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Thanks.....Let me try your fslview overlay suggestion and I will let you know. If I am still having trouble, I will upload the tarfile that you requested. Thanks again! On 10/15/07, Steve Smith <[log in to unmask]> wrote: > > 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 > ------------------------------------------------------------------------ > --- > -- Marc Dubin, MD PhD Resident in Psychiatry - PGY4 Weill Cornell Medical College 212-746-3764 (w) 646-831-8886 (c)