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

[Eugene Zeien]

Christoph,
   Are the red lines on the images you sent the Talairach bounds?
If so, they are nowhere near the correct location.  Try re-defining
the talairach boundaries, then run the neural net again.
   I've attached a picture showing proper talairach boundaries.
The 2 points near the center are supposed to be the anterior and
posterior commissures.
gene

On Fri, 2007-02-16 at 12:35 +0100, Christoph Christmann wrote:
> 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

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