It might make more sense to tweak the settings for the skull stripping (i.e. make sure that –c, –r, and –g are optimally set).  –r should equal the radius of the brain from the center to the farthest edge, -c should be placed in actual center of the brain, and –g can be used to counteract intensity bias.






From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of MCLAREN, Donald
Sent: Friday, March 06, 2009 4:42 PM
To: [log in to unmask]
Subject: Re: [FSL] "Isotropic" DWI


What about using mean diffusivity?

On Fri, Mar 6, 2009 at 9:24 AM, Brittany Copp <[log in to unmask]> wrote:

That would work, except that there are voxels outside the brain with FA
values equal to those found in the brain which makes thresholding difficult.
It would be ideal to have an image where values in the brain are different
than those outside the brain, and I was under the impression that these
isotropic diffusion images fit the bill. Let me know if this is incorrect.


Best Regards, Donald McLaren
D.G. McLaren
University of Wisconsin - Madison
Neuroscience Training Program
Office: (608) 265-9672
Lab: (608) 256-1901 ext 12914
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