= SEEG/Epileptogenicity maps =
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== Dataset description ==
=== License ===
This tutorial dataset  (EEG and MRI data) remains property of the  Grenoble University  Hospital, France. Its use and transfer outside the  ImaGIN and Brainstorm tutorials,  e.g. for research purposes, is prohibited without  written consent. For  questions, please contact Olivier David, PhD  ( olivier.david@inserm.fr ).

=== Clinical description ===
This dataset includes recordings for a patient that was not reported in  the above article, but are part of the same study. The patient presents a  focal epilepsy of the left temporo-occipital junction, MRI-negative,  and was implanted in the surrounding areas. The subfolder "seeg"  contains the recordings of three seizures, all of them showing a  propagation of high-frequency oscillations from the lesion towards the  temporal lobe, bilaterally.

=== SEEG recordings ===
[[http://neuroimage.usc.edu/brainstorm/DatasetEpileptogenicity?action=AttachFile&do=get&target=dixi_am.gif|{{attachment:dixi_am.gif|http://neuroimage.usc.edu/brainstorm/DatasetEpileptogenicity?action=AttachFile&do=get&target=dixi_am.gif|align="right",width="250px"}}]]

The depth electrodes used in this example dataset are [[http://www.diximedical.com/en/microdeep-depth-electrode|DIXI D08-**AM Microdeep electrodes]], with the following specifications:

 * Diameter: 0.8 mm
 * Contact length: 2 mm
 * Insulator length: 1.5 mm
 * Distance between the center of two contacts: 3.5 mm
 * Between 8 and 18 contacts on each electrode

=== Files ===
The dataset we distribute with this tutorial follows the [[http://bids.neuroimaging.io|Brain Imaging Data Structure (BIDS)]] standard for neuroimaging data organization. This specification was first established for MRI and fMRI ([[http://www.nature.com/articles/sdata201644|Gorgolewski, 2016]]) and then refined with an extension dedicated to iEEG ([[https://www.nature.com/articles/s41597-019-0105-7|Holdgraf, 2019]]). The files that will be imported in this tutorial are the  following:

'''tutorial_epimap_bids'''/

 * '''derivatives'''/: Everything that cannot be considered as raw data
  * '''brainvisa'''/'''sub-01_ses-pre'''/: Result of the BrainVISA 4.5 segmentation for the pre-implantation T1 MRI.
 * '''sub-01'''/: Raw data for subject 01
  * '''ses-preimp'''/: Imaging exams performed before the implantation of the sEEG.
   * '''anat'''/'''sub-01_ses-preimp_T1w.nii.gz''': T1-weighted MRI pre-implantation
  * '''ses-postimp'''/: Exams performed with the sEEG devices implanted.
   * '''anat'''/'''sub-01_ses-postimp_T1w.nii.gz''': T1-weighted MRI post-implantation
   * '''ieeg'''/'''..._task-seizure_run-0*_ieeg.eeg''': Three seizure recordings in BrainVision file format, one seizure per file  (with the header files .vhdr and .vmrk)
   * '''ieeg'''/'''..._space-IXI549Space_electrodes.tsv''': Position of the contacts in [[https://neuroimage.usc.edu/brainstorm/CoordinateSystems#MNI_coordinates|MNI space]] ([[https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Anatomical_labelling|SPM12 Segment]] non-linear normalization)
   * '''ieeg'''/'''..._space-ScanRAS_electrodes.tsv''': Position of the contacts in [[https://neuroimage.usc.edu/brainstorm/CoordinateSystems#World_coordinates|world coordinates]], relative to the post-implantation T1 MRI.
 * All the anatomical images have been de-identified with [[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface|mri_deface]] from FreeSurfer 6.

=== References ===
The acquisition methodology is described in the following articles:

David O, Blauwblomme T, Job AS, Chabardès S, Hoffmann D, Minotti L, Kahane P, [[https://academic.oup.com/brain/article/134/10/2898/323878|Imaging the seizure onset zone with stereo-electroencephalography]], Brain. 2011 Oct;134(10):2898-911

Lamarche F, Job AS, Deman P, Bhattacharjee M, Hoffmann D, Gallazzini-Crépin C, Bouvard S, Minotti L, Kahane P, David O, [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5214566/|Correlation of FDG-PET hypometabolism and SEEG epileptogenicity mapping in patients with drug-resistant focal epilepsy]], Epilepsia. 2016 Dec; 57(12):2045–2055

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== Tutorials using this dataset ==
 * [[Tutorials/Epileptogenicity|SEEG epileptogenicity tutorial]]