Dear FreeSurfer Experts and Users, Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical "black spaces" within pial surfaces, compared to FS 5.1?
I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten. At the meantime I keep receiving Emails from people asking me this issue. Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/19/13 7:07 AM, "Yang, Daniel" <yung-jui.y...@yale.edu> wrote: > >Posting one of the brains. > >https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn > > >It seems to me that neither version is perfect; however, 5.2.0 is >capturing more "black spaces" in the region I'm looking at. > >It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20). > >Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the >region I examined with my samples, it's not a systematic "predictable" >bias. > >Any solution? > >-- >Yung-Jui "Daniel" Yang, PhD >Postdoctoral Researcher >Yale Child Study Center >New Haven, CT >(203) 737-5454 > > > > > > >On 3/18/13 6:27 PM, "Matt Glasser" <m...@ma-tea.com> wrote: > >>Do the surfaces look correct in these regions? You might post some >>screenshots of subjects who have a big difference between 5.1 and 5.2 >>with >>the 5.1 and 5.2 white and pial surfaces on volume slices that highlight >>the difference. Without this kind of info, its hard to know which was >>more correct, 5.1 or 5.2. >> >>Peace, >> >>Matt. >> >>On 3/18/13 5:13 PM, "Ritobrato Datta" <rida...@mail.med.upenn.edu> wrote: >> >>>I concur. I have seen similar results in primary visual cortex from ~40 >>>subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to >>>1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3. >>> >>>Ritobrato Datta, Ph.D. >>>Post Doctoral Researcher >>>Department of Neurology >>>University of Pennsylvania School of Medicine >>>3rd Floor, Room 312 >>>3710 Hamilton Walk (Goddard Laboratories) >>>Philadelphia, PA 19104-6241 >>>email - rida...@mail.med.upenn.edu >>> >>> >>>----- Original Message ----- >>>From: Daniel Yang <yung-jui.y...@yale.edu> >>>To: freesurfer@nmr.mgh.harvard.edu >>>Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT) >>>Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0 >>> >>>Dear FreeSurfer Experts, >>> >>>I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161 >>>subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in >>>particular. >>> >>>Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in >>>5.2.0. They are significantly different, t(160) = 56.71. >>> >>>The correlation between the two versions is r = .33 >>> >>>Is this something possible?? I can't see what went wrong in my >>>procedures. >>> >>>Thanks! >>>Daniel >>> >>>-- >>>Yung-Jui "Daniel" Yang, PhD >>>Postdoctoral Researcher >>>Yale Child Study Center >>>New Haven, CT >>>(203) 737-5454 >>> >>>_______________________________________________ >>>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
