iEEG Contact Localization

Authors: Chinmay Chinara, Takfarinas Medani, Raymundo Cassani, Anand Joshi.

Detection, localization and labelling of SEEG depth electrodes is a vital step in studying brain activity.

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 introduction tutorials.

NOT FOR CLINICAL USE:
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.

Dataset description

License

This tutorial dataset (SEEG and MRI data) remains property of the Cleveland Clinic, Ohio, USA. Its use and transfer outside the Brainstorm tutorials, e.g. for research purposes, is prohibited without written consent. For questions, please contact Kenneth Taylor, PhD ( taylork2@ccf.org ).

SEEG recordings

The depth electrodes used in this example dataset are PMT SEEG Depth 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 16 contacts on each electrode

Files

tutorial_seeg_implantation/

• raw/: All the raw MRI and CT scans.

  • seeg_straight/: Bent electrodes not available for this subject

    • preMRI.nii: MRI before the implantation of the SEEG.

    • postCT.nii: CT after the implantation of the SEEG.

  • seeg_curved/: Bent electrodes available for this subject

    • preMRI_curved.nii: MRI before the implantation of the SEEG.

    • postCT_curved.nii: CT after the implantation of the SEEG.

• precomputed/TutorialSeegImplantation_precomputed.zip: The precomputed Brainstorm protocol for this tutorial (Do not unzip this file).

• All the anatomical images have been de-identified with defacing from Brainstorm.

Download and installation

• Requirements: You have already followed all the introduction tutorials and you have a working copy of Brainstorm installed on your computer.

• BrainSuite (optional): Make sure you have the latest version of BrainSuite installed. Follow steps as per the BrainSuite for Brainstorm tutorial. This is required to perform skull stripping when importing CT below in order to remove extracranial regions from the CT.

• SPM: If you are running Brainstorm from the MATLAB environment, you need to have the SPM12 toolbox installed on your computer, as a Brainstorm plugin or a custom installation.
  With the stand-alone compiled version of Brainstorm: all the needed SPM scripts have been compiled and included in the executable. This is required for two purposes:

  • Coregistration between pre-implantation MRI and post-implantation CT volumes.

  • Use mask from SPM based tissue segmentation to remove extracranial regions from the CT.

• ct2mrireg: To have an alternate way of doing the coregistration between pre-implantation MRI and post-implantation CT volumes, you need to have the ct2mrireg plugin installed on your computer, as a Brainstorm plugin. It can be found under the menu Plugins > Anatomy > ct2mrireg. If using Brainstorm with MATLAB, please install the Image Processing Toolbox.

• Download the dataset:

  • Go to the 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

  • Select the menu File > Create new protocol. Name it "TutorialSeegImplantation" and select the options:
    "No, use individual anatomy",
    "No, use one channel file per acquisition run".

Import the anatomy

Pre-implantation MRI

• Right-click on the TutorialSeegImplantation folder > New subject > Subject01.
  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.
  Set the file format: MRI: NIfTI-1 (*.nii;*.nii.gz).
  Select: tutorial_seeg_implantation/seeg_straight/preMRI.nii

• The MRI viewer opens automatically. Click on "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 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, Unified segmentation, NeuroImage 2005..
  
  

• Click on Save to close the MRI viewer. New node named preMRI is created.
  
  

Post-implantation CT

The pre-implantation MRI above 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.
  Select: tutorial_seeg_implantation/seeg_straight/postCT.nii

• Choose No for the NIfTI Scaling. The data scaling feature allows the storage in a wider range than what would be allowed by the datatype. For more info check here.

• Choose Yes for the transformation for MRI orientation.
  Choose SPM for coregistration. See the section Volume coregistration for more details on this option.
  Choose Yes for reslicing so that the CT voxel dimensions match those of the MRI.
  
  

• Choose SPM for skull stripping to remove any non-brain tissues as we need just the electrodes inside the brain. See the section Skull Stripping for more details on this option.
  
  

• 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 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.
  
  

• New node named postCT_spm_reslice_masked_spm is created. The postfix _spm_reslice_masked_spm indicates the different processes it has gone through. Rename the node to postCT for simplicity. This will not change the associated file in the database. To see the history of the processes for this file, right click on postCT > File > View file history.
  
