Scout Delineation in Brainstorm

Discussions
1

Hello everyone! I was wondering if you guys have any insight on these two questions.

  1. How would you delineate a scout region using the MRI and not have it grow the region? We have been trying to delineate a region, specifically the entorhinal cortex, and have found that the using the scout in the MRI would grow the region to a place where we did not delineate. We were wondering if there is a way to constrain inward the scout vertices so that the delineation would be more precise.

  2. Is there a way to map only the scouts onto the cortex? we would like to see the activation of this region and see if the regions are what we would like. We have found a large variation between vertices and would like the have higher precision with the vertices picked.

I think those two questions should cover everything. Thanks you very much!

2

Hello,

  1. Drawing your scouts in the MRI slices in Brainstorm is not a really good solution. The best two options are:
    a) to draw your regions of interest in FreeSurfer/BrainVISA (the software you’re using to extract the cortex surface), and find a way to generate surface-based atlases from those colume-based regions (.label or .annot files in FreeSurfer, .gii in BrainVISA)
    b) to draw your regions in Brainstorm, on the surface (scouts), possibly starting from any of the anatomical atlases already available (Desikan-Killiany, Destrieux, Brodmann…)
    => Note that you don’t have to use the “>” and “>>” buttons to grow the regions, you can also add the vertices one by one on the surface. In the scouts tab, click on the cross (select point), then on the scout again, then add the vertices you want. You can click on the button “edge” in the surface tab to help you select the appropriate vertices

  2. I’m not sure I understand this question. Can you describe better what you are trying to do? Maybe with a screen capture?

Francois

3

Thanks Francois for the reply! I tried delineating the region of interest in FreeSurfer and created a .label file. I tried importing the file into Brainstorm and kept an error saying that the values need to be positive integer. I’m guessing that the labels do not match up with the imported files in Brainstorm. Wondering if anyone has any insight in this. For the second question, it is more along the lines of displaying only the region of interest rather than all of the activations in the brain. Thanks!

Theus

4

Hi Theus,

Your .label file should have the following syntax:

#!ascii label  , from subject  vox2ras=TkReg
154986
0  17.620  -86.460  -14.914 0.0000000000
1  17.044  -86.618  -14.894 0.0000000000
2  15.983  -86.559  -14.974 0.0000000000

Another option is to combine one or several .label files to create a .annot file.

Can you please post the full error message, as well as your .label file?

Francois