Reading SEEG electrodes positions

Discussions
1

Hello,

I want to load the SEEG electrodes on brainstorm, but I am not sure if their position should be in a specific file with a specific format?

Thank you

Hamza

2

Hi Hamza,

The support for sEEG/ECoG recordings in Brainstorm improved a lot over the past months. We are still actively working on it and there is no documentation ready yet.
Hopefully we will release a tutorial with an example dataset later this year.

In the meantime, let’s try to find a way for you to import your recordings.
In terms of interface, it works in a very similar as EEG. I would recommend you start by following the EEG/Epilepsy tutorial:
http://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy

Start by linking your recordings to the database (Review raw files), this should create a “channel file” with the list of recorded channels, saved in the correct order.
If you have to make modifications to the channel file (change the type/group/name of the channels), right-click on the channel file > Edit channel file.
Set to “SEEG” all the depth electrodes contacts. Set the Group field with the name of the depth electrode (ex: “A”) and the contact names to “group+index” (ex: “A1”, “A2”, etc).

Then you have two options to add the position of the contacts:

  1. You have them saved in a file: you can copy their positions in the channel file using the popup menu: channel file > Add EEG positions > Import from file.
    The coordinates can be in any file format supported by Brainstorm (have a look in the list of possible file formats), and are expected to be saved in Brainstorm SCS/CTF coordinates.
    If you save in the same file the position of the three fiducials NAS/LPA/RPA, Brainstorm will convert automatically your position to the correct coordinates system.
    http://neuroimage.usc.edu/brainstorm/CoordinateSystems

  2. If you are looking for an interface to mark the positions, you can use the MRI Viewer in Brainstorm.
    Right-click on the channel file > MRI registration > SEEG: Edit (MRI Viewer)
    Right-click on the MRI Viewer figure to get the “Channels” menu, you’ll find tools to set the electrodes positions.
    If you check the box “MIP: Functional”, you’ll see all the contacts at once, projected on the current slice.
    After this, you can move the contacts in 3D views using the other options in the menu “MRI registration”.

Let me know if you need additional help with this.
Cheers, Francois

There are many more display options and the contacts have to be correctly grouped

3

Hello Francois,

Thank you very much for you detailed answer, it is really helpful. I remember these steps from the workshop you did in Fribourg

But I wonder if “reviewing the data” is an important step before assigning the position on the MRI? I want just to generate a forward model using the brainstorm. So why it is important to read the data? is it for knowing the number of channels?

Then I have a problem in finding a way to put the positions in the file readable by brainstorm, and now by adding the step of “reviewing the data” I have to but my data in a file readable by brainstorm! Is there a way for doing it?

I put the positions with the names on *.elc file, it worked first by choosing “import channel file” but now brainstorm does not read any channel position

BST> Warning: No channel information was read from the file.

It seems that I did something wrong!

Best regards

Hamza

4

This operation creates a channel file with the correct structure and the correct list of channels.
Your forward model is a matrix that connects the sensors with the sources, it is important that your sensors are in the correct order.

Then I have a problem in finding a way to put the positions in the file readable by brainstorm, and now by adding the step of "reviewing the data" I have to but my data in a file readable by brainstorm! Is there a way for doing it?

You don't have to if you don't want to apply your forward model to anything, or if you are sure you will not make any mistake in the manipulation of the leadfield matrix. It was just a suggestion to make your life easier and lower the risks of manipulation errors...
What do you use to record your data? Don't you have an "export to edf" in your acquisition software, or some other standard file format?
http://neuroimage.usc.edu/brainstorm/Introduction#Supported_file_formats
If you are using commercial equipment that is not supported yet, we could work on adding support for it.

I put the positions with the names on *.elc file, it worked first by choosing "import channel file" but now brainstorm does not read any channel position

Just save your positions in a simple text file with one line per sensor "NAME X Y Z".
Then import it using the file filter "EEG: ASCII: Name, XYZ".

Cheers,
Francois

5

Thank you very much Francois,

I did it by adding the electrode position to a *.elc file (ASA electrode file).

Regarding the data, I am using micromid files (*.trc). I did not try yet, but I think that there a way around to read them by brainstorm!

Thank you very much for your help, and have a nice day!

Best,

Hamza

6

Hi,

I’d also like to display some ERP data recorded with SEEG electrodes, but I’ve been unsuccessful so far.
I was able to import MRI data, EEG data, I’ve edited the channel file with electrodes positions and type (SEEG), and was able to process the epoching and averaging of EEG.

My problem is that when I try to visualize the sensors in MRI 3D, all I see is a black screen.
If I display the channels labels, their name appear but nothing else.
If I right click to MRI display => MIP anatomy, nothing happens.

I then run an T1-MRI Segmentation using BrainSuite and import several surfaces like brain, pial cortex, inner cortex, inner skull, outer skull and scalp in the subject anatomy.
If I try to do the MRI registration => Check MRI/surface registration, I obtain an error message: Surface is not registered with the MRI. Please try to import all your surfaces again.
Finally, If I try to display the sensors in the Head, inner skull or cortex, I’m still seeing a black screen.

It seems that I’m missing some steps, would you be kind enough to set me on the right track.

Remi

7

Hi Remi,

First, you should start by importing the full anatomy folder generated with the menu “Import anatomy folder”, as described in the tutorials:
http://neuroimage.usc.edu/brainstorm/Tutorials/TutRawViewer
http://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy (this one is from a new set of tutorials that are under development)

Then you should link your recordings to the database (Review raw file). This would create a channel file with the names of the channels.
You can add electrodes positions by right-clicking on this channel file > Add EEG positions.
Alternatively, you can edit the electrodes positions in the MRI viewer: right-click on the channel file > MRI registration > SEEG: Edit (MRI Viewer)
=> Right-click on the MRI Viewer figure for menus to set the electrodes positions

For more information on the positioning of SEEG electrodes, we have started discussing this on another thread:
http://neuroimage.usc.edu/forums/showthread.php?1958

I’m sorry, those tools that are not correctly documented yet, they are still in an active development phase. We will work this year on a tutorial to explain those steps.

Cheers,
Francois

8

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:
http://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity