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Thank you for your reply. I will use lesser threshold level. Thanks. Mithra. On Thu, Mar 13, 2008 at 9:07 AM, Gwenaëlle DOUAUD <[log in to unmask]> wrote: > Hi Mithra, > > it's normal: there is no voxel above 75% for the > uncinate fasciculus. Looking at the tract, if you want > to be rather conservative, you should go for 20 or > 25%... > > Hope this helps, > Gwenaelle > > > --- Mithra <[log in to unmask]> a écrit : > > > Hello, > > > > I am trying to create a thresholded mask of Uncinate > > Fasciculus (under the > > JHU White matter Tractography atlas). > > > > I created the mask using the FSL atlas. But when I > > try to threshold it to > > 75%, I get nothing. The resulting file ends up being > > a matrix with all > > zeros. > > > > I have done similar steps for sub cortical > > structures (eg, Hippocampus) > > under the Harvard Oxford Subcortical structure atlas > > and I get the > > thresholded masked image. The step works for the > > sub cortical structures. > > > > > > I save the structure from the atlas using 1mm > > standard brain as the > > underlay. > > > > To threshold I use this command: > > > > fslmaths UncinatefasciculusL -thr 75 > > UncinatefasciculusL75 > > > > > > Am I doing this right? > > > > > > > > Thank you. > > -- > > Regards, > > Mithra > > > > Imaging Research Center > > University of Texas, Austin > > 3925-B W Braker Lane > > Austin. TX - 78759 > > Tel: (512) 232-5725 > > Fax: (512) 232-4202 > > > > www.irc.utexas.edu > > > > > > > _____________________________________________________________________________ > Envoyez avec Yahoo! Mail. Une boite mail plus intelligente > http://mail.yahoo.fr > -- Regards, Mithra Imaging Research Center University of Texas, Austin 3925-B W Braker Lane Austin. TX - 78759 Tel: (512) 232-5725 Fax: (512) 232-4202 www.irc.utexas.edu