Hi Bruce and others,

Thanks for the reply! I cloned in all of the brain to the brainmask and ran -autorecon2. What I have so far looks a lot better, but -autorecon2 exited with errors. In recon-all.log it looks like mris_curvature_stats went fine, then it says "INFO: mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file"

I thought ribbon.mgz would be created in -autorecon3. Is it okay to just run -autorecon3 now, or should I fix something first?

Thank you! Sara

On 08/11/2014 11:54 AM, Bruce Fischl wrote:

It looks more likely that it is a problem with the skull stripping. If you clone the brain voxels back in and rerun do things work?

...

On Aug 11, 2014, at 4:11 PM, "Makaretz, Sara Johanna" SMAKARETZ@mgh.harvard.edu wrote:

I am having trouble getting a usable brainmask for one of my subjects - a screenshot of the initial brainmask.mgz is attached as image_1. The talairach transformation looks fine, so I tried running recon-all -multistrip with raised watershed heights to no avail - see image_2.

Does this mean the problem is with the mri_em_register step / lta output? How can I check this, and what can I try changing?

Thank you! <image_1.jpg> <image_2.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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