[Freesurfer] Suggested longitudinal processing stream for already skull stripped images

Hi,

We are attempting to use FreeSurfer in order to process a longitudinal T1 series. Our input data is partly simulated and already skull stripped.

When running

$ recon-all -autorecon1

on one of these images, the check of the Talairach transformation fails. Using the option -notal-check results in a successful execution of the program, but we get a bad Talairach transformation which cannot be manually fixed using tkregister2.

I suppose the problem is that our images are already skull stripped while the pre-processing of FreeSurfer would perform this step after the computation of the Talairach transformation and hence this computation expects non-skull stripped images as input.

What are the suggested processing steps in such case, i.e., having already skull stripped images as input?

Thanks, Andreas