Tibor, We are working to put some exvivo wm segmentation methods into the next FreeSurfer release although I'm not sure where that stands. We do process our exvivo scans with FreeSurfer but we use scripts that use different parameters than recon-all since the contrast is different and as you said there is no skull. Our scripts are specific to our scan protocol. What did you collect and on what scanner? Allison

On Tue, 15 Mar 2011, Auer, Tibor MD. Ph.D. wrote:

Dear Users,

Is there a way to process fixated brain (after autopsy) with Freesurfer?

I have read somewhere that I should just "invert" the image, but what does it mean? And would it not increase the noise and the signal from the CSF?

Of course, the brain is without any skull, pia and dura mater. Does it cause no problem for Freesurfer?

Thanks,

Auer, Tibor M.D. Ph.D.

Biomedizinische NMR Forschungs GmbH

am Max-Planck Institut für Biophysikalische Chemie

Am Fassberg 11

37077 Göttingen

Germany

Phone/Work: +49-(0)551-201-1725

Mobile: +49-(0)176-8012-7921

E-Mail: tauer@gwdg.de mailto:tibor.auer@gmail.com