Vincent, Some may look like holes but as you mention are just sulci being cut through by that plane.

A way to check if it is the above is to put the cursor on the surface that creates this hole and then toggle to the other views (sagittal, axial, coronal). It will become clearer whether it is a sulcus or not in the other views based on where the cursor is located.

It takes some getting used to in order to differentiate the errors that appear as holes vs. sulci if you are not used to looking at the anatomy this way. But the sulci will be in the same areas brain to brain and you will get used to ignoring them. You can also use tksurfer to help identify true errors (they will look like holes or bumps on the surface). Allison

On Feb 22, 2012, at 6:12 PM, cloud.ctrl@me.com wrote:

According to the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits, we should be looking for these holes in the white surface, but when I looked at my processed data using tkmedit SUBJECT brainmask.mgz -aux wm.mgz -surfs, I saw many such holes. They seem to be ubiquitous throughout all 20 of the brains I have processed. Some might be true mistakes in the white matter surface, but I thought maybe some might just be holes that appear because of the shape of sulci moving through 3D space. Or perhaps my Talairach is off? Is there any material that instructs how to tell the difference between holes which need to be fixed and those that don't?

Thank you, Vincent _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer