as I said, I don't think I would trust the ex vivo thicknesses. Definitely
not in an absolute sense
On Mon, 30 Jul 2018,
Fotiadis, Panagiotis wrote:

>
> 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
>
> ____________________________________________________________________________________________________
> 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 4:07:48 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Ex vivo segmentations  
> 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
> > >
> > >
> >
> >
>
>