= 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]].

<<TableOfContents(3,2)>>

<<Include(DatasetEpileptogenicity, ,   from="\<\<HTML\(\<!-- START-PAGE --\>\)\>\>",   to="\<\<HTML\(\<!-- STOP-SHORT --\>\)\>\>")>>

== 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'''".
 * Create a new subject:
  * Right-click on the TutorialEpimap folder > '''New subject''' > '''Subject01'''
  * Keep the default options you defined for the protocol.
 * Import the pre-implantation MRI scan:
  * Switch to the "anatomy" view of the protocol.
  * Right-click on the subject node > '''Import MRI''':<<BR>>Set the file format: "All MRI file (subject space)"<<BR>>Select the file: '''tutorial_epimap/anat/MRI/3DT1pre_deface.nii'''

  * Do you want to apply the transformation to the MRI file? '''YES'''
  * The MRI viewer opens automatically. Click on "[[http://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy#MNI_transformation|Click here to compute MNI transformation]]".  It computes an affine transformation between the subject space and the  MNI ICBM152 space, and sets default positions for all the anatomical landmarks.<<BR>> {{attachment:mni_transformation.gif}}
  * Click on [Save] to close the MRI viewer.

 * Import the post-implantation MRI scan:
  * Right-click on the subject node > '''Import MRI''':<<BR>>Select the file: '''tutorial_epimap/anat/MRI/3DT1post_deface.nii'''
  * Do you want to apply the transformation to the MRI file? '''YES'''
  * How to register the new volume: '''IGNORE'''<<BR>>The two volumes have already been coregistered with SPM. See the section [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Volume_coregistration|Volume coregistration]] for more details on this option.
  * Reslice the volume: '''YES'''
  * The MRI viewer opens automatically, showing the post-implantation volume as an overlay layer on top of the previous volume. Adjust the transparency and amplitude threshold of this layer in the section Data options in the Surface tab. Use this display to validate that the coregistration of the two volume is correct, all the parts of the head must align well. <<BR>><<BR>> {{attachment:anat_overlay.gif||width="591",height="277"}}
 * Generate default cortex and head surfaces for this subject:
  * Right-click on the pre-implantation MRI > '''SPM canonical surfaces'''.
  * Leave the default option selected (20484). This represents the resolution of SPM template surface used in this process. The higher the better, but it will slow down significantly the computation of the epileptogenicity maps.
  * These surfaces will be used later, in the computation of the epileptogenicity maps. Read the advanced sections of this page for information on [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Importing_realistic_surfaces|how to use realistic surfaces]] from BrainVISA or FreeSurfer.<<BR>><<BR>> {{attachment:anat_canonical.gif||width="598",height="161"}}

== Access the recordings ==
.

.

.

== Volume coregistration ==
== Importing realistic surfaces ==