Dear experts,
during the manual correction of freesurfer reconstruction I encountered
following problem:
White surface did not follow gray / white matter boundary probably partly due
to skullstrip error and partly to the insufficient local gray/white matter
contrast. I tried to fix it by editing wm.mgz, in some cases it worked well,
but in some cases white surface "does not respect" my wm.mgz editing and still
leaks out to the areas where wm.mgz has value 1.
The problem is probably at the level of recon-all -white since orig.nofix.mgz
and orig.mgz are OK - does well follow my edits and does not leak to areas with
wm.mgz = 1.
I tried to put some control points to these areas but it still did not help
(the brainmask.mgz at most of the problematic areas has intensity 110).
Processing the data by development version did not help either.
I have uploaded 2 examples to your ftp file exchange:
not_corrected_wm_1
- slice 96 in coronal view, right hemisphere, at the convexity
- slices 97-98, 103, 107,108, in coronal view, left hemisphere, at the
convexity
not_corrected_wm_2
- slices 78 in coronal view, right hemisphere, 2 areas at the convexity
- slices 79-83 in coronal view, two quite large areas in both hemispheres at
the convexity
- slices 88-95 in coronal view, quite large areas at righ hemispheres at the
convexity
and other areas in following slices, there are quite large amount of them in
this subject.
Could you please look at the data to find where could be the problem?
Thank you very much for all your help.
Best regards,
Antonin Skoch
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