We are investigating it. I did fix one thing that you can try if you want - give us your hardware/software info and we will send you a new version of mris_make_surfaces Bruce
P.s. you can also upload and we will take a look On Apr 10, 2013, at 6:11 AM, "Yang, Daniel" <yung-jui.y...@yale.edu> wrote: > 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
