Hi Experts,

I am trying to visualise a brain graph on BNV using Freesurfer as parcellation scheme (cortical+subcortical regions) but I do not know how to obtain coordinates for the centroids of my regions of interest so that I can use those values as XYZ coordinates for my .node file; I am clearly using the wrong coordinates as I end up with a network that does not overlap the surface. Also, network isn't in the same view as the surface (pic attached). I obtained my coordinates using the 'BrainNet_GenCoord.m' script BNV provides, and Freesurfer 'aparc+aseg.nii' as input file.

Is there any script that allows me to obtain correct coordinates for the centroids of both cortical+subcortical regions in MNI to visualise my brain graph using BNV?

Many thanks,
Leila

Hi Leila

The surface provided in BNV is in standard MNI space. BrainNet_GenCoord.m extracts node coordinates as the native space of the nifti file. So, I'm not sure if "aparc+aseg.nii" is in the MNI space. Please try overlap this file onto MNI template like ch2 using MRICroN to have a check. If not, please transfer it to MNI space.

Best,
Mingrui