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