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Hello, I was wondering if there has been any update on this extreme dark/bright classification issue. I am trying segment WMH on FLAIR images. WMH are located around the CSF. I do a skull strip on T1 and mask the FLAIR image using this mask and feed the stripped image to FAST. The number of classes in FAST is set to 3. FAST tends to merge extreme dark (CSF) and extreme bright (WMH) and provide one class. I am using FSL version 4.1.2 and FAST version 4.1. I noticed there is already an update on FSL. If this issue has been addressed, I will update to the new version. If there is any work around, please let me know as well. Thank you very much.. Deniz On Thu, 2 Apr 2009 10:15:58 +0100, Matthew Webster <[log in to unmask]> wrote: >Hi, > The thresh.txt needs 1 value for each class ( 4 in your case ) >which are the _log_ values of the means ( we will be changing the >inputs back to normal intensities in the next release ). We're >currently looking into the extreme dark/bright classification issue... > >Many Regards > >Matthew > >> Hi, I wanted to identify white matter hyperintensities in a >> carefully cleaned up flair image >> (Betted and Grey matter and ventricles pretty well removed). >> I was hoping that the -s (or --manualseg) option in fast would allow >> me to choose a starting value that characterized my wmh, >> but when I try that: >> >> >fast -s thresh.txt combo >> >> (thresh.txt contains a single number, 722 which is 3 SD above the >> mean) >> >> It seems to be doing something else (it lumps together very dark and >> very bright patches....even when I have 4 classes). >> Can anyone explain more about manualseg and how to use it? I've >> looked at the online materials and the forum, but I'm afraid I don't >> see much that is helpful. >> >> Thanks for any insights. >> >> -Dianne >> >> -- >> Dianne Patterson, Ph.D. >> [log in to unmask] >> University of Arizona >> SLHS 328 >> 621-5105 > >