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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of > Fotiadis, Panagiotis <pfotia...@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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of > Bruce Fischl <fis...@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-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of > > Bruce Fischl <fis...@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-boun...@nmr.mgh.harvard.edu > > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf > of > > > Bruce Fischl <fis...@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 > > > > > > > > > > > > > > > > > > > >
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