Sorry for the delayed reply! But that might be a point... In fact, the orig.mgz and the brain.mgz look very bright throughout the brain (especially in the upper part of it). In these files the cortex is even for me very hard to differentiate from the white matter. Interestingly the T1.mgz looks slightly better and the intensity values in cortical regions are a bit lower in T1.mgz than in brain.mgz.

Kind regards

Cindy

-----Ursprüngliche Nachricht----- Von: Bruce Fischl <fischl@nmr.mgh.harvard.edu> Gesendet: 26.06.2010 01:12:16 An: Cindy Eckart <cindy.eckart@web.de> Betreff: Re: [Freesurfer] Serious failure of surface reconstruction >can you check the T1.mgz or brain.mgz and see if the gray matter is still >okay in it? That is, check to make sure that the intensity normalization >didn't make gray matter look like white matter (compare it to the orig.mgz) > >On Fri, 25 Jun 2010, Cindy Eckart wrote: > >> _______________________________________________ >> 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. >> >> ___________________________________________________________ >> GRATIS für alle WEB.DE Nutzer: Die maxdome Movie-FLAT! >> Jetzt freischalten unter http://movieflat.web.de >>  

WEB.DE DSL ab 19,99 Euro/Monat. Bis zu 150,- Euro Startguthaben und     50,- Euro Geldprämie inklusive! https://freundschaftswerbung.web.de