[ENH, MRG] Add intracranial electrode localization GUI

doc/changes/latest.inc

@@ -159,6 +159,7 @@ Enhancements
 
 - Reading EDF files via :func:`mne.io.read_raw_edf` now can infer channel type from the signal label in the EDF header (:gh:`9694` by `Adam Li`_)
 
+- Add :func:`mne.gui.locate_ieeg` to locate intracranial electrode contacts from a CT, an MRI (with Freesurfer ``recon-all``) and the channel names from an :class:`mne.Info` object (:gh:`9586` by `Alex Rockhill`_)
 
 Bugs
 ~~~~

doc/conf.py

@@ -258,6 +258,7 @@
     # unlinkable
     'mayavi.mlab.pipeline.surface',
     'CoregFrame', 'Kit2FiffFrame', 'FiducialsFrame',
+    'IntracranialElectrodeLocator'
 }
 numpydoc_validate = True
 numpydoc_validation_checks = {'all'} | set(error_ignores)

doc/mri.rst

@@ -19,6 +19,7 @@ Step by step instructions for using :func:`gui.coregistration`:
    get_montage_volume_labels
    gui.coregistration
    gui.fiducials
+   gui.locate_ieeg
    create_default_subject
    head_to_mni
    head_to_mri

mne/datasets/utils.py

@@ -254,7 +254,7 @@ def _data_path(path=None, force_update=False, update_path=True, download=True,
     path = _get_path(path, key, name)
     # To update the testing or misc dataset, push commits, then make a new
     # release on GitHub. Then update the "releases" variable:
-    releases = dict(testing='0.123', misc='0.18')
+    releases = dict(testing='0.123', misc='0.19')
     # And also update the "md5_hashes['testing']" variable below.
     # To update any other dataset, update the data archive itself (upload
     # an updated version) and update the md5 hash.
@@ -345,7 +345,7 @@ def _data_path(path=None, force_update=False, update_path=True, download=True,
             bst_raw='fa2efaaec3f3d462b319bc24898f440c',
             bst_resting='70fc7bf9c3b97c4f2eab6260ee4a0430'),
         fake='3194e9f7b46039bb050a74f3e1ae9908',
-        misc='0aa25a9bb4f204b3d4769f0b84e9b526',
+        misc='b5ebe66dbe0f36cba9170a7ce909a66f',
         sample='12b75d1cb7df9dfb4ad73ed82f61094f',
         somato='32fd2f6c8c7eb0784a1de6435273c48b',
         spm='9f43f67150e3b694b523a21eb929ea75',

mne/gui/__init__.py

@@ -239,3 +239,44 @@ def kit2fiff():
     from ._kit2fiff_gui import Kit2FiffFrame
     frame = Kit2FiffFrame()
     return _initialize_gui(frame)
+
+
+@verbose
+def locate_ieeg(info, trans, aligned_ct, subject=None, subjects_dir=None,
+                groups=None, verbose=None):
+    """Locate intracranial electrode contacts.
+
+    Parameters
+    ----------
+    %(info_not_none)s
+    %(trans_not_none)s
+    aligned_ct : str | pathlib.Path | nibabel.spatialimages.SpatialImage
+        The CT image that has been aligned to the Freesurfer T1. Path-like
+        inputs and nibabel image objects are supported.
+    %(subject)s
+    %(subjects_dir)s
+    groups : dict | None
+        A dictionary with channels as keys and their group index as values.
+        If None, the groups will be inferred by the channel names. Channel
+        names must have a format like ``LAMY 7`` where a string prefix
+        like ``LAMY`` precedes a numeric index like ``7``. If the channels
+        are formatted improperly, group plotting will work incorrectly.
+        Group assignments can be adjusted in the GUI.
+    %(verbose)s
+
+    Returns
+    -------
+    gui : instance of IntracranialElectrodeLocator
+        The graphical user interface (GUI) window.
+    """
+    from ._ieeg_locate_gui import IntracranialElectrodeLocator
+    from PyQt5.QtWidgets import QApplication
+    # get application
+    app = QApplication.instance()
+    if app is None:
+        app = QApplication(["Intracranial Electrode Locator"])
+    gui = IntracranialElectrodeLocator(
+        info, trans, aligned_ct, subject=subject,
+        subjects_dir=subjects_dir, groups=groups, verbose=verbose)
+    gui.show()
+    return gui