[Brains-users] Some questions regarding segmentation

[Christoph Christmann]

Hi all,

At first I am facing a serious problem during the segmentation. I did 
skullstrip, import, resample, crop and lighten up a FLASH image. Then 
I created a mask of the brain (with image tools - threshold) the 
Talairach parameters, and sampled ROIs for venous blood and basal 
white and grey matter. Images, ROIs and masks show up in the 
segmentation dialogs (i.e. no appearance of a '-1'). However, after 
running segmentation (without BOOTSTRAP) the tissue qualification 
seems shifted, for example white matter will completely be qualified 
as grey matter. Has anyone an idea what's inducing this behaviour and 
how this can be fixed?

A second question is concerning the skull stripping. Is there any 
tool apart from MRIcro that could be used effectivly to separate the brain?

The last question applies for the use of T2 images. While it seems 
quite reasonable to integrate the T2 images for the ROI analysis I 
wonder if the T2 image is used for the segmentation of the T1 image.

Thanks in advance for any hint!

Christoph





-- 
Christoph Christmann                  christma at as200.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 Neuropsychology         D-68159 Mannheim J5
and Clinical Psychology                

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