[Brains-users] Some questions regarding segmentation

[Eugene Zeien]

Yes, the cran_box is over-inclusive.  Fortunately, by the time we
use it for any measurements, we have a mask which delineates brain.
Combining the cran_box AND the brain.mask (manually inspected and
trimmed) removes the skull and background.

christma at zi-mannheim.de wrote:
> Dear Eugene, dear Ronald,
> 
> I used carefully coregistered T1 and T2 images for 
> segmentation and the cran.box. I got no masks at all. Then I 
> lightened up the T1 images and the T2 images (with image 
> math addition). In the following segmentation with the cran.
> box I got good kappas
> 
> Kappa summary:  gm:  0.9906;  wm:  0.9954;  csf:  1.0000;  
> vb:  0.9792;
> 
> Unfortunenately, the qualification was wrong. I attach an 
> example. 
> 
> The next step was to use the brain.box. Here I got good 
> kappas, too.
> 
> Kappa summary:  gm:  0.9711;  wm:  0.9684;  csf:  1.0000;  
> vb:  0.9976;
> 
> In the end this segmentation was quite good as can be seen 
> in the other attached picture.
> 
> Thanks again a lot for the help. 
> 
> Christoph 
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