= 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 [[http://neuroimage.usc.edu/brainstorm/Tutorials#Get_started|Brainstorm introduction tutorials]].
 * Make sure you complete the [[https://neuroimage.usc.edu/brainstorm/seeg/Introduction|CT to MRI co-registration]] and [[https://neuroimage.usc.edu/brainstorm/seeg/SeegContactLocalization|Contact localization and labeling]] advanced tutorial before proceeding any further.

__'''NOT FOR CLINICAL USE'''__:<<BR>>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.

<<TableOfContents(3,2)>>

== Introduction ==
'''GARDEL''' ('''G'''UI for '''A'''utomatic '''R'''egistration and '''D'''epth '''E'''ectrode '''L'''ocalization) was developed by a multidisciplinary team as part of the [[https://pubmed.ncbi.nlm.nih.gov/29605667/|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 [[https://www.inserm.fr/en/about-us/|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 [[https://neuroimage.usc.edu/brainstorm/seeg/Introduction|CT to MRI co-registration]] to have the data and the required anatomy set up.
 * Follow the tutorial [[https://neuroimage.usc.edu/brainstorm/seeg/SeegContactLocalization|Contact localization and labeling]] to generate the isosurface from the CT
 * '''GARDEL''' [[https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins|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<<BR>><<BR>>''''''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 [[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.
 * 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 [[https://neuroimage.usc.edu/brainstorm/seeg/SeegContactLocalization#Edit_the_contacts_positions|here]].

'''TODO: Show some bad detections with this tutorial data and steps how to correct them here'''

'''TODO: Add relevant screenshots'''

== Additional Documentation ==
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