  

• To just view the CT File, right click on postCT > Display > MRI Viewer.
  
  

Generate isoSurface

This creates a thresholded mesh from the CT to separate the contacts out from rest of the CT. This aids the user towards localization of the electrodes and its contacts more accurately.

• Right click on postCT > CT segmentation > Generate SEEG/ECoG isosurface.
  
  

• This will bring the Generate isosurface window. This window shows 4 values: the Background level, White level, Max Intensity and the suggested Set isoValue, all of them given in the Hounsfield Unit (HU) scale. The first 3 values are calculated automatically from the histogram of the CT and are displayed for reference to help the user to decide on what to set the isoValue for getting a good thresholded mesh. 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.
  
  

• 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.
  
  

Electrode labeling and contact localization (Manual)

Get started

• Right click on Subject01, and choose SEEG/ECOG implantation.

• The SEEG/ECOG implantation menu pops to choose which modalities you want to use for doing your implantation with. Choose MRI+CT+IsoSurf. This takes you to the functional tab. Subject01 > Implantation > SEEG/ECOG (0) channel gets created. An MRI Viewer loads up with the CT overlayed on the MRI. A 3D figure loads up with isoSurface and 3D MRI. Panel iEEG loads up in the panel viewer. Move around the 3D slices to get a clear view of the contacts so that they can be clicked on. See the section SEEG/ECOG Implantation Menu for more details on this option.
  
  
  
  

Create electrodes and plot contacts manually

• After performing steps above, we will have the Panel iEEG along with the MRI Viewer and 3D figures open. We will be working on the electrode marked below.
  
  

• On Panel iEEG Click on the + (Add new electrode). This opens up the Add electrode window. Enter anything under Electrode label based on your convention. For this e.g., enter A and press OK.
  
  

• This creates an electrode A in selected state, and at the bottom the Electrode configuration section of the panel becomes active. Select the following:

  • Type: SEEG

  • Model: Choose PMT 2102-16-091/2102-16-101 from the drop down list. This will automatically set the other parameters in the section. More details for these parameters can be found in the advanced section here.
    
    

• Set tip: Click the button (shortcut: Ctrl+P) and choose the contact (deepest contact) for the electrode in the isosurface in 3D figure which is going to be set as the tip. This should plot a yellow crosshair marker point on the blob and also update the MRI Viewer's crosshair. At the bottom in Panel iEEG click Set tip and the button turns green indicating that the tip has been set. This point in 3D is at the centroid of the blob which gives a more accurate location of the contact compared to the same if chosen from the MRI.
  
  

• Set skull entry: Choose the point in the isoSurface in 3D figure which is going to be set as the skull entry. This point can be any of the contacts other than the tip preferably closer to the skull so that we get an orientation of the electrode. This should plot a yellow crosshair marker point on the blob and also update the MRI Viewer's crosshair. At the bottom in Panel iEEG click Set skull entry and the button turns green indicating that the entry point has been set. 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. The MRI Viewer gets updated with the an electrode based on the above configuration.
  
  

• Click on Contacts > Save Modifications to update the channel information.
  
  

• When you are done with everything, click on Save in the MRI Viewer. It saves the new channel file and updates the number of channels in the database explorer. Also, while closing the windows a prompt appears asking to save the changes. Just click Yes for everything.

Electrode labeling and contact localization (Automatic)

1. Update (Dec 2024): You can refer to this abstract:
   Automatic SEEG Contact Localization and Labeling using Brainstorm presented at AES 2024.

2. Update (Mar 2025): As part of the workshop held in AI in Epilepsy and Neurological Disorders 2025, we provide a prerelease compiled version of Brainstorm with these new features. Please go to Brainstorm prerelease section of the workshop for more details and accessing the software.

Edit contact positions

Until now, we have seen the case where the trajectory of electrode always followed a straight line but practically that is not the case as there could be bending introduced when the neurosurgeon inserts the electrode. In such cases we need to move most of the contacts to more appropriate positions. For this section we will use a precomputed Brainstorm protocol provided in the tutorial dataset.

