Hi Laurel

yes, the lh.orig.nofix is created using the control points and other things, and so the number of holes in it will definitely change if the placement of control points changes

cheers Bruce On Thu, 5 Dec 2019, Laurel Quinlan wrote:

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Hi Doug,

Thank you! Yes, their control point edits were different. Are the number of ?h.orig.nofix defects calculated after reconstruction with control point edits?

-Laurel

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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Tuesday, December 3, 2019 2:16 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surfaceholes in aseg.stats   Those are the number of defects in the ?h.orig.nofix. Not sure why the two people see different numbers. Are you totally sure they are being run in exactly the same way? If they made different edits (control points, brain mask) then it could result in different number of holes

On 12/3/2019 2:38 PM, Laurel Quinlan wrote:

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  Hi Freesurfer Support,

I'm wondering how ?h.surfaceholes prior to fixing and "Total number of defect holes in surfaces prior to fixing" are calculated in the aseg.stats file for each brain. I compared aseg.stats files for the same brain edited by two different people, and I noticed that there were different numbers of holes listed for each person, despite the brain being the same.

For example: lhSurfaceHoles 130 vs 61 rhSurfaceHoles 102 vs 80 Total number of defect holes 232 vs 141 Why would those numbers be so different?

Thanks,

Laurel Quinlan Associate Research Specialist Center for Healthy Minds University of Wisconsin-Madison

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