In order to generate epileptogenicity maps, we need accurate 3D positions for the contacts of the depth electrodes. There are various solutions to get these positions, the best one depending on the information you have access to and the type of material that was implanted. Placing the contacts requires a good understanding of the implantation scheme reported by the neurosurgeon, and some skills in reading MRI scans.
To make this tutorial easier to reproduce and follow, we distribute the positions of the contacts saved in a text file (folder /anat/implantation). Some options to create this text file are documented here, but you don't need to read this before jumping to the next tutorials. You can skip this page if you already know how to get the contact positions in subject or MNI space, or if you are not interested in this particular topic. The sections below are all optional.
Next tutorial: Tutorial 3: Importing and pre-processing
Description of the electrodes
The depth electrodes used in this example dataset are DIXI D08-**AM Microdeep electrodes, with the following specifications:
- Diameter: 0.8 mm
- Contact length: 2 mm
- Insulator length: 1.5 mm
- Distance between the center of two contacts: 3.5 mm
- Between 8 and 18 contacts on each electrode
Using IntrAnat
How to use IntrAnat to get the contact positions.
[ Under construction ]
Using Brainstorm
The online tutorial SEEG epileptogenicity maps explains how to import and process SEEG recordings with Brainstorm. You can use the information on this page to create a text file with the position of all the SEEG contacts, that you can import with ImaGIN. Start by importing the pre- and post-implantation volumes to your Brainstorm database (Import the anatomy), then create a new implantation file (Edit the contacts positions) and finally use the menu "Contacts > Export contacts positions".
Next tutorial: Tutorial 3: Importing and pre-processing