Got you. I will check out ribbon and read more about mri_vol2surf. Thanks for your help! Yue
> Date: Fri, 1 Nov 2013 12:16:48 -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? > > the surfaces can be used to sample in many different ways using options to > mri_vol2surf. For example you could average over the ribbon then display > the histogram of that. For subcortical structures the surfaces don't make > sense, so you are better off just doing it in matlab cheers Bruce > > > On Fri, > 1 Nov 2013, ?? wrote: > > > Hi Bruce, > > Thanks for responding so quickly. > > > > Sorry I probably don't describe my question clearly and my examples are bad. > > This is really new to me. So please correct me if I say something wrong. Let > > me explain again. Hopefully it will make some sense. > > > > What I want to do is first to segment out different cortical and subcorical > > regions(like frontal cortex, occipital cortex, posterior cingulate cortex, > > putamen etc.) and then generate histograms from these regions separately. > > The surfaces give me the histograms that only include the intensities on the > > edges of the regions, right? I am wondering if I can generate histograms > > from the area of one cortical region not just the boundaries. Thanks! > > > > > > Best, > > Yue > > > > > > > Date: Fri, 1 Nov 2013 11:12:46 -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 > > > > > > 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 > > > > > > > > > > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom > > it > > > > is > > > > > addressed. If you believe this e-mail was sent to you in error and the > > > > e-mail > > > > > contains patient information, please contact the Partners Compliance > > > > HelpLine at > > > > > http://www.partners.org/complianceline . If the e-mail was sent to you > > in > > > > error > > > > > but does not contain patient information, please contact the sender > > and > > > > properly > > > > > dispose of the e-mail. > > > > > > > > > > > >
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