Hello Kalyan,

A few questions:

-Is this an error you see frequently in your scans, or just a one-off type of error?

-Is it always in the same places anatomically?

-Did you make sure to put the control points in areas that were 100% white matter, and that had intensity values < 110 ? If you put cps in a partially volumed voxel or an area of gray matter, you will definitely mess up the white surfs.

- Have you tried editing the wm.mgz to add voxels and push the pial surface out? Oftentimes the wm.mgz is more forgiving (so if you add voxels to it, it won't necessarily mess up your wm surface)

Thank you,
Ani

On 07/21/2015 05:45 PM, Tripathy, Kalyan wrote:

Hi,


I am trying to manually correct some segmentation errors through Freesurfer. In particular, I have noticed a number of areas where the pial surface appears to miscalculated and is excluding chunks of grey matter. I tried using control points to push the pial surface out, and this helped reduce the grey matter exclusion, but now there are many places where the white matter surface has been reconstructed too far out, such that it includes a bunch of true grey matter within the white matter territory.

Is there a way that I can combine the original white matter surfaces with the corrected pial surfaces? When I tried to combine them in this manner and run recon-all, I received an error suggesting that the surfaces needed to match. Did I interpret that right, and is there a way around this?


Also, do you have any recommendations as to how I can extend the pial surface to correct grey matter omissions without incurring new errors as a result of the correction method?


Thank you for your time and help.


Kalyan



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