Hi - in general small errors in the BET outline should not be a
problem - I would run the full registration process and ascertain
that the all_FA images look ok, in which case all is well.
Cheers.
On 26 Jul 2007, at 12:16, Agnieszka Burzynska wrote:
> Dear all,
> I am preparing my data for tbss and I believe having a good binary
> mask is
> crucial for good registration and other steps. After using default bet
> setting from GUI I see that ofen the ventral part of medial prefrontal
> cortex is cut off. If I manipulate with -g and -f from the command
> line, I
> et it better, but then too much of non-brain voxels are included
> (like in
> longitudinal fissure or on bottow of the brain).
>
> Is there any ´gold standard´for bet for dtifit/tbss?
>
> How the FA maps registration can be affected by too much non-brain
> matter?
>
> Is it recommended to first center my images and use avwroi to cut
> the sides
> of the image to improve the bet results? Or as long as the mask is
> ´roughly
> ok´I can be happy with the outcome?
>
> Thank you,
> Aga
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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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