The primary objective of GTT is to provide a systematic, automated and fast method to quantify the thickness of tissues in the head. In doing so, GTT aims to provide a tool to understand and control for the influence of tissues on non-invasive brain stimulation and neuroimaging.
The GTT pipeline is discussed in the following this study: https://doi.org/10.1101/2023.04.18.537177
The following persons worked on this project
- Sybren Van Hoornweder
- Marc Geraerts
- Stefanie Verstraelen
- Marten Nuyts
- Kevin A. Caulfield
- Raf L.J. Meesen
Pleaser cite the following article if you use the following script: TBP
The pipeline requires MATLAB and SimNIBS to run.
We have used code from the following projects in this repository:
- [SimNIBS] (https://simnibs.github.io/simnibs/build/html/index.html)
- Triangle/Ray Intersection
- [PointTriangleDistance] (https://www.mathworks.com/matlabcentral/fileexchange/22857-distance-between-a-point-and-a-triangle-in-3d?s_tid=FX_rc1_behav)
To run the pipeline, download the code. An more in-depth discussion of the underlying methods can be found in the accompanying publication. Make sure that the SimNIBS - matlab path is added to the MATLAB environment.
GTT consists of three steps: preparation, initation, and measurement. It requires a structure, as input, containing the following arguments:
- structure.Mesh (Path containing head mesh obtained by CHARM, e.g., ...\m2m_subject1)
- structure.Fiducial (Starting coordinate, e.g., −52.2 −16.4 57.8)
- structure.FiducialType (Coordinate space, can be MNI or Subject space Subject)
- structure.BeginTissue (Whether structure.Coord is a scalp [SCALP] or grey matter [GM] coordinate)
- structure.PlotResults (Boolean statement if results should [1] or should not be plotted [1])
- structure.Direction (1x3 array that defines the vector to use for the SCD measurements (e.g., the TMS coil direction). When this field is absent (default), standard SCD measurements are performed)
Examples of the GTT graphical output are shown below:
This software runs under a GNU General Public License v3.0.
This software uses free packages from the Internet, except MATLAB, which is a proprietary software by the MathWorks. You need a valid Matlab license to run this software.