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 fischl@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.