Is FEM mesh and headmask in MNI space?

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1

Hi all,

I am using Brainstorm to generate a FEM mesh and a head mask with 15000 vertices with a 0.5 vertex density. When I'm creating the FEM mesh, I both use T1w and T2w images and find the fiducials with maff8, and I use SimNIBS to segment the images.
My question is the following: is the head mask compatible with MNI space? If so, where can I find that information?
In my project, I extract the head mask into MATLAB and plot the information that I derive from the head mask such as faces, vertices, and curvature. I need these head mask vertices in the MNI space for further analysis in SimNIBS. Therefore, if the head mask is not in the MNI space how can I convert it?
I should also mention that I use the latest Brainstorm version and R2020b version for MATLAB.

I appreciate your help and time in advance.

2

The structure of the head surface is documented here:
https://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#On_the_hard_drive:_Surface

The various coordinates systems supported by Brainstorm and the conversion between them is documented here:
https://neuroimage.usc.edu/brainstorm/CoordinateSystems#Converting_between_coordinate_systems

You can search the forum for cs_convert or cs_compute to find more code examples.

4

Thank you for the information! Unfortunately, I already tried this and when I tried to convert my headmask which is in subject coordinate space to world coordinates in subject space as below:
Transf = cs_convert(matfile, 'scs', 'world');
It gave this error: Dot indexing is not supported for variables of this type.
the matfile has values such as 0.01, is the dot causing the problem or do you know what could be the reason I can't perform this conversion?

5

This is not the syntax documented in the page I pointed at.
Please read this tutorial more carefully:
https://neuroimage.usc.edu/brainstorm/CoordinateSystems#Converting_between_coordinate_systems

6

Thank you. I have one more question.
When I read this link: https://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#On_the_hard_drive:_Surface
I saw the vertices from the head mask are in SCS coordinates. However, when I plot the head mask with its faces, vertices, and curvature values to visualize the head, I am not sure if all this information is in SCS coordinates which can cause a problem.
In addition, would the origin be the centre of the head or is it the MRI coordinates of the point with SCS coordinates (0,0,0)?

7

I saw the vertices from the head mask are in SCS coordinates. However, when I plot the head mask with its faces, vertices, and curvature values to visualize the head, I am not sure if all this information is in SCS coordinates which can cause a problem.

As you read in the documentation and reported: the Vertices coordinates are stored in the Brainstorm database in SCS coordinates.

In addition, would the origin be the centre of the head or is it the MRI coordinates of the point with SCS coordinates (0,0,0)?

The SCS coordinates are documented here:
https://neuroimage.usc.edu/brainstorm/CoordinateSystems#Subject_Coordinate_System_.28SCS_.2F_CTF.29

I'm only repeating the same thing, so I guess this is not going to help you much...
If you need more assistance, please provide more information about what you are currently trying to do, including screen captures.