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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer