Hi Bruce, Thanks for the quick response. I also used FS v5.1.0. Do I need to use another version or is there another way to fix this?
Laura ________________________________________ From: natalie.h...@gmail.com [natalie.h...@gmail.com] on behalf of Natalie Han [zh...@stanford.edu] Sent: 13 August 2012 19:56 To: Bruce Fischl Cc: Wisse, L.E.M.; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problems with ICV Hi, Bruce, I've been using FS5.1 for segmentation analysis, after I updated the mri_segstats, the ICV does not seem to change at all, only the SupraTentorial Volume changed. If I want to use ICV and SupraTenrotial Volume for my analysis, is that OK to use FS5.1, I don't see more updated version than FS 5.1.0. Thanks. Also, is there a commandline to extract other numbers in the header of aseg.stats? Thanks. Natalie On Mon, Aug 13, 2012 at 9:15 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Laura, > > what version of FS are you running? The ICV is estimated using the talairach > xform, and there were some problems with it in 5.1. > > cheers > Bruce > > > On Mon, 13 Aug 2012, Wisse, L.E.M. wrote: > >> Dear freesurfers, >> >> I tried to calculate ICV with FreeSurfer, but I encountered some problems. >> I >> first ran autorecon 1, 2 and 3, but I noticed afterwards that a few ICV >> values were really off. The values were really high and when I looked at >> brain.finalsurfs.mgz, the segmentation also included skull, eyes and >> sometimes even the nose and ears. (I am not sure that I should look at the >> brainfinal.surfs.mgz for ICV segmentation, but the segmentations seemed to >> correlate with the ICV values.) >> >> So, I decided to try adjusting the watershed parameters and I also tried >> using gcut. I noticed that the segmentation brain.finalsurfs improved a >> lot, >> however in aseg.stats the ICV values did not change at all! >> >> Can anyone help me with this problem? >> >> Kind regards, >> Laura Wisse >> >> >> ____________________________________________________________________________ >> >> >> De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is >> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht >> ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender >> direct >> te informeren door het bericht te retourneren. Het Universitair Medisch >> Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de >> W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat >> geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. >> 30244197. >> >> Denk s.v.p aan het milieu voor u deze e-mail afdrukt. >> >> >> ____________________________________________________________________________ >> >> >> This message may contain confidential information and is intended >> exclusively for the addressee. If you receive this message >> unintentionally, >> please do not use the contents but notify the sender immediately by return >> e-mail. University Medical Center Utrecht is a legal person by public law >> and is registered at the Chamber of Commerce for Midden-Nederland under >> no. >> 30244197. >> >> Please consider the environment before printing this e-mail. >> >> > > _______________________________________________ > 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
