| 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
Regards,
-John
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