How to make a markers spot on 3D brains loaded into brainstorm

Dear all,
I’m looking for a functions or script that let me free to put one or more markers (like sphere or something similar) on the 3D brain and save it with markers.
For example for my goal analysis I found really usefull display 3D brain reconstructions of my subject (segemented with Brainsuite) than I use coordinates to found MRI points. The best thing should be, after found the relevant MRI coordinates, make a markers in the points.
Someone can help me?

Thank you very much,
All the best


Hi Luca,

I’m not sure I understand what you are trying to do. Are you planning on using Brainstorm for selecting vertices of a cortex surface?
You can use the Scout tab for creating a region of interest, then export them to Matlab:

Or if you need just one point, right-click on the 3D view of the cortex > Get coordinates. Then pick a point anywhere on the brain, you’ll get the coordinates in SCS and MRI coordinates.

All those tools are tightly integrated into the Brainstorm interface, they cannot be used outside of the Brainstorm environment.
However, you can generate figures using brainstorm and then add additional graphic objects in them.


Thanks Francois,
I’m going to use Brainstorm for a stimulation study.
We perform a direct electrical stimulation abd recordind ECoG during neurosurgery.
My idea is to reconstruct exactly the location of stimulated cortical (knowing MRI coordinates) site respect to the ECoG contact palced on brain convexity.
I think your sugestion to use Scout Tab could work, I try!
Do you have any other sugestions for this “unusual” use of the brainstorm?

Than you very much
All the best


Hi Luca,

You can process ECOG recordings with Brainstorm, but for now there is no easy way to mark the positions of the electrodes from the interface.
You would need to create a text file with one electrode per line (“NAME X Y Z”), in Brainstorm SCS coordinates.
Then you can import this into your Brainstorm channel file (right-click on the subject > Import channel file > “EEG: ASCII: Name, XYZ”).

In Brainstorm, you could get those coordinates using the “Get coordinates” menu (or the Scout tab, but it’s not as easy to get vertices coordinates).
If you already have them in MRI coordinates, to convert from “Brainstorm MRI” to SCS coordinates, please look at this page:

I will probably develop tools to help defining the position of ECoG grids and deep electrodes in the next six months.


FYI: We improved significantly the tools available in Brainstorm for processing and visualizing SEEG and ECOG data, including new options for volume coregistration. They are now documented in a new tutorial: