14 Nov
2016
14 Nov
'16
7:20 a.m.
Dear Freesurfer's experts,
I come back to you concerning questions of registrations.
Since during the longitudinal process each --long subject directory has been registered onto the common --base template, shouldn't I:
1) Register PET data onto the subject cross-sectional directory (native data) with rigid-body transformation 2) Then take into account the registration between --cross and --long directory subject and apply the registration to the PET first registered onto native space ? In this case, how and where is this transformation has been saved ?
Best regards, Matthieu
2016-09-30 23:05 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Yes
On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote:
Hi Douglas,
Does the surface of the closest MRI time point mean the surface of the -long subject time point directory rather than cross-sectional subject time point directory ?
Best regards, Matthieu
Le 30 sept. 2016 9:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> a écrit :
There is no such long process for PET. The idea is that you process the MRI in a longitudinal way, then sample the PET data onto the surface of the closest MRI time point. Then proceed in a way similar to the thickness analysis On 09/29/2016 11:08 AM, Matthieu Vanhoutte wrote: > Dear Freesurfer's experts, > > Could you answer me about my last question with no response in the > mail below ? > > When using cortical thickness in longitudinal analysis with LME, we > used lh.thickness or rh.thickness from -long subject directories. > These data followed particular processing steps including > registrations in order to use them with more precision in longitudinal > studies, didn't they ? > > My problem is that I would like to perform longitudinal study onPET
> data images with LME. So I wonder if I just have to resample onto > -long cortical subject surface ? Do I need to follow the same steps > than cortical thickness from cross-sectional to -long subject > directories ? If this is the case, which commands should I use to > mimic cortical thickness longitudinal data ? > > Many thanks in advance for helping ! > > Best regards, > Matthieu > > 2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>: > > Hi Martin, > > Thanks for your answer. However, it seems to me that cortical > thickness follow a particular process with the recon-all -long > process, isn’t it ? Is there any resample onto average time > subject then other operation following ? > > Best regards, > Matthieu > > > Le 18 sept. 2016 à 16:26, Martin Reuter > <mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>> > a écrit : > > > > Hi Matthieu, > > > > I never used PET data, but once you manage to resample youpet
> data onto the surface, you will have a file similar to the > thickness file for each subjects. Instead of thickness it holds > you PET information. From that point on everything should be > identical to the thickness analysis. > > > > So this is really more a question how to get your PET data > sampled onto the surface. If no one else replies, write that into > the subject line and repost. > > > > Best, Martin > > > > > >> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > wrote: > >> > >> Dear Freesurfer’s experts, > >> > >> I would like to use the longitudinal mixed-effects model for > surface PET analysis. Although I could find all the process to > follow the longitudinal analysis of cortical thickness, I couldn’t > resolve the steps/commands to apply successively tocoregistered
> PET data on T1 MRI. > >> > >> Could you precise me the process and commands to use for PET > longitudinal analysis ? > >> > >> Many thanks in advance ! > >> > >> Best regards, > >> Matthieu > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > >> > >> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > The information in this e-mail is intended only for theperson
> to whom it is > > addressed. If you believe this e-mail was sent to you inerror
> and the e-mail > > contains patient information, please contact the Partners > Compliance HelpLine at > > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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14 Nov
14 Nov
11:12 a.m.
New subject: Longitudinal surface analysis of PET data
I would just register the pet to the closest (in time) anatomical
On 11/14/2016 07:20 AM, Matthieu Vanhoutte wrote:
Dear Freesurfer's experts,
I come back to you concerning questions of registrations.
Since during the longitudinal process each --long subject directory has been registered onto the common --base template, shouldn't I:
- Register PET data onto the subject cross-sectional directory
(native data) with rigid-body transformation 2) Then take into account the registration between --cross and --long directory subject and apply the registration to the PET first registered onto native space ? In this case, how and where is this transformation has been saved ?
Best regards, Matthieu
2016-09-30 23:05 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
Yes On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote: > > Hi Douglas, > > Does the surface of the closest MRI time point mean the surface of the > -long subject time point directory rather than cross-sectional subject > time point directory ? > > Best regards, > Matthieu > > > Le 30 sept. 2016 9:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> a écrit : > > There is no such long process for PET. The idea is that you > process the > MRI in a longitudinal way, then sample the PET data onto the > surface of > the closest MRI time point. Then proceed in a way similar to the > thickness analysis > > > On 09/29/2016 11:08 AM, Matthieu Vanhoutte wrote: > > Dear Freesurfer's experts, > > > > Could you answer me about my last question with no response in the > > mail below ? > > > > When using cortical thickness in longitudinal analysis with LME, we > > used lh.thickness or rh.thickness from -long subject directories. > > These data followed particular processing steps including > > registrations in order to use them with more precision in > longitudinal > > studies, didn't they ? > > > > My problem is that I would like to perform longitudinal study on PET > > data images with LME. So I wonder if I just have to resample onto > > -long cortical subject surface ? Do I need to follow the same steps > > than cortical thickness from cross-sectional to -long subject > > directories ? If this is the case, which commands should I use to > > mimic cortical thickness longitudinal data ? > > > > Many thanks in advance for helping ! > > > > Best regards, > > Matthieu > > > > 2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>>: > > > > Hi Martin, > > > > Thanks for your answer. However, it seems to me that cortical > > thickness follow a particular process with the recon-all -long > > process, isn’t it ? Is there any resample onto average time > > subject then other operation following ? > > > > Best regards, > > Matthieu > > > > > Le 18 sept. 2016 à 16:26, Martin Reuter > > <mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>>> > > a écrit : > > > > > > Hi Matthieu, > > > > > > I never used PET data, but once you manage to resample you pet > > data onto the surface, you will have a file similar to the > > thickness file for each subjects. Instead of thickness it holds > > you PET information. From that point on everything should be > > identical to the thickness analysis. > > > > > > So this is really more a question how to get your PET data > > sampled onto the surface. If no one else replies, write that > into > > the subject line and repost. > > > > > > Best, Martin > > > > > > > > >> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>> > > wrote: > > >> > > >> Dear Freesurfer’s experts, > > >> > > >> I would like to use the longitudinal mixed-effects model for > > surface PET analysis. Although I could find all the process to > > follow the longitudinal analysis of cortical thickness, I > couldn’t > > resolve the steps/commands to apply successively to coregistered > > PET data on T1 MRI. > > >> > > >> Could you precise me the process and commands to use for PET > > longitudinal analysis ? > > >> > > >> Many thanks in advance ! > > >> > > >> Best regards, > > >> Matthieu > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >> > > >> > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
11:43 a.m.
New subject: Longitudinal surface analysis of PET data
Still using rigid-body registration on --long subject directory ?
Or is affine registration in this case needed ?
Best regards, Matthieu
2016-11-14 17:12 GMT+01:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
I would just register the pet to the closest (in time) anatomical
On 11/14/2016 07:20 AM, Matthieu Vanhoutte wrote:
Dear Freesurfer's experts,
I come back to you concerning questions of registrations.
Since during the longitudinal process each --long subject directory has been registered onto the common --base template, shouldn't I:
- Register PET data onto the subject cross-sectional directory
(native data) with rigid-body transformation 2) Then take into account the registration between --cross and --long directory subject and apply the registration to the PET first registered onto native space ? In this case, how and where is this transformation has been saved ?
