Hi Yue
tksurfer will only display cortical histograms. For subcortical regions
you are probably best off using something like matlab (which would be
pretty trivial)
cheers
Bruce
On Fri, 1 Nov 2013, ?? wrote:
Hi Bruce,
Thanks for the information. The surface works for me. These histograms
generated from the surfaces, if I understand correctly, are based on the
intensities along the boundaries of one region. Can I also generate
histograms including the whole region? Like Pick putamen or caudate and
generate histograms and statistic summaries based on all the pixels in those
regions. Or can I generate binary masks of putamen or caudate from the
labels then I can apply those masks and generate histograms in other
softwares? Thanks a lot!
Best,
Yue
> Date: Fri, 1 Nov 2013 08:45:35 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: moonblue...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] How to generate histograms of intensities in one
anatomical region?
>
> Hi Yue
>
> if you sample them on to the surface with mri_vol2surf you can use the
> overlay histogram facility in tksurfer to do what you want. You can also
> use mask_label to remove values outside of an ROI if that is what you are
> interested in.
>
> cheers
> Bruce
> On Fri, 1 Nov 2013, ?? wrote:
>
> > Hi All,
> > I have T1-weighted MPRAGE images and I run recon-all to generate
surfaces
> > and labels in freesurfer. Then I would like to do statistical analysis
in
> > the regions I am interested in. For example, I would like to generate a
> > histogram of intensities in frontal cortex or in occipital. I can
display
> > these regions in different color in freeview based on the look-up table
but
> > I don't know how to use them to generate histograms in freesurfer or
create
> > binary masks then I can do the analysis with these masks in matlab.
> >
> > I use freesurfer to do this because I see these beautiful color
> > segmentations. It would be really painful to manually create regional
masks
> > for a group study. I am new to freesurfer and I really appreciate if
someone
> > can point out a direction.
> >
> > Thanks!
> >
> >
> > Best,
> > Yue
> >
> >
>
>
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