= 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]].

__'''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(2,2)>>

== 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.

== Dataset description ==
Link to SEEG analysis dataset description.

== Download and installation ==
 * '''Prerequisites''':
  * '''Brainstorm Installation''': Ensure you have a working copy of Brainstorm installed on your computer.
  * '''Familiarity with Brainstorm''': This tutorial assumes that you have completed all the [[https://neuroimage.usc.edu/brainstorm/Tutorials|Brainstorm introduction tutorials]] and are comfortable with its interface and basic functionalities.
 * '''SPM12 (Statistical Parametric Mapping)'''
  * '''Purpose''': SPM12 is required for:
   * Coregistration between pre-implantation MRI and post-implantation CT volumes.
   * Utilizing [[https://andysbrainbook.readthedocs.io/en/latest/SPM/SPM_Short_Course/SPM_04_Preprocessing/04_SPM_Segmentation.html|tissue segmentation masks]] to remove extracranial regions from the CT.
  * '''Installation''':
   * '''MATLAB Users''': If you are running Brainstorm within MATLAB, install SPM12 either as a [[https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins|Brainstorm plugin]] or through a custom installation.
   * '''Standalone Brainstorm Users''': If you are using the standalone compiled version of Brainstorm, SPM12 functionalities are included in the executable, and no additional installation is necessary.
 * '''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)'''

== Contact localization ==
=== Generate Isosurface ===
 * Link to SEEG analysis tutorial to create a thresholded mesh from the CT.

'''TODO: Add relevant screenshots'''

=== 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/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.
 * 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 ==
=== Forum discussions ===
=== Articles ===
=== Related tutorials ===