Dear FreeSurfer Experts,

We have two high resolution datasets (T1 and T2* images). T2* is co-registered to the T1 volume. The T1 volume was processed in freesurfer using the recon-all and we want to use the segmented cortex (by freesurfer) as a mask to extract the cortex from the T2* volume.

Would it be possible, please, to let us know which command to use to transfer the segmented cortex to the native space of T1 and T2*?. 

Many thanks in advance,

Ali