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
