Hi Nazanin
those steps are already incorporated into recon-all - you don't need to do anything special
cheers Bruce On Fri, 20 Jan 2017, N Saf wrote:
Dear Bruce,
I read this article "Atlas Renormalization for Improved Brain MR Image Segmentation Across Scanner Platforms(2007)" and I wonder if theses steps "normalization" and "normalization2" do the Atlas Renormalization which mentioned at that article or should I use another command myself to do the Atlas Renormalization that the article proposed? (sorry if the question is basic)
Best, Nazanin
On Fri, Jan 20, 2017 at 9:16 AM, N Saf nalives@gmail.com wrote: Dear Bruce,
thank you for your comprehensive explanation.
Best, Nazanin
On Thu, Jan 19, 2017 at 7:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Nazanin
there is no easy way to display a partial volume. You can still use Dice/Jaccard on the hard segmentations, but we have found that the partial volume correction improves e.g. test/retest reliability and probably accuracy, although that is harder to prove. cheers Bruce On Thu, 19 Jan 2017, N Saf wrote: Dear Bruce is there any 3D image file which shows the segmentation regions after this correction ?and if there is not is it right to use aseg.mgz file for reporting Dice or Jaccard Index (I have manual segmentation as gold standard)? Best Regards, Nazanin On Wed, Jan 18, 2017 at 5:18 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Nazanin the volumes reported in the aseg.stats file have been corrected for partial volume effects. cheers Bruce On Wed, 18 Jan 2017, N Saf wrote: Dear FreeSurfers, I have a question about aseg file. I load the aseg file of bert subject in itk-snap and read the volume for 17 and 53 label but it is a bit larger of the volume in bert stats file. I do the same for some of my subjects too and I see the same result .I don't know why it is like that ?would you please clear the reason for me.because I need to compare the FreeSurfer result and I should use of aseg file labels but I'm afraid the comparison I'm doing is not valid. Sincerely yours, Nazanin _______________________________________________ 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.
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.