Computational protocol: Rapid and efficient localization of depth electrodes and cortical labeling using free and open source medical software in epilepsy surgery candidates

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Protocol publication

[…] The whole pre-processing stage was accomplished semi-automatically using predefined auto-analysis pipelines.We determined the final exact position of each IE and individual contacts in all patients with respect to the underlying labeled cortex using a visualization procedure in the 3D Slicer platform.To locate the anatomical structures adjacent to each electrode we visually inspected 2D multi-planar reconstructions of the co-registered CT and MR images. We used 3D surface renderings of the pial surfaces and the IEs, for a global overview of the final implantation process and also to assist in the localization of 2D multiplanar navigation.Both approaches are described in the following sections.Multiplanar 2D Visualization. Brain MR image of each patient along with its corresponding cortical labels and CT scan containing the IEs were jointly explored. This procedure, also used by other epilepsy centers (Desai et al., ; Gonzalez-Martinez et al., ; Kubota et al., ) allows one to identify the location of individual contacts on different anatomical cuts and its position according to the surrounding cortex.The process involved setting an accurate density threshold and window level for the CT volumes containing the IEs along with appropriate adjustment of display and transparency options for the cortical parcellations. At that point each contact was manually selected in order to obtain additional information as anatomical cortical location and spatial coordinates that were displayed in the visualization panel.Additionally; using the display function in SPM8 (freely available at, we were able to manually select contacts that evidenced ictal onset activity providing individual MNI spatial coordinates; important to conduct group analysis (See Table ). It was achieved registering and normalizing the previously aligned post-implant CT volume and T1 structural images to a standardized MNI template as described before (Ashburner and Friston, ) through the utility “Normalize (Estimate and Write)” in SPM8. (See more details in the supplementary material section and also at Please note that the SPM software is a suite of MATLAB functions and subroutines from The MathWorks, Inc that requires commercial licensing.Brain 3D surface reconstructions. For a global overview of the final implantation process, automatic 3D Pial reconstructions obtained from the freesurfer output were then overlaid with the IEs on the surface. We automatically implemented the Marching Cubes algorithm (Cline et al., ) to generate 3D representations of the electrodes by using the volume rendering technique (Drebin et al., ) which enables real-time 3D visualization and quantitative analysis of volumetric data. We accomplished the aforementioned steps by combining the use of “Model” and “Volume Render” modules for the Pial surface and IEs representations, respectively with adequate transparency and 3D display settings to the 3D visualization panel.Thus the cortical surface renders clarified the deep trajectory of IEs and its relation with cortical structures. This procedure is also essential to assist operators during the 2D multi-planar navigation when the implantation planning is uncertain. […]

Pipeline specifications

Software tools SPM, FreeSurfer
Application Computerized tomography scan imaging
Organisms Homo sapiens
Diseases Epilepsy