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. Peace, Matt. _____ 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. Brittany -- Best Regards, Donald McLaren ===================== D.G. McLaren University of Wisconsin - Madison Neuroscience Training Program Office: (608) 265-9672 Lab: (608) 256-1901 ext 12914 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (608) 265-9672 or email.