Table 1.
Examples of Software Packages that Can Be Used to Render icEEG Surface Data
| Name | Developer | Comments |
|---|---|---|
| MRI-based surface rendering | ||
| BioImage Suite 3.01—Orthogonal Viewer | Yale University | A segmentation-based method with a relatively short runtime. The resulting cortical surface can be exported as a text file that stores the vertex and face coordinates of the surface. |
| FreeSurfer 5.1.0 | Harvard/MGH | A segmentation-based process for generating high-definition cortical surfaces with a relatively long run-time. Includes several other anatomical analysis tools. |
| Curry 7—Image Analysis Package | Compumedics | A segmentation algorithm is used to generate a triangular mesh surface. |
| Constrained Laplacian Anatomic Segmentation using Proximity (CLASP) | McConnell Brain Imaging Center | An iterative morphing-based technique that minimizes the repulsion-based cost function by deforming a voxel-enclosed surface. |
| Mapping electrodes to the brain surface | ||
| BioImage Suite 3.01—Electrode Editor | Yale University | The electrode editor allows export of a map file with x/y/z coordinates in the MRI space. |
| Statistical Parametric Mapping (SPM) | University College London | A software suite that executes in Matlab. It can also be used for fMRI, SPECT, MEG, and EEG analysis. |
| Flirt 5.5 | University of Oxford | An automated tool for linear image registration between different acquisition methods (i.e., MRI and CT). |
| Curry 7—Image Analysis Package | Compumedics | Electrodes are mapped to the cortical surface through co-registration of MRI and CT images using reference landmarks. |
| Computational processing of icEEG data | ||
| Matlab 7.13 (R2011B) | Mathworks | This software provides a programming environment in which scripts can be written to process electrical data. |
| BCI2000 | Wadsworth Center | A broad collection of signal processing routines and experimental paradigms that are free for research and academic institutions. |
| Displaying icEEG data on the cortical surface | ||
| Matlab 7.13 (R2011B) | Mathworks | The MRI-based mesh surface and postprocessed icEEG data can be combined using the “plot,” “surf,” and “contour” functions in a custom-written script. |
| Curry 7—Image Analysis Package | Compumedics | Data can be rendered on a three-dimensional cortex or shown on a two-dimensional scalp plot. The user retains full control over viewing angle and zoom. |
| Brain Computer Interface 2000 | Wadsworth Center | The SIGFRIED module of BCI2000 can be used to process and display data obtained through icEEG. Data can also be exported and visualized using external software. |
| Producing a 3D color movie of icEEG information | ||
| Matlab 7.13 (R2011B) | Mathworks | After generating projections for each frame of an icEEG recording, code can easily be written to assemble the files into a single *.avi or *.mpg movie. |
| Curry 7—Image Analysis Package | Compumedics | Projections are rendered in real time and allow threedimensional rotation of the cortical surface at any point during playback. |
IcEEG = intracranial electro-encephalography.