Hi - thanks for the email.
Yes - the default setting for the fractional threshold of 0.5 gives a very
small amount of brain loss at the top. If you reduce this to 0.4 (on the
command line - ie if you're not using the GUI - this means using -f 0.4)
then the results are very good.
I don't think you need to change your sequence - these results look close
to perfect.
Thanks, Steve.
Stephen M. Smith
Head of Image Analysis, FMRIB
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
On Mon, 3 Sep 2001, Antonio Algaze wrote:
> I am acquiring a hi-res SPGR 3D volume (2.5 mm slice and 0.9 mm in-plane res)
> for intermediate registration between EPI data and the standard brain.
>
> BET does some brain erosion on these SPGR volumes, especially at the topmost
> slices. Lacking experience for how well BET should be doing given this input,
> I would appreciate your opinion on the result. The dataset and its
> corresponding BET brain-removed version are here:
> http://www.bme.ohio-state.edu/aalgaze/bet
>
> Does it merit changing the "advanced options"?
>
> I would like to tailor my acquisitions to optimize FSL analysis. Any
> suggestions for best BET performance?
>
> Again, thank you so much for the help.
>
> Cheers,
> Antonio
>
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