From 65b48d012da4d40e761d04c2fea031e4c1c95741 Mon Sep 17 00:00:00 2001
From: Hamza Abdelhedi <hamza.abdelhedii@gmail.com>
Date: Wed, 14 Oct 2026 18:15:49 -0400
Subject: [PATCH 1/2] BUG: Exclude bad channels in annotate_muscle_zscore

---
 mne/preprocessing/artifact_detection.py            | 2 +-
 mne/preprocessing/tests/test_artifact_detection.py | 6 ++++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/mne/preprocessing/artifact_detection.py b/mne/preprocessing/artifact_detection.py
index b8786c765b2..ad8e69688f1 100644
--- a/mne/preprocessing/artifact_detection.py
+++ b/mne/preprocessing/artifact_detection.py
@@ -117,7 +117,7 @@ def annotate_muscle_zscore(
         logger.info("Using %s sensors for muscle artifact detection", ch_type)
     else:
         _check_option("ch_type", ch_type, ["mag", "grad", "eeg"])
-    raw_copy.pick(ch_type)
+    raw_copy.pick(ch_type, exclude="bads")
 
     raw_copy.filter(
         filter_freq[0],
diff --git a/mne/preprocessing/tests/test_artifact_detection.py b/mne/preprocessing/tests/test_artifact_detection.py
index d3f6e8f75fa..fe91f965b85 100644
--- a/mne/preprocessing/tests/test_artifact_detection.py
+++ b/mne/preprocessing/tests/test_artifact_detection.py
@@ -174,6 +174,12 @@ def test_muscle_annotation(meas_date, events):
     onset = onset.astype(int)
     assert_array_equal(scores[onset].astype(int), np.array([23, 10]))
     assert annot_muscle.duration.size == 2
+    # Bad channels are excluded
+    raw.info["bads"] = ["MEG0111"]
+    _, scores_bads = annotate_muscle_zscore(raw, ch_type="mag", threshold=10)
+    raw_drop = raw.copy().drop_channels(raw.info["bads"])
+    _, scores_drop = annotate_muscle_zscore(raw_drop, ch_type="mag", threshold=10)
+    assert_allclose(scores_bads, scores_drop)
     raw.set_annotations(annot_muscle)
 
 

From 463bbe745c81527589c217864eac17390d83913a Mon Sep 17 00:00:00 2001
From: Hamza Abdelhedi <hamza.abdelhedii@gmail.com>
Date: Wed, 14 Oct 2026 18:16:52 -0400
Subject: [PATCH 2/2] Add changelog entry

---
 doc/changes/dev/14418.bugfix.rst | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 doc/changes/dev/14418.bugfix.rst

diff --git a/doc/changes/dev/14418.bugfix.rst b/doc/changes/dev/14418.bugfix.rst
new file mode 100644
index 00000000000..093e0141592
--- /dev/null
+++ b/doc/changes/dev/14418.bugfix.rst
@@ -0,0 +1 @@
+Fix bug with :func:`mne.preprocessing.annotate_muscle_zscore` where channels in ``raw.info["bads"]`` were included in the computation of the muscle artifact scores, by `Hamza Abdelhedi`_.