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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
