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Thx Doug, much appreciated.
Jim
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve
Sent: Tuesday, August 31, 2021 12:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces
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Hi Jim, I know it has been a while, but I have tracked down the source of the
problem with the pial surface. I can go into detail if you want, but the fix
is to add -no-numakeuchar to recon-all. I noticed that there are some places
where the white surface does not extend far enough. This is due to the WM
strands being very thin and partial voluming with GM. The fix for this is to
edit the wm.mgz and rerun recon-all with -autorecon-wm -autorecon3.
doug
On 5/27/2021 2:19 PM, Alexopoulos, Dimitrios wrote:
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Hi users,
We're having some issues with running some of our 2-3yo data (0.8mm isotropic)
through FS7 with and without the -hires flag.
There are persistent issues with the frontal lobe regions where the pial has
not extended to outer surface as illustrated below.
The WM surface contour look reasonable but the pial has underestimated the
outer cortex resulting in an incorrect surface (below).
I don't think control points will work (low intensity values in the 50-60s),
and no WM to add to the WM.mgz.
Any suggestion on how to push the pial surface out to capture the cortical
surface??
Thx.
Jim
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[cid:image003.png@01D79E6C.D1C47A10] [cid:image004.png@01D79E6C.D1C47A10]
&nb sp;
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