= iEEG Contact Localization (UNDER CONSTRUCTION) =
''Authors: Chinmay Chinara, Takfarinas Medani.''

Detection, localization and labeling of SEEG depth electrodes is a vital step in studying brain activity. This tutorial can be considered as a precursor to the [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity|Epileptogenicity]] tutorial.

__'''NOT FOR CLINICAL USE'''__:<<BR>>The performance characteristics of the methods  and software implementation presented in this tutorial have not been  certified as medical devices and should be used for research purposes  only.

<<TableOfContents(3,2)>>

== Download and installation ==
 * '''Requirements''': You have  already  followed all the introduction tutorials and you have a working copy of   Brainstorm installed on your computer.
 * '''CT2MRIREG''': If you are running Brainstorm from the MATLAB environment,  for the coregistration between pre-implantation MRI and post-implantation CT volumes,  you need to have the '''ct2mrireg''' plugin installed on your computer, as a [[https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins|Brainstorm plugin]]. It can be found under the menu '''Plugins > Anatomy > ct2mrireg'''.
 * '''Download the dataset''':
  * Go to the [[http://neuroimage.usc.edu/bst/download.php|Download]] page of this website, and download the file: '''tutorial_seeg_contact_localization.zip'''.
  * Unzip   it in a folder that is not in any of the Brainstorm folders (program   folder or database folder).
 * '''Brainstorm''':
  * Start Brainstorm (MATLAB scripts or stand-alone version).
  * Select the menu '''File > Create new protocol'''. Name it "'''TutorialSeegImplantation'''" and select the options: <<BR>>"'''No, use individual anatomy'''",<<BR>>"'''No, use one channel file per acquisition run'''".

== Import the anatomy ==
=== Pre-implantation MRI ===
 * Right-click on the TutorialSeegImplantation folder > '''New subject''' > '''Subject01'''.<<BR>>Keep the default options you defined for the protocol.

 * 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: '''tutorial_epimap_bids/sub-01/ses-preimp/anat/sub-01_ses-preimp_T1w.nii.gz'''

 * Do you want to apply the transformation to the MRI file? '''YES'''
 * The MRI viewer opens automatically. The positions of all the anatomical fiducials are already defined, they were read from the .json file located in the same folder.
 * Click on "[[http://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy#MNI_normalization|Click here to compute MNI normalization]]", option "'''segment'''".  It computes a non-linear transformation between the subject space and the  MNI ICBM152 space. <<BR>><<BR>> {{attachment:mni_transformation.gif}}
 * Click on [Save] to close the MRI viewer.
 * Rename the new file: '''T1pre'''. <<BR>><<BR>> {{attachment:import_t1pre.gif}}