Hi Bruce,

Thanks for your prompt response! I see, in that case I will disregard cortical thickness for now. I was also interested in measuring the average signal intensities of the gray and white matter in those ex vivo brains. Do you think it would be prudent to use the resulting surfaces from the ex vivo pipeline (after of course checking their accuracy and making sure the gray/white segmentations look accurate) to measure said intensities, or would you recommend another way?

Thanks,
Panos

Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Sent: Monday, July 30, 2018 3:56:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ex vivo segmentations

Hi Panos

I wouldn't trust the thickness from the ex vivo pipeline, and in any case
those number are way to narrow a range. The normal cortex thickness ranges
from about 1.5mm to 4 or 4.5mm. Getting reasonable thickness from ex vivo
data is high on our to-do list

cheers
Bruce

On Mon, 30 Jul 2018, Fotiadis, Panagiotis wrote:

>
> Hi Bruce and Doug,
>
>
> I have processed a few ex vivo brains with the help of the ex vivo freesurfer pipeline (outlined
> in https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon), and have extracted their cortical
> thickness. So far the range of the cortical thicknesses have been approximately between
> 3.70-3.90 mm. Does that number sound reasonable for ex vivo brains? I am asking because the typical
> cortical thickness that I would expect to find on an in vivo brain would be between 2.05 - 2.35 mm.
>
> Thanks in advance for any advice!
>
> Best,
>
> Panos
>
>
> Panagiotis Fotiadis
> Senior Imaging Research Technologist
> J. P. Kistler Stroke Research Center, Department of Neurology
> Massachusetts General Hospital, Boston, MA
> T: (617) 643-3869
>
>