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, Panagiotis wrote:

>
> Hi Bruce,
>
>
> That's actually great for visualizing the new surface as well, thanks! And to calculate the actual
> intensity at that distance, would I need to resample with mri_vol2surf and then use MATLAB or should
> I go another way?
>
>
> Thanks again,
>
> 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: Thursday, August 2, 2018 10:24:23 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 a follow-up question concerning measuring the signal intensity of the gray and white
> matter in
> > those ex vivo brains:
> >
> >
> > I used mri_vol2surf to create an mgh surface that goes 1mm outside the white matter (to estimate
> > intensity in the gray matter) and another surface that goes 1mm into the white matter (to estimate
> > the signal intensity within the white matter). However, I don't think I can use mri_segstats here
> to
> > calculate the actual intensity value, as the ex vivo pipeline does not come up with a segmentation
> > option I can use (or at least that is my impression), so I ended up using MATLAB (by MRIreading
> the
> > mgh file and then calculating a mean of the non-zero array values of the mgh file). Would you
> > recommend a different way to calculate the intensity in those mgh files or do you think that my
> > current MATLAB approach should suffice?
> >
> >
> > Thanks again for all your help!
> >
> >
> > 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
> > Fotiadis, Panagiotis <PFOTIADIS@mgh.harvard.edu>
> > 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 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 4:29:35 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:
> >
> > >
> > > 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
> > > > >
> > > > >
> > > >
> > > >
> > >
> > >
> >
> >
>
>