thanks Bruce :) -Mojdeh On 07/20/2012 04:27 PM, Bruce Fischl wrote: > 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 >>>> >>>> >>>> >>> >>> >>> The information in this e-mail is intended only for the person to >>> whom it is >>> addressed. If you believe this e-mail was sent to you in error and >>> the e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to >>> you in error >>> but does not contain patient information, please contact the sender >>> and properly >>> dispose of the e-mail. >>> >> >> >>
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