OK, it's not an issue in rh.orig.nofix, but it is an issue in rh.white and rh.orig. There are actually no WM voxels in wm.mgz to fix, as you can see in the pictures.

To be clear control points would be the best route here? Along the sulcus?

On Mon, Oct 21, 2013 at 1:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

Hi Jon

yes, we'll need images or just upload the subject as we can't diagnose it from only this information. If I had to guess, I would think it's an incorrectly fixed topological defect. See if the ?h.orig.nofix surface has the sulcus that is missing from the ?h.orig surface. If so, you'll need to fix the defect by either adding control points or manually editing the wm.mgz

cheers Bruce

On Mon, 21 Oct 2013, Jonathan Holt wrote:

Hi Guys,

...

I'm having an issue with a brain involving both inaccurate surfaces and incorrectly segmented voxels. Basically, a sulcus is being skipped over by the main surface where and a bunch of basically empty space is being segmented as white matter. I've edited the segmentation myself by removing it and then I ran

recon-all -autorecon2-noaseg -subjid <SUBJID>

The problem is still persisting and the surface is still inaccurate. I can attach photos if needed.

jon

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