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Dear Freesurfer community,

I have a .nii volume atlas (CAREN), defining 5 networks, in MNI (ICBM152) space.

However, I wish to do my analysis in surface rather than volume space, and for the software I am using, that means I need to load in a .annot file. 

For the first step, I used:

mri_vol2label --c CAREN_5networks.nii --id 1 --l 1.label 


and did this for values 1 to 5 (for each of the networks). However, looking at the resulting label file, the first column is nothing but -1 values. I believe this should be the vertex number, and trying to combine these labels into an .annot file is not working.


Apologizes for the naive question, but can anyone share as to how I can ultimately create a surface atlas when I have the volume.nii atlas file? Was I wrong with mri_vol2label as my first step?


I am using Freesurfer version 7.2.0.


Thank you,
Paul