Best regards, Matthieu
2016-09-30 23:05 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
Yes On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote: > > Hi Douglas, > > Does the surface of the closest MRI time point mean the surface of the > -long subject time point directory rather than cross-sectional subject > time point directory ? > > Best regards, > Matthieu > > > Le 30 sept. 2016 9:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> a écrit : > > There is no such long process for PET. The idea is that you > process the > MRI in a longitudinal way, then sample the PET data onto the > surface of > the closest MRI time point. Then proceed in a way similar tothe
> thickness analysis > > > On 09/29/2016 11:08 AM, Matthieu Vanhoutte wrote: > > Dear Freesurfer's experts, > > > > Could you answer me about my last question with no response in the > > mail below ? > > > > When using cortical thickness in longitudinal analysis with LME, we > > used lh.thickness or rh.thickness from -long subject directories. > > These data followed particular processing steps including > > registrations in order to use them with more precision in > longitudinal > > studies, didn't they ? > > > > My problem is that I would like to perform longitudinal study on PET > > data images with LME. So I wonder if I just have to resample onto > > -long cortical subject surface ? Do I need to follow the same steps > > than cortical thickness from cross-sectional to -long subject > > directories ? If this is the case, which commands should I use to > > mimic cortical thickness longitudinal data ? > > > > Many thanks in advance for helping ! > > > > Best regards, > > Matthieu > > > > 2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>>:
> > > > Hi Martin, > > > > Thanks for your answer. However, it seems to me that cortical > > thickness follow a particular process with the recon-all -long > > process, isn’t it ? Is there any resample onto average time > > subject then other operation following ? > > > > Best regards, > > Matthieu > > > > > Le 18 sept. 2016 à 16:26, Martin Reuter > > <mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>>>
> > a écrit : > > > > > > Hi Matthieu, > > > > > > I never used PET data, but once you manage to resample you pet > > data onto the surface, you will have a file similar tothe
> > thickness file for each subjects. Instead of thickness it holds > > you PET information. From that point on everything should be > > identical to the thickness analysis. > > > > > > So this is really more a question how to get your PET data > > sampled onto the surface. If no one else replies, write that > into > > the subject line and repost. > > > > > > Best, Martin > > > > > > > > >> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>>
> > wrote: > > >> > > >> Dear Freesurfer’s experts, > > >> > > >> I would like to use the longitudinal mixed-effects model for > > surface PET analysis. Although I could find all the process to > > follow the longitudinal analysis of cortical thickness, I > couldn’t > > resolve the steps/commands to apply successively to coregistered > > PET data on T1 MRI. > > >> > > >> Could you precise me the process and commands to use for PET > > longitudinal analysis ? > > >> > > >> Many thanks in advance ! > > >> > > >> Best regards, > > >> Matthieu > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >> > > >> > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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11:48 a.m.
New subject: Longitudinal surface analysis of PET data
Rigid.
On 11/14/2016 11:43 AM, Matthieu Vanhoutte wrote:
Still using rigid-body registration on --long subject directory ?
Or is affine registration in this case needed ?
Best regards, Matthieu
2016-11-14 17:12 GMT+01:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
I would just register the pet to the closest (in time) anatomical On 11/14/2016 07:20 AM, Matthieu Vanhoutte wrote: > Dear Freesurfer's experts, > > I come back to you concerning questions of registrations. > > Since during the longitudinal process each --long subject directory > has been registered onto the common --base template, shouldn't I: > > 1) Register PET data onto the subject cross-sectional directory > (native data) with rigid-body transformation > 2) Then take into account the registration between --cross and --long > directory subject and apply the registration to the PET first > registered onto native space ? In this case, how and where is this > transformation has been saved ? > > Best regards, > Matthieu > > 2016-09-30 23:05 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: > > Yes > > > On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote: > > > > Hi Douglas, > > > > Does the surface of the closest MRI time point mean the surface > of the > > -long subject time point directory rather than cross-sectional > subject > > time point directory ? > > > > Best regards, > > Matthieu > > > > > > Le 30 sept. 2016 9:14 PM, "Douglas N Greve" > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> a écrit : > > > > There is no such long process for PET. The idea is that you > > process the > > MRI in a longitudinal way, then sample the PET data onto the > > surface of > > the closest MRI time point. Then proceed in a way similar to the > > thickness analysis > > > > > > On 09/29/2016 11:08 AM, Matthieu Vanhoutte wrote: > > > Dear Freesurfer's experts, > > > > > > Could you answer me about my last question with no > response in the > > > mail below ? > > > > > > When using cortical thickness in longitudinal analysis > with LME, we > > > used lh.thickness or rh.thickness from -long subject > directories. > > > These data followed particular processing steps including > > > registrations in order to use them with more precision in > > longitudinal > > > studies, didn't they ? > > > > > > My problem is that I would like to perform longitudinal > study on PET > > > data images with LME. So I wonder if I just have to > resample onto > > > -long cortical subject surface ? Do I need to follow the > same steps > > > than cortical thickness from cross-sectional to -long subject > > > directories ? If this is the case, which commands should I > use to > > > mimic cortical thickness longitudinal data ? > > > > > > Many thanks in advance for helping ! > > > > > > Best regards, > > > Matthieu > > > > > > 2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte > > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>>>: > > > > > > Hi Martin, > > > > > > Thanks for your answer. However, it seems to me that > cortical > > > thickness follow a particular process with the > recon-all -long > > > process, isn’t it ? Is there any resample onto average > time > > > subject then other operation following ? > > > > > > Best regards, > > > Matthieu > > > > > > > Le 18 sept. 2016 à 16:26, Martin Reuter > > > <mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>>>> > > > a écrit : > > > > > > > > Hi Matthieu, > > > > > > > > I never used PET data, but once you manage to > resample you pet > > > data onto the surface, you will have a file similar to the > > > thickness file for each subjects. Instead of thickness > it holds > > > you PET information. From that point on everything > should be > > > identical to the thickness analysis. > > > > > > > > So this is really more a question how to get your > PET data > > > sampled onto the surface. If no one else replies, > write that > > into > > > the subject line and repost. > > > > > > > > Best, Martin > > > > > > > > > > > >> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte > > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>>> > > > wrote: > > > >> > > > >> Dear Freesurfer’s experts, > > > >> > > > >> I would like to use the longitudinal mixed-effects > model for > > > surface PET analysis. Although I could find all the > process to > > > follow the longitudinal analysis of cortical thickness, I > > couldn’t > > > resolve the steps/commands to apply successively to > coregistered > > > PET data on T1 MRI. > > > >> > > > >> Could you precise me the process and commands to > use for PET > > > longitudinal analysis ? > > > >> > > > >> Many thanks in advance ! > > > >> > > > >> Best regards, > > > >> Matthieu > > > >> _______________________________________________ > > > >> Freesurfer mailing list > > > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > >> > > > >> > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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. 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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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11:49 a.m.
New subject: Longitudinal surface analysis of PET data
Thank you !
Best regards, Matthieu
2016-11-14 17:48 GMT+01:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Rigid.
On 11/14/2016 11:43 AM, Matthieu Vanhoutte wrote:
Still using rigid-body registration on --long subject directory ?
Or is affine registration in this case needed ?
Best regards, Matthieu
2016-11-14 17:12 GMT+01:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
I would just register the pet to the closest (in time) anatomical On 11/14/2016 07:20 AM, Matthieu Vanhoutte wrote: > Dear Freesurfer's experts, > > I come back to you concerning questions of registrations. > > Since during the longitudinal process each --long subject directory > has been registered onto the common --base template, shouldn't I: > > 1) Register PET data onto the subject cross-sectional directory > (native data) with rigid-body transformation > 2) Then take into account the registration between --cross and --long > directory subject and apply the registration to the PET first > registered onto native space ? In this case, how and where is this > transformation has been saved ? > > Best regards, > Matthieu > > 2016-09-30 23:05 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: > > Yes > > > On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote: > > > > Hi Douglas, > > > > Does the surface of the closest MRI time point mean the surface > of the > > -long subject time point directory rather thancross-sectional
> subject > > time point directory ? > > > > Best regards, > > Matthieu > > > > > > Le 30 sept. 2016 9:14 PM, "Douglas N Greve" > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> a écrit : > > > > There is no such long process for PET. The idea is that you > > process the > > MRI in a longitudinal way, then sample the PET data onto the > > surface of > > the closest MRI time point. Then proceed in a way similar to the > > thickness analysis > > > > > > On 09/29/2016 11:08 AM, Matthieu Vanhoutte wrote: > > > Dear Freesurfer's experts, > > > > > > Could you answer me about my last question with no > response in the > > > mail below ? > > > > > > When using cortical thickness in longitudinal analysis > with LME, we > > > used lh.thickness or rh.thickness from -long subject > directories. > > > These data followed particular processing steps including > > > registrations in order to use them with more precision in > > longitudinal > > > studies, didn't they ? > > > > > > My problem is that I would like to perform longitudinal > study on PET > > > data images with LME. So I wonder if I just have to > resample onto > > > -long cortical subject surface ? Do I need to followthe
> same steps > > > than cortical thickness from cross-sectional to -long subject > > > directories ? If this is the case, which commands should I > use to > > > mimic cortical thickness longitudinal data ? > > > > > > Many thanks in advance for helping ! > > > > > > Best regards, > > > Matthieu > > > > > > 2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte > > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>>>: > > > > > > Hi Martin, > > > > > > Thanks for your answer. However, it seems to methat
> cortical > > > thickness follow a particular process with the > recon-all -long > > > process, isn’t it ? Is there any resample onto average > time > > > subject then other operation following ? > > > > > > Best regards, > > > Matthieu > > > > > > > Le 18 sept. 2016 à 16:26, Martin Reuter > > > <mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>>>> > > > a écrit : > > > > > > > > Hi Matthieu, > > > > > > > > I never used PET data, but once you manage to > resample you pet > > > data onto the surface, you will have a file similar to the > > > thickness file for each subjects. Instead of thickness > it holds > > > you PET information. From that point on everything > should be > > > identical to the thickness analysis. > > > > > > > > So this is really more a question how to get your > PET data > > > sampled onto the surface. If no one else replies, > write that > > into > > > the subject line and repost. > > > > > > > > Best, Martin > > > > > > > > > > > >> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte > > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>>> > > > wrote: > > > >> > > > >> Dear Freesurfer’s experts, > > > >> > > > >> I would like to use the longitudinal mixed-effects > model for > > > surface PET analysis. Although I could find all the > process to > > > follow the longitudinal analysis of cortical thickness, I > > couldn’t > > > resolve the steps/commands to apply successively to > coregistered > > > PET data on T1 MRI. > > > >> > > > >> Could you precise me the process and commands to > use for PET > > > longitudinal analysis ? > > > >> > > > >> Many thanks in advance ! > > > >> > > > >> Best regards, > > > >> Matthieu > > > >> _______________________________________________ > > > >> Freesurfer mailing list > > > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > >> > > > >> > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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. 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18 Nov
18 Nov
5:18 a.m.
New subject: Longitudinal surface analysis of PET data
Hi Matthieu,
to clarify, you can directly register to the long time point.
If, for some reason, the pet and MR (cross) are already very close in space, it may make sense to first register to that, then concatenate that transform with the one from cross to long and then map the PET there. Don’t map it twice, instead concatenate the transforms. mri_concatenate_lta will do that.
You find the transforms from base to each time point in the long mri/transforms directory and probably also in the base/mri/transforms dir.
Best, Martin
On Nov 14, 2016, at 5:49 PM, Matthieu Vanhoutte matthieuvanhoutte@gmail.com wrote:
Thank you !
Best regards, Matthieu
2016-11-14 17:48 GMT+01:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>: Rigid.
On 11/14/2016 11:43 AM, Matthieu Vanhoutte wrote:
Still using rigid-body registration on --long subject directory ?
Or is affine registration in this case needed ?
