Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
Daniel, Unfortunately, since I run all the individuals again with FreeSurfer 5.2, I just saved from the 5.1 the info I was using for comparison between version - the aseg stats. I don't have cortical thickness information for 5.1 unless we run all the cases again in 5.1 - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Thu, Apr 11, 2013 at 2:47 PM, Yang, Daniel wrote: > Hi PPJ and all, > > I found that the 5.2 – 5.1 difference is primarily seen in the cortical > thickness, and much less so in the aseg.volume. > > Here, I picked right-amygdala volume as an example of aseg.volume and > rh_bankssts_thickness as an example of rh.aparc.thickness. > > While the correlation between the two versions of right-amygdala is r = > .92 (n = 161), that of the rh_bankssts_thickness is r = .45. > > Presumably I believe the correlation should be > .90 for a strong > continuity between the two versions? > > Do you have anything in the cortical thickness? > > 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 > Date: Wednesday, April 10, 2013 11:07 AM > To: Daniel Yang > Cc: Bruce Fischl , " > freesurfer@nmr.mgh.harvard.edu" > > Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0 > > 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 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 >> Date: Wednesday, April 10, 2013 10:49 AM >> To: Bruce Fischl >> Cc: Daniel Yang , "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 wrote: >>> >>>> Dear FreeSurfer Expert
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
The 5.2 image has been smoothed, by a small degree, relative to 5.1. Either prior to FS processing or by FS, it would seem. On Mon, Apr 15, 2013 at 3:29 AM, Christopher Bell < christopherbell2...@gmail.com> wrote: > Looking at the image posted previously. > > https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn > > I think it is pretty clear the 5.1 picture has better gray/white contrast. > It is a very subtle difference, but you can see it if you look at some > pieces of > wm that were "missed" by 5.2 in this image. > > > > > On Thu, Apr 11, 2013 at 12:33 PM, Yang, Daniel wrote: > >> Thanks Nick! I have uploaded the relevant files to you. >> >> Thanks, >> Daniel >> >> -- >> Yung-Jui "Daniel" Yang, PhD >> Postdoctoral Researcher >> Yale Child Study Center >> New Haven, CT >> (203) 737-5454 >> >> >> >> >> >> >> On 4/10/13 1:19 PM, "Nick Schmansky" wrote: >> >> >Daniel, >> > >> >We're repeating our paired-analysis of thickness measures between 5.1 >> >and 5.2. In the meantime, to check for correctness, open the >> >brain.finalsurfs.mgz file with the surfaces overlayed, and check the >> >intensity value of the voxels which appear to be non-cortical 'black >> >spaces', relative to neighboring gm voxels. ignore the aseg.mgz gm >> >voxels, as those are not accurate (ie, dont load aseg.mgz when >> >inspecting surfaces, or at least turn if off when inspecting gm >> >regionsits still handy to see where hippocampus sits). >> > >> >Nick >> > >> > >> >On Wed, 2013-04-10 at 11:11 +, Yang, Daniel 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 >> >> >> > >> > >> > >> > >> >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 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.
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
Looking at the image posted previously. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn I think it is pretty clear the 5.1 picture has better gray/white contrast. It is a very subtle difference, but you can see it if you look at some pieces of wm that were "missed" by 5.2 in this image. On Thu, Apr 11, 2013 at 12:33 PM, Yang, Daniel wrote: > Thanks Nick! I have uploaded the relevant files to you. > > Thanks, > Daniel > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454 > > > > > > > On 4/10/13 1:19 PM, "Nick Schmansky" wrote: > > >Daniel, > > > >We're repeating our paired-analysis of thickness measures between 5.1 > >and 5.2. In the meantime, to check for correctness, open the > >brain.finalsurfs.mgz file with the surfaces overlayed, and check the > >intensity value of the voxels which appear to be non-cortical 'black > >spaces', relative to neighboring gm voxels. ignore the aseg.mgz gm > >voxels, as those are not accurate (ie, dont load aseg.mgz when > >inspecting surfaces, or at least turn if off when inspecting gm > >regionsits still handy to see where hippocampus sits). > > > >Nick > > > > > >On Wed, 2013-04-10 at 11:11 +, Yang, Daniel 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 > >> > > > > > > > > > >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 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.
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
Thanks Nick! I have uploaded the relevant files to you. Thanks, Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 4/10/13 1:19 PM, "Nick Schmansky" wrote: >Daniel, > >We're repeating our paired-analysis of thickness measures between 5.1 >and 5.2. In the meantime, to check for correctness, open the >brain.finalsurfs.mgz file with the surfaces overlayed, and check the >intensity value of the voxels which appear to be non-cortical 'black >spaces', relative to neighboring gm voxels. ignore the aseg.mgz gm >voxels, as those are not accurate (ie, dont load aseg.mgz when >inspecting surfaces, or at least turn if off when inspecting gm >regionsits still handy to see where hippocampus sits). > >Nick > > >On Wed, 2013-04-10 at 11:11 +, Yang, Daniel 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 >> > > > > >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
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
Hi PPJ and all, I found that the 5.2 – 5.1 difference is primarily seen in the cortical thickness, and much less so in the aseg.volume. Here, I picked right-amygdala volume as an example of aseg.volume and rh_bankssts_thickness as an example of rh.aparc.thickness. While the correlation between the two versions of right-amygdala is r = .92 (n = 161), that of the rh_bankssts_thickness is r = .45. Presumably I believe the correlation should be > .90 for a strong continuity between the two versions? Do you have anything in the cortical thickness? 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 mailto:p...@netfilter.com.br>> Date: Wednesday, April 10, 2013 11:07 AM To: Daniel Yang mailto:yung-jui.y...@yale.edu>> Cc: Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu>>, "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0 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<http://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 mailto: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 mailto:p...@netfilter.com.br>> Date: Wednesday, April 10, 2013 10:49 AM To: Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu>> Cc: Daniel Yang mailto:yung-jui.y...@yale.edu>>, "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto: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<http://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 mailto: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 Juniormailto: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<http://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 mailto: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" mailto: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). >
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
Daniel, We're repeating our paired-analysis of thickness measures between 5.1 and 5.2. In the meantime, to check for correctness, open the brain.finalsurfs.mgz file with the surfaces overlayed, and check the intensity value of the voxels which appear to be non-cortical 'black spaces', relative to neighboring gm voxels. ignore the aseg.mgz gm voxels, as those are not accurate (ie, dont load aseg.mgz when inspecting surfaces, or at least turn if off when inspecting gm regionsits still handy to see where hippocampus sits). Nick On Wed, 2013-04-10 at 11:11 +, Yang, Daniel 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 > ___ 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.
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
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 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 > Date: Wednesday, April 10, 2013 10:49 AM > To: Bruce Fischl > Cc: Daniel Yang , "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 > 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 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" 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 >>> > >>> > >>> > >>> > >>> > >>>
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
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 mailto:p...@netfilter.com.br>> Date: Wednesday, April 10, 2013 10:49 AM To: Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu>> Cc: Daniel Yang mailto:yung-jui.y...@yale.edu>>, "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto: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<http://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 mailto: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 Juniormailto: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<http://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 mailto: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" mailto: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" mailto: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" >>mailto: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 1910
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
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 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 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" 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" 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" 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 > >>>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. > >>> > >> > >> > > > > > ___
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
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 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" 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" 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" > 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 > >>>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.m
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
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" 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" 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" 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" 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 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
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
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" 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" 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" 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 >>>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
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
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" 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" 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 >>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
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
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" 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 >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
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
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 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.
