Place SEEG electrodes with Brainstorm
How to place SEEG electrodes on a post-implantation volume using Brainstorm, and produce a standardized implantation file you can use in the rest of your analysis.
Load a post-implantation volume into Brainstorm, mark each electrode and its contacts against the implantation scheme, and export a standardized implantation file. This is the manual route; CiCLONE automates much of the same work.
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 - Brainstorm, launched from the Applications catalogue.
Data - the Epimap tutorial dataset, in particular the defaced post-implantation T1 volume (anat/MRI/3DT1post_deface.nii). Tutorial datasets are provided read-only; copy the file into your own workspace before you start.
Knowledge - accurate placement is not a mechanical exercise. You need to know the implantation procedure and the scheme that was used, the specification of the electrodes implanted, and enough brain anatomy to recognize what you are looking at. You also need imaging with high enough resolution to see the individual contacts.
The workflow
Prepare your working copy
Copy the post-implantation volume from the tutorial dataset into your own workspace, and open a session with Brainstorm running.
Load the post-implantation volume
Import the volume as the anatomy for a new subject, so electrode positions are recorded against it.
Set up the implantation
Create the implantation and declare the electrodes it contains, matching the type and contact count actually used.
Position each electrode
Working slice by slice, set the entry and target points for each electrode so its contacts fall on the visible trajectory.
Check and adjust the contacts
Review the placed contacts against the imaging and correct any that have drifted off the trajectory.
Export the implantation file
Write out the implantation in the standardized format, ready to use in later analysis.
This covers the procedure as it applies on the platform. For the full detail of editing implantations and positioning contacts in Brainstorm, the official Brainstorm tutorials go further.
Where to go next
With electrodes placed, Compute an epileptogenicity map uses the same Epimap dataset.
If you would rather automate the localization, see Localize electrodes with CiCLONE.