I think nick has a patch he can distribute before we release 5.2 Bruce
On Aug 14, 2012, at 3:13 AM, "Wisse, L.E.M." <l.e.m.wi...@umcutrecht.nl> wrote: > 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
