Ok, I'll try to put together a stat from aparc too. --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
On Wed, Apr 10, 2013 at 12:04 PM, Yang, Daniel <yung-jui.y...@yale.edu>wrote: > Hi PPJ, > > Thanks! It looks interesting. I also found FS 5.2 is faster. Is there > any chance you could also provide the cortical thickness of the 2009 atlas > (e.g., rh)? > > I will take a look into the aseg.volume in my data too. > > Best, > Daniel > > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454 > > From: Pedro Paulo de Magalhães Oliveira Junior <p...@netfilter.com.br> > Date: Wednesday, April 10, 2013 10:49 AM > To: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Cc: Daniel Yang <yung-jui.y...@yale.edu>, "freesurfer@nmr.mgh.harvard.edu" > <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0 > > You'll find attached some preliminary data of the comparison we did > among versions. > > --------------------------------------------------------------------- > Pedro Paulo de Magalhães Oliveira Junior > Netfilter & SpeedComm Telecom > -- www.netfilter.com.br > -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 > > > > On Wed, Apr 10, 2013 at 10:42 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu > > wrote: > >> Hi PPJ >> That's exactly what we are doing. Good to hear its stable for you >> Bruce >> >> >> >> On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalhães Oliveira Junior< >> p...@netfilter.com.br> wrote: >> >> I have processed more that 600 brains with both versions in the last >> weeks and the only difference I'm seeing between version 5.2.0 and 5.1, >> besides the obvious new features, is processing time. >> >> Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance. >> >> Besides that there's no visible difference in terms of cortical >> thickness, volumes, etc. >> >> If you have access to computer resources to spare you can run recon-all >> of both versions in some well known database of images and do a more formal >> test. >> >> >> >> >> >> >> --------------------------------------------------------------------- >> Pedro Paulo de Magalhães Oliveira Junior >> Netfilter & SpeedComm Telecom >> -- www.netfilter.com.br >> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 >> >> >> >> On Wed, Apr 10, 2013 at 8:11 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 >> >> >
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