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


------------------------------------------------------------ ------------
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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
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---



--
Marc Dubin, MD PhD
Resident in Psychiatry - PGY4
Weill Cornell Medical College

212-746-3764 (w) 646-831-8886 (c)