I have eight definite cases and I think I've seen it in a few more.
What works is running bet twice, once with a low fractional intensity
threshold (around 0.2, which seems to be needed for atrophic brains,
but results in these occasional holes), and once with a higher value
(which gets rid of the holes, at the cost of cut-off gyri etc.). Then
I combine the two masks with boolean OR. It's annoying, because it
means that I have to supervise the brain extraction, instead of
running it as a batch process (I need to do about 5000 in the medium
term).
Here's the visual example again:
http://www.soundray.org/bet-punchedout.jpg
Cheers
Rolf
On Thu, Dec 24, 2009 at 07:40:19AM +0000, Stephen Smith wrote:
>
> HI - unusual - maybe because you have such large ventricles the BET
> surface is getting messed up, with self-intersections etc.
>
> Have you tried initialising it close to the final solution using
> options such as -c and -r ?
>
> Cheers.
> On 23 Dec 2009, at 11:27, Rolf Heckemann wrote:
>
> I occasionally observe punched-out holes in bet masks, like in the
> attached screenshot. I run bet after pre-masking with
> standard_space_roi -b. The pre-masked brain looks complete.
> Any advice appreciated.
> Rolf
> --
> Rolf A Heckemann, MD PhD
> Médecin chercheur
> Fondation Neurodis
> CERMEP - Imagerie du Vivant
> Hôpital Neurologique Pierre Wertheimer
> 59 Boulevard Pinel
> 69003 Lyon
> France
> 1261567251
>
> ----------------------------------------------------------------------
> -----
> 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)
> [1][log in to unmask] [2]http://www.fmrib.ox.ac.uk/~steve
> ----------------------------------------------------------------------
> -----
>
> References
>
> 1. mailto:[log in to unmask]
> 2. http://www.fmrib.ox.ac.uk/~steve
--
Rolf A Heckemann, MD PhD
Médecin chercheur
Fondation Neurodis
CERMEP - Imagerie du Vivant
Hôpital Neurologique Pierre Wertheimer
59 Boulevard Pinel
69003 Lyon
France
1261657189
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