Sorry, I wasn't suggesting binarizing your FA maps, just your tract mask. My example wasn't clear. Then you can change the transparency of your FA map to show the tracts, or use a cut-out (press the B key to get the box to change your cut-out).
Joe
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Joseph M. Orr, PhD.
Post-Doctoral Fellow
Institute of Cognitive Science
594 UCB - CINC 182D
University of Colorado at Boulder
Boulder, CO 80309-0594
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From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Derek Archer [[log in to unmask]]
Sent: Friday, May 03, 2013 7:49 AM
To: [log in to unmask]
Subject: Re: [FSL] 3dviewer - probtrackx output
Hi Joe,
I think I might just be confused, but wouldn't that just give me a 3d brainmask of the FA map? I want to be able to see the FA map with tracts overlayed, but in 3d.
On the "3D controls" (http://fsl.fmrib.ox.ac.uk/fsl/fslview/3D-vtkkbd.html) page, it says there are X,Y,Z slice planes available, and I would be happy with this for now, but it doesn't explain how to get these planes to appear.
Thanks,
Derek
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