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Hi - no, that's not quite right I'm afraid - I suggest you read the original TBSS paper in NeuroImage. The only thing that is seletonised is the group-mean-FA image, after an initial nonlinear reg of all subjects into standard space, and averaging. Then all subject's data is 'projected' onto the skeleton - see the paper for details. Cheers. On 23 Jul 2009, at 16:12, John Kuster wrote: > Thanks, Steve, that makes sense. > > I also have a question, in my current understanding, TBSS will > skeletonise > FA data and then align all the skeletons, this is one of the > advantages of > using TBSS, that it uses the skeletons to attain a better > registration. > However, this alignment is only applied to the skeletons, that is, NOT > applied to the full FA maps at any point. Am I correct in this? > > Thanks! > > > On 7/23/09 1:24 AM, "Steve Smith" <[log in to unmask]> wrote: > >> Er....because you didn't set any output options....you need to choose >> one or more of >> -T >> --T2 >> -x >> -c >> etc. >> Cheers. >> >> >> On 22 Jul 2009, at 21:28, John Kuster wrote: >> >>> Dear FSLers, >>> >>> If anyone could tell me why I am getting an aborted command, I would >>> really appreciate it! I am not sure why it says no output options >>> selected, >>> >>> Thanks in advance, >>> >>> Jake >>> >>> >>> striatum:stats] (nmr-std-env) randomise -i all_FA_skeletonised -o >>> tbss_msk >>> -m mean_FA_skeleton_mask_ROI_masked -d design.mat -t design.con -n >>> 5000 >>> randomise options: -i all_FA_skeletonised -o tbss_msk -m >>> mean_FA_skeleton_mask_ROI_masked -d design.mat -t design.con -n 5000 >>> Loading Data: *********************** >>> Data loaded >>> 1.14407e+06 permutations required for exhaustive test of t-test 1 >>> Doing 5000 random permutations >>> Warning! No output options selected. Outputing raw tstat only >>> Starting permutation 1 (Unpermuted data) >>> 1.14407e+06 permutations required for exhaustive test of t-test 2 >>> Doing 5000 random permutations >>> Warning! No output options selected. Outputing raw tstat only >>> Starting permutation 1 (Unpermuted data) >>> Finished, exiting. >>> >> >> >> --------------------------------------------------------------------------- >> Stephen M. Smith, Professor of Biomedical Engineering >> Associate Director, Oxford University FMRIB Centre >> >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >> +44 (0) 1865 222726 (fax 222717) >> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >> --------------------------------------------------------------------------- >> >> > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------