Dear John,
Thanks for this, it removed the scalp outline from the images very well.
However, before I analyse the cleaned up segmented images, should I
normalise them again?
Many thanks
Xavier
>
>| I am trying to analyse some old T1-weighted scans. They were done on a 1.0T
>| scanner, and so the image contrast is not good. When normalising and
>| segmenting the scans, a thin ribbon of scalp is consistently left around
>| the brain. I have analysed plenty of other scans very successfully, so I
>| think this is due to poor scan quality. However, before I give up, I was
>| wondering if anyone had any suggestions.
>
>This may be due to lower scan quality, but often a thin ribbon of scalp is
>to be expected. The segmentation does not yet work perfectly, and it does
>not fully know the difference between brain and non-brain when the voxels
>have similar intensities. However, it may be possible to automatically
>remove most of this ribbon by the <Xtract brain> button (hidden in the
>render pulldown).
>
>Select the xxx_seg1.img and xxx_seg2.img images that need to be cleaned up,
>and specify the "Save Extracted Brain" option. This produces an image
>called brain_xxx.img. Then you would use the <ImCalc> button to multiply
>xxx_seg1.img by brain_xxx.img:
>
>Select xxx_seg1.img and brain_xxx.img, and specify an output filename.
>The expression to be evaluated would be:
> i1.*i2
Xavier Chitnis
Section of Cognitive Psychopharmacology
Dept. of Psychological Medicine
Institute of Psychiatry
De Crespigny Park
London, SE5 8AF.
Tel: 0171 919 3977
Pager: 07669 028 121
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