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Hi - you can do your tracking directly in standard space if you provide probtrackx with the appropriate transformation. This is explained in the doc. Cheers Saad On 28 Mar 2013, at 20:43, Randall Benson wrote: > We ran a study on tinnitus and non-tinnitus hearing impaired individuals with TBSS and found some areas of increased FA in the tinnitus + group. Now we want to do fiber tracking to determine: 1) the origin and target of these fibers containing the differences; 2) determine the differential strengths, FAs, etc. on these tracts. I'm not sure what makes sense to do in order to first identify the origin and terminus of the group as a whole. I thought maybe doing a tracking in standard space on the group averaged FA image might be good but not sure if this is feasible in FSL. Would vecreg be the way to do this? > > Has anybody done fiber tracking actually in standard space? On an average of several normalized FA images? > > If you don't have a prior anatomical loci as seeds and are doing a whole brain TBSS then what can you do to do an "ROI" analysis as our reviewers are requesting? > > Thanks. > > Randy > -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi