sounds like you'll need control points. Is the WM so dark because of bias fields, or is there some pathology-induced changes to wm intensities?
On Fri, 28 Jun 2013, Jonathan Holt wrote:
Bruce,
in brainmask.mgz it ranges from about 90-60, as for the wm.mgz values there are only sporadic voxels, most in the 80-90 range. Where the LH inf lat ventricle should be there are some wm voxels at 250.
I agree there are segmentation issues, but there is also a complete lack of WM voxels, what should I do about both?
jon On Jun 28, 2013, at 11:08 AM, Bruce Fischl wrote:
Hi Jonathan
so you lose that entire gyrus? What are the intensity values of the wm in the brain.mgz in that region? And it's not present in the wm.mgz either? That means it's a segmentation problem not a topology one (which is what I would have guessed)
Bruce On Fri, 28 Jun 2013, Jonathan Holt wrote:
Hi all, I'm having a bit of trouble with one particular subject for which we brains for 4-5 different time points. The pial surface is consistently misplaced in the same area, see attached main/aux volume images. I'm hesitant to manually replace the white matter myself as I fear it wouldn't be as accurate. Suggestions on other methods to fix this? The problem is always in the LH temporal right around the lateral inferior ventricle and the fusiform and other subcortical structures.
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