Visualizing electrodes on default anatomy

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1

Hi all,

Sorry if this is a repeat question, I didn't find anything exactly like it in the forum, but could have missed something.

I have several subjects each with a single ECOG strip, and would like to visualize them all together on the default/ICBM152 cortex surface. I've computed the MNI normalization for each subject's MRI, and localized the electrodes on each subject's CT registered to their MRI.

I can't seem to find a method of adding electrodes to the default cortex. I've tried creating a new subject using the default anatomy, but can't add electrodes or anything to it (not sure if this is a bug or not). I've also tried creating a new subject and directly adding the ICBM152 MRI/cortex, but I'm not sure how to warp the electrode positions to the new subject.

Any thoughts would be appreciated!

Thanks,
Zach

2

So I've found a solution, but I'm hoping there's a more straightforward way.

  • Create new subject ("COREG"), copy over ICBM152 mri and surface files
  • Export each subject's individually localized channel and MRI files to the MATLAB workspace
  • Convert each subject's channel locations to MNI using cs_convert
  • Write out all MNI channels to a single file
  • Import the combined channel file to the COREG subject
  • Fix the channel file in the GUI to correctly identify channels as ECOG type, with separate group IDs for each subject.

I'm hoping that either this functionality exists already, or that I can write a process to automate it

Zach

3

Dear Zach,

Unfortunately there are no tools to do what you described in your post, but this is already identified as an important feature to add. In the next few years, we have planned to develop new SEEG/ECOG features, including automatic detection from CT and tools for group analysis.

The approach you described sounds reasonable, and at the moment I don't have better options to propose. If you need to repeat this task multiple times, you might be interested in automating it with scripts.
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting

Francois

4

Hi Francois,

Thank you for the info.

I haven't had time to learn the actual process/scripting pipeline, but I put together a Matlab script to automate a very basic version of this. I've attached the script in case anybody finds it useful. It expects the user to have already created a new subject called 'COREG' with the ICBM152 MRI and a channel file (which will be overwritten, so it doesn't matter what it contains). It will then take all the other subjects' channel files, convert them into the ICBM152 local space, and save them all to the COREG channel file. Then you should be able to view them all together on the cortical surface.

BrainstormCoregisterChannels.m (5.0 KB)