Hi Freesurfer Experts,

I have a question about calculating voxelwise % change. 

We have collected T1-MRI across 3 time points in a couple of subjects and the aim is to produce individual surfaces/maps showing the % of cortical thinning with respect to the baseline data. 

Each time point has been processed using the standard recon-all. Next, the base template was created using data from all 3 time points. The longs were processed accordingly. I am thinking of using something like FSCALC to get the new surface, showing the % difference compared to T1. Would all of these steps be correct?

Many thanks for your help in advance.

Best Wishes,

Elijah