Hi Jim,

Yes, there is a -3T switch for recon-all. This enables two 3T specific options: different parameters for the Nu Intensity Correction stage, and an atlas of young adults scanned at 3T for the Tailairach stage. By default, this isn't enabled.

More information on Freesurfer flags can be found here: https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags

Best, Lee

On Tue, 19 Jan 2016, EJ Nikelski wrote:

Hi all,

I'm testing Freesurfer 5.3 and have a question about processing 1.5T versus 3.0T scans. Specifically, is there a switch in recon-all?

I've observed some using a "-3T" switch, but I can't see this option documented in the "recon-all -help" output. I've executed test runs on a VM both with and without this option ... which seems to produce different results in the ROI quantification stats, although no change in the nu_correct arguments (I would have expected a different -distance value, but always appears to be set to 50).

So, in sum, is there as 1.5T/3.0T switch in recon-all, and what does it do?

Thanks,

-jim