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: fischl@nmr.mgh.harvard.edu To: moonblue412@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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