From ba8a36a0d3777306618634f23bfff1601649aeeb Mon Sep 17 00:00:00 2001
From: PragnyaKhandelwal <prag1704@gmail.com>
Date: Fri, 14 Aug 2026 01:38:14 +0530
Subject: [PATCH 1/2] ENH: read EGI MFF channelStatus into raw.info['bads']

When categories.xml is present in an MFF directory, collect the union of all
channels marked exclusion="badChannels" across every category segment and
populate raw.info["bads"] with their MNE channel names.
---
 doc/changes/dev/14156.newfeature.rst |  1 +
 mne/io/egi/egimff.py                 | 44 ++++++++++++++++++++++++++++
 mne/io/egi/tests/test_egi.py         | 29 ++++++++++++++++++
 3 files changed, 74 insertions(+)
 create mode 100644 doc/changes/dev/14156.newfeature.rst

diff --git a/doc/changes/dev/14156.newfeature.rst b/doc/changes/dev/14156.newfeature.rst
new file mode 100644
index 00000000000..514fba3e9fc
--- /dev/null
+++ b/doc/changes/dev/14156.newfeature.rst
@@ -0,0 +1 @@
+:func:`mne.io.read_raw_egi` now reads bad channels from ``categories.xml`` (when present in the MFF directory) and populates :attr:`mne.Info.bads` with channels marked ``exclusion="badChannels"`` in NetStation. By `Pragnya Khandelwal`_.
diff --git a/mne/io/egi/egimff.py b/mne/io/egi/egimff.py
index 8dfee16292e..ea56a33ec1c 100644
--- a/mne/io/egi/egimff.py
+++ b/mne/io/egi/egimff.py
@@ -67,6 +67,42 @@ def _disk_range_to_epochs(egi_info, disk_start, disk_stop):
         yield ei, t0, dt, ov_start - disk_start, ov_stop - disk_start
 
 
+def _read_channel_status_bads(filepath, ch_names, pns_names):
+    """Return bad channel names from categories.xml channelStatus, if present.
+
+    EGI NetStation writes per-epoch bad-channel lists into ``categories.xml``
+    as ``<channelStatus>`` elements.  This function collects the union of all
+    channels marked ``exclusion="badChannels"`` across every category and
+    segment and maps them back to MNE channel names.
+
+    Returns an empty list when ``categories.xml`` is absent or unparseable.
+    """
+    cats_path = op.join(filepath, "categories.xml")
+    if not op.isfile(cats_path):
+        return []
+    from mffpy.xml_files import XML
+
+    try:
+        cats_obj = XML.from_file(cats_path)
+    except Exception:
+        return []
+    bads = set()
+    for segments in cats_obj.categories.values():
+        for seg in segments:
+            for entry in seg.get("channelStatus") or []:
+                if entry["exclusion"] != "badChannels":
+                    continue
+                if entry["signalBin"] == 1:
+                    for ch in entry["channels"]:
+                        if 1 <= ch <= len(ch_names):
+                            bads.add(ch_names[ch - 1])
+                elif entry["signalBin"] == 2:
+                    for ch in entry["channels"]:
+                        if 1 <= ch <= len(pns_names):
+                            bads.add(pns_names[ch - 1])
+    return sorted(bads)
+
+
 def _read_mff_header(filepath):
     """Read mff header."""
     _soft_import("mffpy", "reading EGI MFF data")
@@ -514,6 +550,14 @@ def __init__(
                     if chan["kind"] == FIFF.FIFFV_EEG_CH:
                         chan["loc"][3:6] = ref_coords
 
+        # Mark bad channels from categories.xml channelStatus if present
+        bads = _read_channel_status_bads(
+            input_fname, ch_names, egi_info.get("pns_names", [])
+        )
+        if bads:
+            with info._unlock():
+                info["bads"] = bads
+
         file_bin = op.join(input_fname, egi_info["eeg_fname"])
         egi_info["egi_events"] = egi_events
         egi_info["mff_path"] = input_fname
diff --git a/mne/io/egi/tests/test_egi.py b/mne/io/egi/tests/test_egi.py
index 10a7435666e..88d9377724c 100644
--- a/mne/io/egi/tests/test_egi.py
+++ b/mne/io/egi/tests/test_egi.py
@@ -604,6 +604,35 @@ def test_egi_mff_bad_xml(tmp_path):
     assert "DIN1" in raw.annotations.description
 
 
+@requires_testing_data
+def test_egi_mff_channel_status(tmp_path):
+    """Test that bad channels from categories.xml channelStatus are read."""
+    mff_fname = copytree_rw(egi_pause_fname, tmp_path / "paused_status.mff")
+    # Minimal categories.xml marking EEG channels 5 and 23 as bad
+    cats_xml = """\
+<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
+<categories xmlns="http://www.egi.com/categories_mff">
+    <cat>
+        <name>Recording</name>
+        <segments>
+            <seg status="unedited">
+                <beginTime>0</beginTime>
+                <endTime>1300000</endTime>
+                <evtBegin>0</evtBegin>
+                <evtEnd>0</evtEnd>
+                <channelStatus>
+                    <channels signalBin="1" exclusion="badChannels">5 23</channels>
+                </channelStatus>
+            </seg>
+        </segments>
+    </cat>
+</categories>
+"""
+    (mff_fname / "categories.xml").write_text(cats_xml, encoding="utf-8")
+    raw = read_raw_egi(mff_fname, events_as_annotations=False, verbose=False)
+    assert raw.info["bads"] == ["E23", "E5"]  # sorted alphabetically
+
+
 @requires_testing_data
 @pytest.mark.parametrize(
     "fname, expected",

From 5b70061d3fac974e19278459f9a5c501304cd032 Mon Sep 17 00:00:00 2001
From: PragnyaKhandelwal <prag1704@gmail.com>
Date: Fri, 14 Aug 2026 01:54:37 +0530
Subject: [PATCH 2/2] fix codespell: unparseable -> unparsable

---
 mne/io/egi/egimff.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mne/io/egi/egimff.py b/mne/io/egi/egimff.py
index ea56a33ec1c..8091b34b721 100644
--- a/mne/io/egi/egimff.py
+++ b/mne/io/egi/egimff.py
@@ -75,7 +75,7 @@ def _read_channel_status_bads(filepath, ch_names, pns_names):
     channels marked ``exclusion="badChannels"`` across every category and
     segment and maps them back to MNE channel names.
 
-    Returns an empty list when ``categories.xml`` is absent or unparseable.
+    Returns an empty list when ``categories.xml`` is absent or unparsable.
     """
     cats_path = op.join(filepath, "categories.xml")
     if not op.isfile(cats_path):