Hi Ben
our primary cortical segmentation of the wm is not probabilistic. In any
case you want partial volume fractions I expect, not posterior
probabilities. I would use mris_fill to create a mask of the WM from the
?h.white surfaces, if you want the most accuracy
cheers
Bruce
On Tue, 7
Aug 2018, Ben M wrote:
External Email - Use Caution
Hi,
I would like to create a mask of the WM for fMRI analysis. I read a previous
post in which it was
suggested to get the wm segmentation and erode it, since the result will be
exclusively WM. My
question is why is this so? Why can I assume that getting the WM mask from the
aseg file will almost
certainly get me high probability WM, >0.9 for example? In most segmentation
algorithms we get
posterior probabilities at each voxel, so that we can then select voxels with
posterior
probabilities >0.90 for example. Why is freesurfer's WM segmentation so
accurate that we do not need
posterior probabilities? Are these very high probabilities somehow already
coded in freesurfer's
segmentation algorithm?
Thanks,
Ben
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