I would like to compare cortical thickness between two timepoints.

Timepoint 1 has 1mm^3 data.

Timepoint 2 has 0.8mm^3 data.

I realize that there are limitations with this change in resolution between timepoints and that no analysis is going to be perfect, but I am trying to come up with the best possible solution.

Would it work to resample both timepoints' raw data into 0.9mm^3 ( mri_convert --conform_size 0.9 invol outvol ), and then run the 0.9mm data through Freesurfer 6.0 submilimeter recon? If so, are there any special considerations I need to take into account after the initial recon, or would longitudinal processing after this point be per normal?

Thanks,

James