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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