Hi Patrick,

no images were attached.

If the skull strip removes any brain, you edit the brainmask and fill the voxels back (or adjust the watershed parameter if lot's of brain is missing). In you case it sounds like the brain is not missing from the brainmask, but the surfaces don't grab all of it. Is the white matter surface also undersegmented in that area? Then try adding control points in white matter that should help with both surfaces.

Best, Martin

On 09/10/2014 05:40 AM, Jan-Patrick Stellmann wrote:

Dear all,

we observe some segmentation faults in the temporal lobe in single patients. Gyri are within the brain mask but outside the pail boundaries. Editing brain mask.mgz or wm.mgz does not resolves the problem.
Examples are attached.

How can we add missing brain? we are using free surfer v5.3.0 on a linux mint workstation.

Thanks in advance.

Best regards,
Patrick

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