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"all_FA_skeletonised" is going to only contain the voxels that are part of the FA skeleton (see Steve Smith's 2006 NeuroImage paper, and the wiki), which are the data that would be included in a TBSS analysis. I won't say if one way or the other is "better" (because I don't know the answer), but I would choose the skeletonised data for my own study. For an ROI such as the cerebellar peduncle, it might turn out that there are too few skeletonised voxels to give you reliable data (depends on your particular group). In that case, if the raw data are good enough (e.g. not too many partial volume effects), you may wish to use "all_FA". But inspecting the raw data *and* the processed data is important. Regarding "fslmeants" vs. "fslstats", and whether or not to include nonzero voxels: I would say you should always exclude zero voxels, because they will just increase the N, if you're taking the mean FA of a given region. But those voxels won't contribute, and should be excluded. I don't know if the commands do something different in this case; I think they should give the same result. ________________________________________ From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Evan Stone [[log in to unmask]] Sent: Friday, February 07, 2014 1:38 AM To: [log in to unmask] Subject: Re: [FSL] Data Extraction Yes thank you, but why would this be different from using allFA? Is this the right way to gather the data, or is there a better way? And how would i use fslmeants for nonzero voxels?