If you replace "all_FA" with "all_FA_skeletonised", that should only give you FA in the peduncle for only those voxels that are also in the skeleton.

On 02/06/2014 08:01 AM, Evan Stone wrote:

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Hey all,

What would be the best way to extract regional DTI data?! I have skeletonized diffusion data for all major parameters (FA, MD, RD, and AD) and have created masks for the CBM-JHU atlas for each region/threshold. Should I use skeletonised data despite the fact that the masks are not skeletonised? I have used, for example, fslmeants -i all_FA -o MiddleCerebellarPeduncle.txt -m MiddleCerebellarPeduncle.nii.gz...should I use fslstats instead? Should I count or exclude non-zero voxels if I do?

HELP! :-)

-Evan