Hi Bruce,

Thanks, that is actually really helpful.

Also, I realized I misspoke earlier when I was talking about the cortical thickness range. The 3.7-3.9 mm range that I mentioned was referring to global cortical thickness across (not within) the different brains I have processed. The range of cortical thickness within individual brains was indeed wider ( between 2 - 5mm). I was just curious about why the average cortical thickness across brains was higher than what I've seen in the in vivo brains.

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

Hi Panos

I think you can trust the white surface (more or less), it's the pial
that is tougher. So you might sample say 1mm out from the white and not
use the pial at all
cheers
Bruce
On Mon, 30 Jul 2018, Fotiadis, Panagiotis wrote:

>
> 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
> >
> >
>
>