Hi Reza

the surface labels are sets of vertex indices (and voxel coords). Neither of these applies to a surface constructed from a different session. You need to use mri_label2label to transform the surface from one timepoint to another. You can either use the surface registration, which is a bit indirect (since it goes through an atlas), or you can use mri_robust_register and compute a rigid transform and use that. Or maybe even better process the subject through the longitudinal stream in which case they will be in register across time by construction.

cheers Bruce

On Sun, 8 Nov 2015, Reza Rajimehr wrote:

Hi, We have run recon-all twice on a single subject, both times without any error. Using a functional localizer, we have made a surface-based label for an ROI (FFA) in the ventral temporal cortex of the inflated surface from the first recon. When we visualize the same label on the inflated surface of the second recon, the label shows up as scattered points in the lateral parietal cortex! Why do we see such a huge difference in the vertex coordinates across the two recons of a single subject?

Reza