There might be a couple things happening. First, I would try adding a
few control points in that area; make sure they are in true WM in voxels
that have a value less than 110 on the brain.mgz file. This might help
push the white surface further out (the WM in that gyrus is very thin).
It might also help push the pial surface out. The next thing you can try
is to increase the maximum distance over which the edge is searched for.
These young subjects have very plump/thick cortices. You can do that
with an expert options file. Create a text file with the following content:
PlaceT1PialSurf --max-cbv-dist 6
Where "6" tells it to search 6 mm rather than the default 5. You may
need to play with the number
You can then run recon-all with
recon-all -s subject -expert yourexpertoptions.txt -pial -lh
The above command will run just the pial of just the lh hemi, so you
should have your answer in a few minutes
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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