Hi Qi,

you should process both time points together via the freesurfer longitudinal stream. Independent processing is less sensitive. Selecting one of the time points as a template is also bad, as it induces processing bias, see:

https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing
and the References there.

I cannot answer the other question about FA.

Best, Martin

On 05/05/2016 06:52 PM, Zeng, Qi wrote:

Hi All,

I was running freesurfer for a patient case of two time points. Will you suggest to run it as a group, such as one time point as a template and followed by longitudinal study, discussing atrophy or run these two time points separately as two individual, running everything such recon-all, dt-recon twice and comparing the result, such as thickness, volume and FA? BTW, I post a question about FA display before: will anything lead to a rectangular FA display, with extra diffusion out of the brain skull (no errors during recon and dt …)?

Best,

Qi
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-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu