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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