Dear Martin,

sorry for the missing pictures. I tried all correction steps recommended in the tutorial. Results are now attached… As you can see even control points did not completely correct the failure. WM mask recognizes the grey/white matter correctly, but surfaces are still not correct. Thank you very much for your help.

Best regards, Patrick

Dr. med. Jan-Patrick Stellmann Institut für Neuroimmunologie und MS (inims) Klink für Neurologie Universitätsklinikum Eppendorf (UKE) Martinistrasse 52 20246 Hamburg Germany tel.: 040-7410-54076 fax: 040-7410-56973 email: j.stellmann@uke.uni-hamburg.de

Am 12.09.2014 um 15:39 schrieb Martin Reuter mreuter@nmr.mgh.harvard.edu:

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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