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| Please note that this tutorial is intended for users already familiar with Brainstorm. It does not provide detailed explanations of the software's interface or theoretical foundations. | Please note that this tutorial is intended for users already familiar with Brainstorm. It does not provide detailed explanations of the software's interface or theoretical foundations. |
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| * Follow the tutorial [[https://neuroimage.usc.edu/brainstorm/seeg/SeegContactLocalization|Contact localization and labeling]] to generate the isosurface from the CT | * Follow the tutorial [[https://neuroimage.usc.edu/brainstorm/seeg/SeegContactLocalization|Contact localization and labeling]] to generate the isosurface from the CT |
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| == Contact localization == === Generate Isosurface === * Link to SEEG analysis tutorial to create a thresholded mesh from the CT. * Talk about why this is required for automatic detection '''TODO: Add relevant screenshots''' |
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| * Choose '''MRI+CT+IsoSurf''' from the popup menu (more details about the menu can be found [[https://neuroimage.usc.edu/brainstorm/Tutorials/SeizureFingerprinting#Start_implantation|here]]). This takes you to the functional tab. '''Subject01 > Implantation > SEEG/ECOG (0)''' channel gets created. All expected figures open up. Panel iEEG loads up in the panel viewer. * Click on '''Auto > GARDEL'''. Click '''Yes''' on the disclaimer that pops up. |
* Choose '''MRI+CT+IsoSurf''' from the popup menu (more details about the menu can be found [[https://neuroimage.usc.edu/brainstorm/seeg/SeegContactLocalization#Start_implantation|here]]). While any of the options can be chosen from the menu, this gives the option to visualize and interact both in 3D and 2D. * In the iEEG panel, click on '''Electrodes > Automatic localization > GARDEL'''. Click '''Yes''' on the disclaimer that pops up. |
Automatic SEEG Contact Localization using GARDEL
Authors: ***
This tutorial describes how to perform automatic SEEG contact localization in Brainstorm using GARDEL.
Please note that this tutorial is intended for users already familiar with Brainstorm. It does not provide detailed explanations of the software's interface or theoretical foundations.
For comprehensive introductory material, refer to the Brainstorm introduction tutorials.
Make sure you complete the CT to MRI co-registration and Contact localization and labeling advanced tutorial before proceeding any further.
NOT FOR CLINICAL USE:
The methods and software implementations presented in this tutorial have not been certified as medical devices. They are intended for research purposes only and should not be used for clinical decision-making.
Contents
Introduction
GARDEL (GUI for Automatic Registration and Depth Eectrode Localization) was developed by a multidisciplinary team as part of the EpiTools suite, led by Samuel Medina Villalon (Aix‑Marseille University & AP‑HM, Marseille), Rodrigo Manuel Paz (University of Buenos Aires–CONICET), Nicolas Roehri, Stanislas Lagarde, Fabrice Pizzo, Bruno Colombet, Fabrice Bartolomei, Romain Carron, and Christian Bénar, all contributing through INSERM and partnering institutions across France, Argentina, and Switzerland. This international group combined clinical neurophysiology and advanced imaging expertise to create GARDEL, enabling fully automatic detection and anatomical labeling of SEEG contacts thereby laying a strong foundation for streamlining SEEG analysis in research workflows.
Prerequisites
Complete the CT to MRI co-registration to have the data and the required anatomy set up.
Follow the tutorial Contact localization and labeling to generate the isosurface from the CT
GARDEL Brainstorm plugin needs to be installed for doing the automatic detection of the contacts.
Import the anatomy
Link to SEEG analysis tutorial to import the MRI and CT along with generating the CAT12 surfaces.
TODO: Add relevant screenshots
TODO: Talk about working in the CT space (better resolution -> better automatic localization)
Automatic contact localization using GARDEL
Right click on Subject01, and choose SEEG/ECOG implantation.
Choose MRI+CT+IsoSurf from the popup menu (more details about the menu can be found here). While any of the options can be chosen from the menu, this gives the option to visualize and interact both in 3D and 2D.
In the iEEG panel, click on Electrodes > Automatic localization > GARDEL. Click Yes on the disclaimer that pops up.
- In few minutes, you can see the electrodes being rendered live on the figures. While GARDEL is a great tool but there could be some bad detections due to factors mentioned in the disclaimer. It is always good to verify the results carefully.
If there are any bad detections, they can be post-processed using editing features available within Brainstorm. More details can be found here.
TODO: Show some bad detections with this tutorial data and steps how to correct them here
TODO: Add relevant screenshots
Additional Documentation
Forum discussions
Articles