Hi,

I am having an issue with the 3D/Glass brain when I want to see the results of the second-level analysis using FreeSurfer surfaces. The connectivity matrix and ring diagrams work pretty well, but I think I have an issue with the coordinates of the FreeSurfer parcellation. Nodes are off the glass brain, and their locations don't make any sense. Please see the attached screenshot.

I used "lh.aparc.annot" file from the fsaverage subject in the Setup.ROIs dialog box which automatically changed it to "aparc.surf.nii" to create an atlas file for all subjects. I tried both  "Compute average time-series" from "surface-space data (secondary dataset #4)" and "smoothed data (secondary dataset #5)" with the atlas file but it didn't make any difference.

I read some older posts somehow related to this issue but couldn't find an exact solution for me.

I am using CONN ver 22.a and FreeSurfer 7.4.1 on Ubuntu 22.04 machine.

I have FreeSurfer surface files in /conn/utils/surf folder.

Any help or suggestions are greatly appreciated.

Best wishes,

Oz