Hi Andrea,
Take a look at the ?h.orig.nofix surfaces. Does it look like the wm edits
were picked up in those initial surfaces? Also, just check that the edits
to the wm.mgz were 255 and that there are no major disconnects anywhere.
-Louis
On Fri, 4 Apr 2014, Andrea Grant wrote:
I was able to quickly edit my WM.mgz file using the contour edit that Louis
suggested.
However, when I then re-run the recon-all with -autorecon2-wm and -autorecon3,
it doesn't
correct the problem. I'm attaching two figures (with and without the edited
WM.mgz overlay).
What are my next steps to correct the segmentation?
Thanks,
Andrea
On Fri, Mar 7, 2014 at 3:25 PM, Louis Nicholas Vinke
<vi...@nmr.mgh.harvard.edu> wrote:
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
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