Hi Mojdeh
it's really hard to say how much you should correct. In general we don't do that much. A couple of control points or a few voxels added to the wm.mgz can have a big effect if you are experienced. Mostly just see if the ?h.white and pial surface are visually accurate, and if not see if some small intervention might fix them.
cheers Bruce
On Fri, 20 Jul 2012, Mojdeh Zamyadi wrote:
Hi Bruce,
Thank's for the reply! I'm not concerned about hippocampal volume for now, mostly needing cortical thickness for my project! Yes, I am using v5.1. So in case of cortical thickness I shouldn't worry too much about Talairach registration? could you please tell me what are the main things I should check and pay attention to for cortical thickness? I'm following the troubleshooting page (http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction) and I see some discrepancies in the pial/WM surfaces but again I am not sure how much I should correct!
Thanks again, -Mojdeh
On 07/20/2012 04:15 PM, Bruce Fischl wrote:
Hi Mojdeh
it won't affect any individual thickness measures, *but* will affect the estimated total intracranial volume (eTIV). We don't typically use eTIV for thickness correction, but do for things like hippocampal volume. Are you using version 5.1? If so, that's the problem. Nick has a fix for this that he can direct you about, or you can wait for 5.2 and rerun the Talairach registration then.
cheers Bruce
On Fri, 20 Jul 2012, Mojdeh Zamyadi wrote:
Hi all,
Sorry for re-posting this but it seems it didn't get through!
I've just started to do cortical thickness analysis on some subjects and I'm noticing some miss-registrations, more specifically the Talairach image is smaller than the target image no matter what subject I look at! I just wanted to make sure if this is something normal and to what extend it's going to effect the individual cortical thickness calculations. I guess I'm not sure how the Talairach transformation is used in further steps of the cortical thickness calculation.
I tried to attach example coronal, sagittal and horizontal slices of one of my subjects but apparently it was too big for the mailing list. Pleas let me know if there is a way to attach images here.
I greatly appreciate your advice.
Thanks, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospital for Sick Children 555 University Avenue Toronto, ON, M5G 1X8 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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