Analyzing Radial Angle Patterns in Brain MR Images through Coronal, Sagittal, and Horizontal Cross-Sections

Discussions
1

Hi,

After importing all the anatomy files from the Freesurfer folder, I am currently focusing on surface orientation. I am wondering if it's possible to generate plots displaying the values across different cross-sections of the brain MR image (such as coronal, sagittal, and horizontal views) to see if it looks like the radial angle based on vert Normals.
Could you please help me in this way?
Thank you so much

2

Hi @sarach

I'm not sure that I understand what you want to do.

In brainstorm you can display the MRI in 3D or with the coronal, sagittal, and axial views.

If you want to view surfaces, you can display them in all directions as well.

Check this tuto:
https://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy

3

Thank you for your response!
Yes, I know it!
Actually, I would like to make plots of the VertNormals of each vertex in my ROIs through various cross-sections of brain MR image (coronal, sagittal, horizontal examples) to see if it looks like the radial angle.

4

If you want to plot the VertNormals, export the surface file to Matlab and then use the quiver3 Matlab function.

5

Thank you so much,
Is there a way to import the matrix of angles (or any values) to brainstorm in. mat format and plot it on the cortex?
Actually, I possess the cosine of angles as a value within a matrix that shares the same dimensions as the cortex.

6

This is not implemented for this purpose.
You can display the vectors on the cortex using the LeadField functions, but you must adapt the code for your application:
https://neuroimage.usc.edu/brainstorm/Tutorials/ReviewForward?highlight=(view)|(leadfield)#The_forward_model_.26_lead_field_visualisation

I'm unsure if the sinus is sufficient for the 3D vector visualization;
you need both the azimuth and the elevation,
and you need to have it as a 3D coordinate vectors (similar to the vert Normals )