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

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.
 * '''SPM''': If you are running Brainstorm from the MATLAB environment, you need to have the SPM12 toolbox installed on your computer, as a [[https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins|Brainstorm plugin]] or a custom installation. <<BR>>With the stand-alone compiled  version of Brainstorm: all the needed SPM scripts have been compiled and  included in the executable.
 * '''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_implantation.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_seeg_implantation/preMRI.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_normalization|Click here to compute MNI normalization]]", option "'''maff8'''".  This method is embedded in Brainstorm and does not require the installation of SPM12. However, it requires the automatic download of the file SPM12 Tissue Probability Maps. If you do not have access to internet, see the instructions on the [[https://neuroimage.usc.edu/brainstorm/Installation#No_internet_access|Installation]] page. It is based on an affine co-registration   with the MNI ICBM152 template from the SPM software, described in the   following article: Ashburner J, Friston KJ, [[http://www.ncbi.nlm.nih.gov/pubmed/15955494|Unified segmentation]], NeuroImage 2005.. <<BR>><<BR>> {{attachment:1.png}} {{attachment:2.png}}
 * Click on '''Save''' to close the MRI viewer.
 * Rename the new file: '''preMRI'''. <<BR>><<BR>> {{attachment:3.png}}

=== Post-implantation CT ===
 * The pre-implantation MRI will be used as the anatomical reference for this subject. We will now import a second scan done after the SEEG implantation, on which we can see the SEEG contacts. In this dataset, the post-implantation volume is a CT scan (contacts hypersignal appear in white).
 * Right-click on the subject node > '''Import CT''':<<BR>>Select: '''tutorial_seeg_implantation/postCT.nii'''
 * Follow steps  [[https://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy#Import_CT|here]] to complete the process on importing a CT.
 * The MRI viewer opens automatically, showing the post-implantation CT volume as a colored layer on top of the previous volume. Adjust the transparency and amplitude threshold of this layer in the section '''Data options''' of the '''Surface '''tab, adjust its [[Tutorials/Colormaps|colormap]] with the popup menu of the figure. 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:4.png}}
 * Rename the new file: '''postCT'''.<<BR>><<BR>> {{attachment:5.png}}

=== Generate isoSurface ===
This creates a thresholded mesh from the CT to separate the contacts out from rest of the CT. This allows the user to better see and localize the electrodes and its contacts.

 * Right click on '''postCT > CT segmentation > Generate threshold mesh from CT'''.<<BR>><<BR>> {{attachment:6.png}}
 * This will bring the '''Generate isosurface''' window. This window shows 4 things in '''Hounsfield Unit (HU)''' i.e. the Background level, the White level, the Max Intensity and the '''Set isoValue''' field. The first 3 values are calculated automatically from the histogram of the CT and is displayed for reference. This is to help the user to decide on what to set the isoValue for getting a good thresholded mesh. Another way is to refer to the [[https://en.wikipedia.org/wiki/Hounsfield_scale|Wiki]]. The editable isoValue field shows an estimated best guess based on mean of White Level and Max Intensity. Just let that value be and press '''OK'''.<<BR>><<BR>> {{attachment:7.png}}
 * An isosurface is generated showing the contact as blobs overlayed on the 3D MRI slices. The '''Thresh''' slider under '''Surface options''' can be used to fine tune and regenerate mesh with different isoValues.<<BR>><<BR>> {{attachment:8.png}}

=== Electrode labelling and contact localization ===
=== Get started ===
 * Right click on '''postCT''', and choose '''SEEG/ECOG implantation'''. This takes you to the functional tab and '''Subject01 > Implantation > SEEG/ECOG (0)''' channel gets created. Also the '''MRI Viewer with the CT''' loaded and '''3D Viz with the isoSurface+3D MRI Slices''' loaded opens up along with the '''Panel iEEG'''.<<BR>><<BR>> {{attachment:9.png}}

