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 <nali...@gmail.com> wrote: > Dear Bruce, > > thank you for your comprehensive explanation. > > Best, > Nazanin > > > On Thu, Jan 19, 2017 at 7:00 PM, Bruce Fischl <fis...@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 < >>> fis...@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. >> >> >
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