Hi Andrea,
You can use the contour tool in the voxel edit mode to quickly and roughly
fill in wm. Use the tool with the wm.mgz selected in the volume layer
list but set the brainmask (or T1) as the reference. Set brush value to
255, and then do crtl+alt+leftbutton while dragging the mouse to adjust
the contour, and then crtl+leftclick to fill in selected regions. Note
that the cerebellar white matter may be outlined by the contour as well,
but if it doesn't connect with the cortical wm then it won't be filled in.
-Louis
On Thu, 6 Mar 2014, Andrea Grant wrote:
Hello,
I'm working with T1 weighted scans obtained at 7T and have a problem with a
subject. I preprocess the images to deal
with the B1 inhomogeneity (normalize to PD and mask noisy pixels), and have
successfully segmented about 20 scans. I
often need to use control points, but they normally work just as I expect.
However, I have one subject where large
areas of the brain are completely excluded from the segmentation (basically
the entire occipital lobe). I added control
points and re-ran, to no effect.
I'm attaching a screenshot of the brainmask with surfaces, my control points,
and the white matter mask. Clearly, the
skull stripping wasn't very successful (I adjusted the watershed threshold
manually, but at one value I got the current
result and at a single integer lower I lost half the brain). I have
successfully segmented other subjects with equally
poor skull strips, though, so I don't believe this has any bearing on the
current issue.
Is editing the white matter mask the only way to fix this? If so, do I need
to carefully fill in on every slice, or can
I just brush in here and there to sort of goose the white matter into that
region? I can do the slice by slice fix,
but if there's a way to avoid the several hours it will take me, I would love
to know!
Thanks,
Andrea
-
Andrea Grant
Visual Neuroimaging Technologist
Center for Magnetic Resonance Research, University of Minnesota
2021 6th St. SE, Minneapolis, MN 55455, 612-626-4948
gran0...@umn.edu
umn.edu/~gran0260
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