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Tutorials

Place SEEG electrodes with 3D Slicer

Tutorial

How to prepare implantation imaging and then place SEEG electrodes on it in 3D Slicer, including electrodes that do not follow a straight trajectory - and how to export the contact positions afterwards.

In short

Prepare the imaging with MRIcroGL and FSL, then place the electrodes in 3D Slicer and export the contact positions. Unlike a straight-trajectory approach, this route lets you follow electrodes that bend.

Research use only

The methods and software used in this tutorial have not been certified for clinical practice, and should be considered for research purposes only.

What you will need​

Applications - MRIcroGL and FSL for the preparation, then 3D Slicer for the placement. All three are in the Applications catalogue.

Data - the Data for electrodes labelling tutorial dataset, specifically the Case1 folder. Copy it into your own workspace before you start.

Knowledge - as with any electrode placement, you need to know the implantation procedure and scheme, the electrode specifications, and the anatomy well enough to interpret what you see. High-resolution post-implantation imaging - CT or T1 MRI - is essential.

The workflow​

  1. Prepare your working copy

    Copy the Case1 folder from the tutorial dataset into your own workspace, and open a session.

  2. Convert and inspect the imaging

    Use MRIcroGL to convert the imaging into the format you will work with, and check that the contacts are visible.

  3. Coregister and extract with FSL

    Align the post-implantation imaging to the anatomical reference, and extract the brain so the electrodes can be read against clean anatomy.

  4. Load the prepared volumes into 3D Slicer

    Open the prepared volumes and set up the views you need to follow each trajectory.

  5. Place the electrodes and contacts

    Mark each electrode along its actual path, contact by contact - including where the trajectory curves.

  6. Export the contact positions

    Write out the labelled contact positions, ready for the analysis that follows.

Where to go next​

Localize electrodes with CiCLONE automates most of this and produces BIDS-compatible output directly.

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Place SEEG electrodes with Brainstorm
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Localize electrodes with CiCLONE