Best regards, Matthieu
2016-11-14 17:12 GMT+01:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>:
I would just register the pet to the closest (in time) anatomical On 11/14/2016 07:20 AM, Matthieu Vanhoutte wrote: > Dear Freesurfer's experts, > > I come back to you concerning questions of registrations. > > Since during the longitudinal process each --long subject directory > has been registered onto the common --base template, shouldn't I: > > 1) Register PET data onto the subject cross-sectional directory > (native data) with rigid-body transformation > 2) Then take into account the registration between --cross and --long > directory subject and apply the registration to the PET first > registered onto native space ? In this case, how and where is this > transformation has been saved ? > > Best regards, > Matthieu > > 2016-09-30 23:05 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>: > > Yes > > > On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote: > > > > Hi Douglas, > > > > Does the surface of the closest MRI time point mean the surface > of the > > -long subject time point directory rather than cross-sectional > subject > > time point directory ? > > > > Best regards, > > Matthieu > > > > > > Le 30 sept. 2016 9:14 PM, "Douglas N Greve" > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> a écrit : > > > > There is no such long process for PET. The idea is that you > > process the > > MRI in a longitudinal way, then sample the PET data onto the > > surface of > > the closest MRI time point. Then proceed in a way similar to the > > thickness analysis > > > > > > On 09/29/2016 11:08 AM, Matthieu Vanhoutte wrote: > > > Dear Freesurfer's experts, > > > > > > Could you answer me about my last question with no > response in the > > > mail below ? > > > > > > When using cortical thickness in longitudinal analysis > with LME, we > > > used lh.thickness or rh.thickness from -long subject > directories. > > > These data followed particular processing steps including > > > registrations in order to use them with more precision in > > longitudinal > > > studies, didn't they ? > > > > > > My problem is that I would like to perform longitudinal > study on PET > > > data images with LME. So I wonder if I just have to > resample onto > > > -long cortical subject surface ? Do I need to follow the > same steps > > > than cortical thickness from cross-sectional to -long subject > > > directories ? If this is the case, which commands should I > use to > > > mimic cortical thickness longitudinal data ? > > > > > > Many thanks in advance for helping ! > > > > > > Best regards, > > > Matthieu > > > > > > 2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte > > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>>>>: > > > > > > Hi Martin, > > > > > > Thanks for your answer. However, it seems to me that > cortical > > > thickness follow a particular process with the > recon-all -long > > > process, isn’t it ? Is there any resample onto average > time > > > subject then other operation following ? > > > > > > Best regards, > > > Matthieu > > > > > > > Le 18 sept. 2016 à 16:26, Martin Reuter > > > <mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>>>>> > > > a écrit : > > > > > > > > Hi Matthieu, > > > > > > > > I never used PET data, but once you manage to > resample you pet > > > data onto the surface, you will have a file similar to the > > > thickness file for each subjects. Instead of thickness > it holds > > > you PET information. From that point on everything > should be > > > identical to the thickness analysis. > > > > > > > > So this is really more a question how to get your > PET data > > > sampled onto the surface. If no one else replies, > write that > > into > > > the subject line and repost. > > > > > > > > Best, Martin > > > > > > > > > > > >> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte > > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>>>> > > > wrote: > > > >> > > > >> Dear Freesurfer’s experts, > > > >> > > > >> I would like to use the longitudinal mixed-effects > model for > > > surface PET analysis. Although I could find all the > process to > > > follow the longitudinal analysis of cortical thickness, I > > couldn’t > > > resolve the steps/commands to apply successively to > coregistered > > > PET data on T1 MRI. > > > >> > > > >> Could you precise me the process and commands to > use for PET > > > longitudinal analysis ? > > > >> > > > >> Many thanks in advance ! > > > >> > > > >> Best regards, > > > >> Matthieu > > > >> _______________________________________________ > > > >> Freesurfer mailing list > > > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > 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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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > > -- > > Douglas N. 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>>> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>>> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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5:27 a.m.
New subject: Longitudinal surface analysis of PET data
Hi Martin,
Thank you for clarifications !
1) What do you mean by "If, for some reason, the pet and MR (cross) are already very close in space" ?
2) How could it be possible to directly register to the long time point ? Since I use a rigid registration, the long time point T1 will not have been deformed (affine or non linear) ?
Best regards, Matthieu
2016-11-18 11:18 GMT+01:00 Martin Reuter mreuter@nmr.mgh.harvard.edu:
Hi Matthieu,
to clarify, you can directly register to the long time point.
