Bruce Fischl
Sent: Thursday, August 2, 2018 11:13:02 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ex vivo segmentations
yes, use vol2surf. I'm not sure what you want to do with the results, but
certainly matlab will give you the max flexibility
On Thu, 2 Aug 2018,
Fotiadis, Panag
___
_
> From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
> Fotiadis, Panagiotis
> Sent: Monday, July 30, 2018 4:33 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Ex vivo segmentatio
AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ex vivo segmentations
Hi Panos
we typically use mri_expand to move the surface inwards and outwards, then
sample with the resulting surfaces.
cheers
Bruce
On Thu, 2 Aug 2018, Fotiadis, Panagiotis
wrote:
>
> Hi Bruce,
>
>
> I had
July 30, 2018 4:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ex vivo segmentations
Cool. Thanks again!
Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643
lf of Fotiadis, Panagiotis
Sent: Monday, July 30, 2018 4:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ex vivo segmentations
Cool. Thanks again!
Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts Ge
Bruce Fischl
Sent: Monday, July 30, 2018 4:29:35 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ex vivo segmentations
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:
>
&g
) 643-3869
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
Bruce Fischl
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
t: 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,
urfer] 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
ch
Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce Fischl
Sent: Monday, July 30, 2018 3:56:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ex vivo
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
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 betwe
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