[Brains-users] brain mask - problems with automatic definition

[Christoph Christmann]

hi,

the segmented image looks reasonable. I attach some pictures 
elucidating the actual situation. I am especially surprised that the 
cerebellum border is not found correctly although it seems to be 
obvious as you can see in the brain_mask_cor_seg.jpg file. You can 
see in the other two images, that T1 and T1 is realigned quite well 
(cost function < 0.45).

If you would have any idea to use other programs to get the brain 
mask I would try this way, too. Actually, we started with BrainSuite 
but found it to be less precise, too - although in other regions. 
Maybe we end up with an SPM or FSL segmentation for the mask.

Best regards

Christoph




At Thursday 15.02.2007 20:18, Eugene Zeien wrote:
>The segmented image looks reasonable?
>
>And, when you use
>     Workup -> Run Neural -> MR5 -> Brain...
>the segmented image's filename ends up in the first field?
>
>Any chance you could send a screenshot of the segmented image?
>Or was that the segmented image under the mask in the previous pictures?
>
>gene
>
>On Tue, 2007-02-13 at 19:51 +0100, Christoph Christmann wrote:
> > The result is based on a segmentation of a T1 and a T2 weighted
> > image. The problem occurs with every data set. Until now we correct
> > the brain mask manually, however as you can imagine this is 
> rather boring...
> >
> > Christoph
> >
> > At Tuesday 13.02.2007 19:44, Gene Zeien wrote:
> > >Looks like the results I get when I feed the Neural Net a T1 image
> > >rather than a segmented image.
> > >
> > >Anyone else seen this type of problem?
> > >
> > >http://www.psychiatry.uiowa.edu/pipermail/brains-
> > >users/attachments/20070213/c7f972c9/brain_mask_axi-0001.jpg
> > >
> > >On Tue, 2007-02-13 at 18:37 +0100, Christoph Christmann wrote:
> > > > sorry, here are the pictures
> > > >
> > > >
> > > > >http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users
> > > >
> > > > --
> > > > Christoph 
> Christmann                  christoph.christmann at zi-mannheim.de
> > > > Psychologist, MEE                     Fon/Fax +49 621 1703 63 18/05
> > > > Central Institute of Mental Health    http://www.zi-mannheim.de
> > > > Department of Clinical                D-68159 Mannheim J5
> > > > and Cognitive Psychology
> > > > _______________________________________________ Brains-users
> > > mailing list Brains-users at www.psychiatry.uiowa.edu
> > > http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users
> > >--
> > >Gene Zeien <gene at psychiatry.uiowa.edu>
> > >
> > >_______________________________________________
> > >Brains-users mailing list
> > >Brains-users at www.psychiatry.uiowa.edu
> > >http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users
> >

-- 
Christoph Christmann                  christoph.christmann at zi-mannheim.de
Psychologist, MEE                     Fon/Fax +49 621 1703 63 18/05
Central Institute of Mental Health    http://www.zi-mannheim.de
Department of Clinical                D-68159 Mannheim J5
and Cognitive Psychology                       
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