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Hi - I'm suprised that you get this with the -T option. If you load in all_FA first into FSLView, and then overlay the FMRIB58_FA (threshold this, change its colour to red-yellow, and make it a little transparent) and then move through the timepoints, do all subjects behave in a similar way to what you've described? We can have a look and advise on what's happening; Please upload the files in a single compressed tarfile to http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi and then email me the upload ID. Cheers. On 15 Oct 2007, at 02:36, Marc Dubin wrote: > Hello FSL Users, > > Using the TBSS tools I have been carrying out the tbss_2_reg step > with the -T option (FMRIB58_FA). I > then go through all of the remaining steps of TBSS and then when I > visualise with: > > fslview MNI152 mean_FA_skeleton -l Green -b 2000,8000 tbss_tstat1 - > l Red-Yellow -b 3,6 > tbss_tstat2 -l Blue-Lightblue -b 3,6 > > the mean_FA_skeleton significantly overshoots the brain, > terminating in or even beyond the skull > (the overall extent of the skeleton is significantly larger that > the brain). > > Any ideas about what might be going on here would be greatly > appreciated! > > Thanks, > Marc ------------------------------------------------------------------------ --- 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 ------------------------------------------------------------------------ ---