_scores = detect_bad_components_mne(
+            cfg=cfg,
+            which="eog",
+            epochs=epochs_eog,
+            ica=ica,
+            ch_names=cfg.eog_channels,
+            subject=subject,
+            session=session,
+        )
+    else:
+        eog_ics = eog_scores = []
+
     # Run MNE-ICALabel if requested.
     if cfg.ica_use_icalabel:
+        icalabel_ics = []
+        icalabel_labels = []
+
         msg = "Performing automated artifact detection (MNE-ICALabel) …"
         logger.info(**gen_log_kwargs(message=msg))
 
         label_results = label_components(inst=epochs, ica=ica, method="iclabel")
-        icalabel_ics = []
-        icalabel_labels = []
         for idx, label in enumerate(label_results["labels"]):
             if label not in ["brain", "other"]:
                 icalabel_ics.append(idx)
@@ -484,36 +512,10 @@ def run_ica(
             f"in {len(epochs)} epochs."
         )
         logger.info(**gen_log_kwargs(message=msg))
-        ica.exclude = sorted(icalabel_ics)
     else:
-        # Run MNE's built-in ECG and EOG component detection
-        if epochs_ecg:
-            ecg_ics, ecg_scores = detect_bad_components_mne(
-                cfg=cfg,
-                which="ecg",
-                epochs=epochs_ecg,
-                ica=ica,
-                ch_names=None,  # we currently don't allow for custom channels
-                subject=subject,
-                session=session,
-            )
-        else:
-            ecg_ics = ecg_scores = []
-
-        if epochs_eog:
-            eog_ics, eog_scores = detect_bad_components_mne(
-                cfg=cfg,
-                which="eog",
-                epochs=epochs_eog,
-                ica=ica,
-                ch_names=cfg.eog_channels,
-                subject=subject,
-                session=session,
-            )
-        else:
-            eog_ics = eog_scores = []
+        icalabel_ics = []
 
-        ica.exclude = sorted(set(ecg_ics + eog_ics))
+    ica.exclude = sorted(set(ecg_ics + eog_ics + icalabel_ics))
 
     # Save ICA to disk.
     # We also store the automatically identified ECG- and EOG-related ICs.
@@ -534,6 +536,7 @@ def run_ica(
     )
 
     if cfg.ica_use_icalabel:
+        assert len(icalabel_ics) == (icalabel_labels)
         for component, label in zip(icalabel_ics, icalabel_labels):
             row_idx = tsv_data["component"] == component
             tsv_data.loc[row_idx, "status"] = "bad"

From 421ac0f86c274c6bc1b7e422dc2808e9ae3fd567 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Wed, 8 Nov 2023 15:16:11 +0100
Subject: [PATCH 16/17] Typo

---
 mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
index b748a016d..dd6355c05 100755
--- a/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
+++ b/mne_bids_pipeline/steps/preprocessing/_06a_run_ica.py
@@ -536,7 +536,7 @@ def run_ica(
     )
 
     if cfg.ica_use_icalabel:
-        assert len(icalabel_ics) == (icalabel_labels)
+        assert len(icalabel_ics) == len(icalabel_labels)
         for component, label in zip(icalabel_ics, icalabel_labels):
             row_idx = tsv_data["component"] == component
             tsv_data.loc[row_idx, "status"] = "bad"

From e5d426ba7b483a7758d60dca22182767e276c6b1 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Wed, 8 Nov 2023 09:34:35 -0500
Subject: [PATCH 17/17] FIX: Clearer test

---
 mne_bids_pipeline/_config.py               |  8 ++++----
 mne_bids_pipeline/tests/test_documented.py | 18 +++++++++++-------
 2 files changed, 15 insertions(+), 11 deletions(-)

diff --git a/mne_bids_pipeline/_config.py b/mne_bids_pipeline/_config.py
index e72f5e222..9d1782585 100644
--- a/mne_bids_pipeline/_config.py
+++ b/mne_bids_pipeline/_config.py
@@ -1237,7 +1237,7 @@
 """
 Peak-to-peak amplitude limits to exclude epochs from ICA fitting. This allows you to
 remove strong transient artifacts from the epochs used for fitting ICA, which could
-negatively affect ICA performance. 
+negatively affect ICA performance.
 
 The parameter values are the same as for [`reject`][mne_bids_pipeline._config.reject],
 but `"autoreject_global"` is not supported.
@@ -1262,7 +1262,7 @@
     to **not** specify rejection thresholds for EOG and ECG channels here –
     otherwise, ICA won't be able to "see" these artifacts.
 
-???+ info 
+???+ info
     This setting is applied only to the epochs that are used for **fitting** ICA. The
     goal is to make it easier for ICA to produce a good decomposition. After fitting,
     ICA is applied to the epochs to be analyzed, usually with one or more components
@@ -1367,7 +1367,7 @@
 false-alarm rate increases dramatically.
 """
 
-ica_use_icalabel = False
+ica_use_icalabel: bool = False
 """
 Whether to use MNE-ICALabel to automatically label ICA components. Only available for
 EEG data.
@@ -1398,7 +1398,7 @@
 
 If `None` (default), do not apply artifact rejection.
 
-If a dictionary, manually specify rejection thresholds (see examples). 
+If a dictionary, manually specify rejection thresholds (see examples).
 The thresholds provided here must be at least as stringent as those in
 [`ica_reject`][mne_bids_pipeline._config.ica_reject] if using ICA. In case of
 `'autoreject_global'`, thresholds for any channel that do not meet this
diff --git a/mne_bids_pipeline/tests/test_documented.py b/mne_bids_pipeline/tests/test_documented.py
index 097fc1032..7bb622dc4 100644
--- a/mne_bids_pipeline/tests/test_documented.py
+++ b/mne_bids_pipeline/tests/test_documented.py
@@ -18,15 +18,19 @@ def test_options_documented():
     with open(root_path / "_config.py", "r") as fid:
         contents = fid.read()
     contents = ast.parse(contents)
-    in_config = [
+    unannotated = [
+        item.targets[0].id for item in contents.body if isinstance(item, ast.Assign)
+    ]
+    assert unannotated == []
+    _config_py = [
         item.target.id for item in contents.body if isinstance(item, ast.AnnAssign)
     ]
-    assert len(set(in_config)) == len(in_config)
-    in_config = set(in_config)
+    assert len(set(_config_py)) == len(_config_py)
+    _config_py = set(_config_py)
     # ensure we clean our namespace correctly
     config = _get_default_config()
-    config_names = set(d for d in dir(config) if not d.startswith("_"))
-    assert in_config == config_names
+    _get_default_config_names = set(d for d in dir(config) if not d.startswith("_"))
+    assert _config_py == _get_default_config_names
     settings_path = root_path.parent / "docs" / "source" / "settings"
     assert settings_path.is_dir()
     in_doc = set()
@@ -51,8 +55,8 @@ def test_options_documented():
                         assert val not in in_doc, "Duplicate documentation"
                     in_doc.add(val)
     what = "docs/source/settings doc"
-    assert in_doc.difference(in_config) == set(), f"Extra values in {what}"
-    assert in_config.difference(in_doc) == set(), f"Values missing from {what}"
+    assert in_doc.difference(_config_py) == set(), f"Extra values in {what}"
+    assert _config_py.difference(in_doc) == set(), f"Values missing from {what}"
 
 
 def test_datasets_in_doc():