Anatomical registration of intracranial electrodes. Robust model-based localization and deformable smooth brain-shift compensation methods

Alejandro Omar Blenkmann, Sabine Liliana Leske, Anaïs Llorens, Jack J. Lin, Edward F. Chang, Peter Brunner, Gerwin Schalk, Jugoslav Ivanovic, Pål Gunnar Larsson, Robert Thomas Knight, Tor Endestad, Anne Kristin Solbakk

Research output: Contribution to journalReview articlepeer-review


Background: Intracranial electrodes are typically localized from post-implantation CT artifacts. Automatic algorithms localizing low signal-to-noise ratio artifacts and high-density electrode arrays are missing. Additionally, implantation of grids/strips introduces brain deformations, resulting in registration errors when fusing post-implantation CT and pre-implantation MR images. Brain-shift compensation methods project electrode coordinates to cortex, but either fail to produce smooth solutions or do not account for brain deformations. New methods: We first introduce GridFit, a model-based fitting approach that simultaneously localizes all electrodes’ CT artifacts in grids, strips, or depth arrays. Second, we present CEPA, a brain-shift compensation algorithm combining orthogonal-based projections, spring-mesh models, and spatial regularization constraints. Results: We tested GridFit on ∼6000 simulated scenarios. The localization of CT artifacts showed robust performance under difficult scenarios, such as noise, overlaps, and high-density implants (<1 mm errors). Validation with data from 20 challenging patients showed 99% accurate localization of the electrodes (3160/3192). We tested CEPA brain-shift compensation with data from 15 patients. Projections accounted for simple mechanical deformation principles with < 0.4 mm errors. The inter-electrode distances smoothly changed across neighbor electrodes, while changes in inter-electrode distances linearly increased with projection distance. Comparison with existing methods: GridFit succeeded in difficult scenarios that challenged available methods and outperformed visual localization by preserving the inter-electrode distance. CEPA registration errors were smaller than those obtained for well-established alternatives. Additionally, modeling resting-state high-frequency activity in five patients further supported CEPA. Conclusion: GridFit and CEPA are versatile tools for registering intracranial electrode coordinates, providing highly accurate results even in the most challenging implantation scenarios. The methods are implemented in the iElectrodes open-source toolbox.

Original languageEnglish
Article number110056
JournalJournal of Neuroscience Methods
StatePublished - Apr 2024


  • Depth electrodes
  • EEG (iEEG)
  • Electrocorticography (ECoG)
  • Intracranial
  • Simulations
  • Stereo electroencephalography (SEEG)
  • Subcortical grids
  • Subdural grids


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