=== Panel iEEG ===
 * When opening SEEG/ECOG recordings, the panel iEEG is added to the Brainstorm window. You can use it to edit the display properties of the depth electrodes. In this interface, "'''electrode'''" refers to entire depth electrode implanted in the head of the patient while "'''contact'''" refers to recording sites on the electrode. There are multiple contacts on an electrode, and one contact corresponds to one channel of data in the channel file and the recordings. <<BR>><<BR>> {{attachment:10.png}}
 * SEEG depth electrodes are graphical objects, they are defined independently from the SEEG contacts available in the channel file and recordings. A contact/channel is associated to a depth electrode using the '''Group''' property of the channel, accessible with a right-click on the channel file > '''Edit channel file'''.
 * In this example, the depth electrodes available in the Panel iEEG have been manually set by using this Panel features. In the convention used here, the contact names must start with one or more letters (the name of the electrode) followed by a number representing the index of the contact on the electrode. '''Contact #1''' is at the tip of the electrode, and is therefore the deeper contact of the electrode. If the convention used in your recordings is different, you may have to edit the electrodes properties in order to get them displayed correctly.
 * Buttons in the toolbar:
  * '''Add an electrode''': Adds an entry for a new depth electrode. The new electrode will not be displayed until you set its properties and position. This will not add or remove SEEG contacts or channels of data.
  * '''Remove selected electrodes''': Deletes a depth electrode from the list, but does not modify the list of SEEG contacts or channels of data.
  * '''Set color for selected electrodes''': Self explanatory.
  * '''Show/hide selected electrodes''': To hide an electrode in the 3D figures and MRI viewer, select it in the list then click on this button. Select all the electrodes with the standard shortcut Ctrl+A.
  * '''Display contacts as''': Depth electrodes / Spheres.
  * '''Contacts > Set default positions''': For each of the selected electrodes, the current positions of the SEEG contacts are discarded and replaced with the default positions of the contacts on the electrode. The properties used for setting the position of the contacts are the contact spacing, the tip of the electrode and the entry point in the skull. Contact #i is placed along the electrode at (i-1)*contact_spacing millimeters from the tip of the electrode.
  * '''Contacts > Project on electrode''': For each of the selected electrodes, the contacts are projected orthogonally on the electrode. This menu can be useful for aligning contacts that were marked one by one.
  * '''Contacts > Line fit through contacts''': Performs line fitting through the contacts in 3D Viz.
  * '''Contacts > Save modifications''': Save the current modifications to the channel file. Otherwise, the modifications are saved only when you close the figure (dialog box "Save modifications to channel file?")
  * '''Contacts > Export contacts positions''': Save the 3D positions of the SEEG contacts in a text file, using one of the file formats supported by Brainstorm.
 * Electrode properties: ''Properties that have an impact on the position of the contacts''.<<BR>>
  * If you edit the properties, the modifications will apply to all the selected electrodes in the current channel file. Check what is selected before making changes.
  * '''Type''': SEEG/ECOG
  * '''Model''': List of electrode models. If you select an entry in this menu, it will copy the default properties for this model to the selected electrodes. If you are using electrodes that are not in this list, please post on the specification of your devices on the user forum and we will add them to this list.
  * '''Number of contacts''': Number of recording sites on the electrode. By default, this is set for SEEG to the maximum index found in a group of contacts. Example: electrode s' is associated to channels s'1, s'2, s'3, s'10, s'11, s'12 => detected number of contacts is 12.
  * '''Contact spacing''': Distance between the centers of two consecutive contacts in the electrode. In this example dataset, the default value corresponds to the average distance observed between pairs of adjacent contacts.
  * '''Set tip''': Select one electrode in the list, then move the cursor of the MRI viewer to the tip of the selected electrode (center of the first contact) or choose the contact from the isoSurface in the 3D Viz and finally click on [Set tip].
  * '''Set skull entry''': Select one electrode in the list, then move the cursor of the MRI viewer to the point where the depth electrode enters the skull or choose the point from the isoSurface in the 3D Viz, and finally click on [Set skull entry]. This position does not actually correspond to any contact, it is used only to estimate the direction of the depth electrode. [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Edit_the_contacts_positions|More details]].
 * Display options: Properties that only affect the way the electrodes are renderer graphically.
  * '''Contact length''': Defines the length of the yellow cylinder that represents the contacts along the electrode axis, or the diameter of the sphere when the electrodes are not rendered.
  * '''Contact diameter''': Diameter of the yellow cylinders representing the contacts. By default, this value is slightly larger than the electrode diameter so that it is rendered correctly. If you use the same value as the electrode diameter, the contacts might not be visible.
  * '''Electrode diameter''': Diameter of the cylinder representing the SEEG depth electrode.
  * '''Electrode length''': Length of the cylinder representing the SEEG depth electrode.