You mean the T1.mgz from the recon-all output? Don't use that. Use the orig.mgz.from the long stream (you'd only need to run it long enough to produce the orig.mgz)External Email - Use Caution
Hello Freesurfer Experts,
I am using Freesurfer version 7.1.1 to perform longitudinal Samseg processing (using run_samseg_long) on my T1 longitudinal data.
1) First, I run the mri_robust_template to generate the mean.mgz using T1.mgz from the cross sectional recon-all pipeline. Would it be better to use T1.mgz from the longitudinally processed data?
You can run the recon-all long stream on that one time point; it will apply a registration designed to not introduce bias, then use the orig.mgz
2) There are few subjects who do not have followup data. How do I process these subjects to avoid the bias introduced by the longitudinal Samseg pipeline?
In general I would say samseg, but that is a pretty big difference. Can you take a look and see if one looks better than the other?
3) For the same subject, I see that the subcortical volumes from longitudinal recon-all pipeline from aseg.stats (e.g Left-Hippocampus volume is 3321.5mm3) are different to the subcortical volumes from longitudinal samseg pipeline from samseg.stats (e.g Left-Hippocampus volume is 3899.628686mm3). Which of these measures would be recommended?
Thank you very much for your support!
Best wishesJay
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