Hi Bruce,

That worked. Thanks!

Ana

On 05.10.2015 17:56, Bruce Fischl wrote:

Hi Ana

you might need to fix the labeling in the aseg. If you can't get this to work feel free to upload and we will take a look

cheers Bruce On Mon, 5 Oct 2015, Anastasia Klimovich-Smith wrote:

...

Dear freesurfer experts,

I have an issue with -autorecon2-wm stage results (freesurfer v.5.3.0). Sometimes the ventricles are not fully filled and the white matter is localized within the remaining gaps. After manually filling the gaps in the wm.mgz (following the wiki - Fixing Common Geometric Inaccuracies in White Matter Surfaces) and rerunning (-autorecon2-wm) I still have the wm surface following the ventricle holes, even though I can see they are filled on wm.mgz. I used freesurfer v.5.1.0 before and didn't have these issues. How would you recommend fixing this?

Thanks a lot, Ana _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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