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There is a lot of WM that is not labeled properly. The only way to really fix it is to continue to edit the wm.mgz. However, it looks like there is a lot of WM that is labeled properly that is not being included. This is likely a topological defect. Try loading the ?h.smoothwm.nofix to see where the defects are, then try fixing them by hand. This may get you a long way toward fixing this case

On 8/10/2023 11:33 PM, Krystal Xiwing Yau wrote:

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Dear FreeSurfer experts,

It has been a problem for me to fix this kind of issue, and am struggling to obtain the accurate data from it.

I tried to edit wm.mgz as well as adding control points in attempt to expand the pial surface all the way up to the gyrus in temporal lobe. However, it only shows a tiny area calculated as pial surface in the right temporal lobe as shown below:

During the process of autorecon2-cp, I saw a message saying "An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz." May I know where I can spot out the defect?

Moreover, does it relate to the quality of images?

Thank you.

Regards, Krystal

Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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