= SEEG epileptogencity maps =
'''[TUTORIAL UNDER DEVELOPMENT: NOT READY FOR PUBLIC USE] '''

''Authors: Francois Tadel, Olivier David.''

This tutorial introduces some concepts that are specific to the management of SEEG recordings in the Brainstorm environment, and explains how to compute maps of epileptogenicity from ictal recordings. It is based on a clinical case from the Grenoble University Hospital, France.

Note that the operations used here are not detailed, the goal of this  tutorial is not to introduce Brainstorm to new users. For in-depth  explanations of the interface and theoretical foundations, please refer  to the [[http://neuroimage.usc.edu/brainstorm/Tutorials#Get_started|introduction tutorials]].

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== Download and installation ==
How to get the example dataset:

 * '''Requirements''': You have  already  followed all the introduction tutorials and you have a working copy of   Brainstorm installed on your computer.
 * Go to the [[http://neuroimage.usc.edu/bst/download.php|Download]] page of this website, and download the file: '''tutorial_epimap.zip'''
 * Unzip   it in a folder that is not in any of the Brainstorm folders (program   folder or database folder)

Files included in this package:

 * anat/MRI/3DT1pre_deface.nii: Subject MRI before SEEG implantation
 * anat/MRI/3DT1post_deface.nii: Subject MRI after SEEG  implantation
 * anat/MRI/brainvisa: Cortical surface extracted with BrainVISA 4.5
 * anat/implantation/*: Positions of the SEEG contacts in various formats (MNI or subject space)
 * seeg/SZ*.TRC: Seizure recordings in Micromed format, one seizure per file
 * MRI scans were de-identified with FreeSurfer's mri_deface.

== Import the anatomy ==
 * Start Brainstorm (Matlab scripts or stand-alone version)
 * Select the menu File > Create new protocol. Name it "'''TutorialEpimap'''" and select the options:
  * "'''No, use individual anatomy'''",
  * "'''No, use one channel file per acquisition run'''".

 *