GeodesicSlicer: a Slicer Toolbox for Targeting Brain Stimulation

Abstract

NonInvasive Brain Stimulation (NIBS) is a potential therapeutic tool with growing interest, but neuronavigation-guided software and tools available for the target determination are mostly either expensive or closed proprietary applications. To address these limitations, we propose GeodesicSlicer, a customizable, free, and open-source NIBS therapy research toolkit. GeodesicSlicer is implemented as an extension for the widely used 3D Slicer medical image visualization and analysis application platform. GeodesicSlicer uses cortical stimulation target from either functional or anatomical images to provide functionality specifically designed for NIBS therapy research. The provided algorithms are tested and they are accessible through a convenient graphical user interface. Modules have been created for NIBS target determination according to the position of the electrodes in the 10-20 system electroencephalogram and calculating correction factors to adjust the repetitive Transcranial Magnetic Stimulation (rTMS) dose for the treatment. Two illustrative examples are processing with the module. This new open-source software has been developed for NIBS therapy: GeodesicSlicer is an alternative for laboratories that do not have access to neuronavigation system. The triangulation-based MRI-guided method presented here provides a reproducible and inexpensive way to position the TMS coil that may be used without the use of a neuronavigation system.

A new toolbox to compare target localizations for non-invasive brain stimulation: An application of rTMS treatment for auditory hallucinations in schizophrenia

“…The ST localization corresponding to a particular scalp position (T3P3) and the PT localization determined by computerized cortical MRI scan must be in a common space to be properly compared. To reach this goal, we developed the open-source tool GeodesicSlicer (The code and description are available in the Wikipage) (Briend et al, 2020). This software is based on the geodesic distance measurement (defined as the shortest path between two points in a curved space) at scalp-surface calculated on a mesh morphed to participantspecific brain MRI.…”

“…In addition to anatomical variability, rTMS efficacy could also be related to different frequencies and study designs used (Dollfus et al, 2018(Dollfus et al, , 2016b. A strong effort to individualize these approaches should have be done, as for example calculating the correction factors for each patient to adjust the rTMS dose for the treatment (Briend et al, 2020).…”

“…This module can compute geodesic paths between any rTMS targets, whether localized by MRI-guided TMS neuronavigation or localized by 10-20 EEG position. Based on Andoh's triangulation-based MRI-guided method (Andoh et al, 2009), this module could also calculates the geodesic distances between the projected stimulation target and the position of the 3 nearest electrodes in the individualized 10-20 system EEG in order to guide the stimulation (Briend et al, 2020). Please refer to the toolbox documentation on our Wikipage for detailed steps.…”

“…Please refer to the toolbox documentation on our Wikipage for detailed steps. This method provides a reliable and inexpensive way to position the TMS coil that can be used in case of unavailable online neuronavigation like in a clinical setting (Briend et al, 2020), but also in comparing different localizations due to different target modalities via the "Parameters to find the shortest path" module of the software. For any sort of questions, feedback, suggestions, or critique, please visit the 3D slicer support forum.…”

“…We therefore postulated that choosing ST using 10-20 EEG system over PT using anatomical landmarks could induce an anatomical bias able to explain clinical outcomes. In order to precisely quantify this anatomical bias, and because using different TMS targeting methods will lead to somewhat different scalp targets, we developed a free open-source software: GeodesicSlicer (Briend et al, 2020), that computes the shortest path at scalp-surface between any rTMS targets, whether localized by MRI-guided neuronavigation or by the 10-20 EEG system.…”