• Go to File > Load Protocol > Load from zip file. Browse and select tutorial_seeg_implantation/precomputed/TutorialSeegImplantation_precomputed.zip and click Open. From the loaded protocol we can see there are three subjects. We will be working on the subject named Curved that has electrodes implanted that are bent.
  
  

• Right click on Curved > SEEG/ECOG implantation. Click Continue for working on the existing implantation. Choose MRI+CT+IsoSurf to show the figures. Select the 3D figure and toggle between the electrode ( ) and sphere ( ) modes to get the figures as under using buttons in Panel iEEG. Keep it in the sphere mode for better visibility. The contacts definitely need to be corrected and moved to their right positions.
  
  

• Display the contact labels in 3D figure by right clicking Channels > Display labels. It can be seen that the contacts A2-A15 are incorrect. Let us first correct contact A2.
  
  

• Since the isoSurface blobs are the correct ones, we can use them as ground truth guide to correct the contacts. Click the button (shortcut: Ctrl+P) and choose the correct blob. That places a yellow crosshair on the blob and updates the MRI Viewer crosshair as well.
  
  

• Without clicking anywhere else, move your cursor to the MRI Viewer, right click and go to Electrodes > Set electrode position (or press Ctrl+S). From the Set electrode position window choose A2 and press OK. This will update the position of A2 only in the MRI Viewer.
  
  

• Click on Save and it closes all the windows and updates the channel file and number of channels in the database explorer.
  
  

• Right click on Curved > SEEG/ECOG implantation. Click Continue for working on the existing implantation. Choose MRI+CT+IsoSurf to show all the figures. Select the 3D figure and in the Panel iEEG, choose the sphere ( ) mode for display. You will now see the updated contact in the 3D figure as well.
  
  

• Follow the above steps to update all the remaining contacts as required. Unfortunately, Brainstorm currently does not have a way to handle curved electrodes display yet: if you move the contacts, the electrode remains represented as a straight line. This is a display issue only, which has no impact on any computation, but we hope to improve it at some point.
  
  

• We have a functionality called line fitting that can help better view the trajectory in the 3D figure with sphere ( ) display mode. Choose the electrode and click Contacts > Show/Hide line fit through contacts.
  
  

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.
  
  

• 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:

  • Coordinates (millimeters) radio buttons: Users can switch between the different coordinate systems (SCS, MRI, World, MNI) to change the coordinate values of the contacts.

  • (Add new 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.

  • (Select surface point): Activates coordinate selection in 3D figure window. (Shortcut: Ctrl+P)

  • (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 > Show/Hide line fit through contacts: Performs line fitting through the contacts in 3D figure.

  • 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. 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 A is associated to channels A1, A2...A14 => detected number of contacts is 14.

  • 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 figure 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 figure, 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. 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.

SEEG/ECOG Implantation Menu

While starting manual implantation on an volume by right click on subject node > SEEG/ECOG implantation, the menu below pops up allowing the user to choose which modality or modalities to proceed with.

• MRI: MRI viewer loads up with MRI volume only.

• CT: MRI viewer loads up with CT volume only.

• MRI+CT: MRI viewer loads up with the CT overlayed on the MRI.

• MRI+CT+IsoSurf: MRI viewer loads up with the CT overlayed on the MRI. 3D figure loads up with the isoSurface and 3D MRI slices.

• Cancel: Abort the process.

Skull Stripping

Skull stripping is done on the MRI volume to get a binary volumetric mask of just the brain region. On applying this mask to volumes like CT, it helps in removing any non-brain tissues like skull, scalp, fat, and any other head tissues from the CT volume. In this tutorial, we have a CT scan of a subject with intracranial electrodes, so on applying this mask not only removes the non-brain tissues but also the hanging extracranial wires. Brainstorm has the following menu options for skull stripping:

• SPM: Uses SPM toolbox's Tissue Segmentation.

• BrainSuite: Uses BrainSuite's Brain Surface Extractor.

• Skip: Proceed without skull stripping.

Walkthrough Video

TODO

Additional Documentation

Forum discussions

• Updating SEEG coordinates

Related tutorials

• Epileptogenicity

• ECoG/sEEG tutorial