I want to calculate the volume of subcortical structure using my own atlas. But my altlas is not in the fsaverage space. In order to achieve my goal, I plan to use the mri_vol2vol command to register my atlas to the fsaverage subject and then register every subject to the fsaverage subject. At last, I want to use the mris_segstats command to calculate the volume of subcortical structure. I have two questions:

1. Is the plan above can get the right results?

2. If the plan above can get the right results, what registration matrix should I use for mri_vol2vol and how can I get the matrix?

Thanks!

Tianqi Wang