Hi Tianqi

you mean you want to warp your atlas onto a subject, then measure the volume of the warped structures? You can certainly do that, but in general we have found it to be less accurate than explicit segmentation. Note that mri_vol2vol doesn't compute a transform, it just applies one. And also note that you will want a nonlinear transform, not a matrix

cheers Bruce

On Wed, 20 Jan 2016, Tianqi Wang wrote:

Dear freesurfers, 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