If, for some reason, the pet and MR (cross) are already very close in space, it may make sense to first register to that, then concatenate that transform with the one from cross to long and then map the PET there. Don’t map it twice, instead concatenate the transforms. mri_concatenate_lta will do that.
You find the transforms from base to each time point in the long mri/transforms directory and probably also in the base/mri/transforms dir.
Best, Martin
On Nov 14, 2016, at 5:49 PM, Matthieu Vanhoutte < matthieuvanhoutte@gmail.com> wrote:
Thank you !
Best regards, Matthieu
2016-11-14 17:48 GMT+01:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Rigid.
On 11/14/2016 11:43 AM, Matthieu Vanhoutte wrote:
Still using rigid-body registration on --long subject directory ?
Or is affine registration in this case needed ?
Best regards, Matthieu
2016-11-14 17:12 GMT+01:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
I would just register the pet to the closest (in time) anatomical On 11/14/2016 07:20 AM, Matthieu Vanhoutte wrote: > Dear Freesurfer's experts, > > I come back to you concerning questions of registrations. > > Since during the longitudinal process each --long subjectdirectory
> has been registered onto the common --base template, shouldn't I: > > 1) Register PET data onto the subject cross-sectional directory > (native data) with rigid-body transformation > 2) Then take into account the registration between --cross and --long > directory subject and apply the registration to the PET first > registered onto native space ? In this case, how and where is this > transformation has been saved ? > > Best regards, > Matthieu > > 2016-09-30 23:05 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: > > Yes > > > On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote: > > > > Hi Douglas, > > > > Does the surface of the closest MRI time point mean the surface > of the > > -long subject time point directory rather thancross-sectional
> subject > > time point directory ? > > > > Best regards, > > Matthieu > > > > > > Le 30 sept. 2016 9:14 PM, "Douglas N Greve" > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> a écrit : > > > > There is no such long process for PET. The idea is that you > > process the > > MRI in a longitudinal way, then sample the PET data onto the > > surface of > > the closest MRI time point. Then proceed in a way similar to the > > thickness analysis > > > > > > On 09/29/2016 11:08 AM, Matthieu Vanhoutte wrote: > > > Dear Freesurfer's experts, > > > > > > Could you answer me about my last question with no > response in the > > > mail below ? > > > > > > When using cortical thickness in longitudinal analysis > with LME, we > > > used lh.thickness or rh.thickness from -long subject > directories. > > > These data followed particular processing steps including > > > registrations in order to use them with more precision in > > longitudinal > > > studies, didn't they ? > > > > > > My problem is that I would like to performlongitudinal
> study on PET > > > data images with LME. So I wonder if I just have to > resample onto > > > -long cortical subject surface ? Do I need to followthe
> same steps > > > than cortical thickness from cross-sectional to -long subject > > > directories ? If this is the case, which commands should I > use to > > > mimic cortical thickness longitudinal data ? > > > > > > Many thanks in advance for helping ! > > > > > > Best regards, > > > Matthieu > > > > > > 2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte > > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>>>: > > > > > > Hi Martin, > > > > > > Thanks for your answer. However, it seems to methat
> cortical > > > thickness follow a particular process with the > recon-all -long > > > process, isn’t it ? Is there any resample onto average > time > > > subject then other operation following ? > > > > > > Best regards, > > > Matthieu > > > > > > > Le 18 sept. 2016 à 16:26, Martin Reuter > > > <mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>>>> > > > a écrit : > > > > > > > > Hi Matthieu, > > > > > > > > I never used PET data, but once you manage to > resample you pet > > > data onto the surface, you will have a file similar to the > > > thickness file for each subjects. Instead of thickness > it holds > > > you PET information. From that point on everything > should be > > > identical to the thickness analysis. > > > > > > > > So this is really more a question how to getyour
> PET data > > > sampled onto the surface. If no one else replies, > write that > > into > > > the subject line and repost. > > > > > > > > Best, Martin > > > > > > > > > > > >> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte > > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>>> > > > wrote: > > > >> > > > >> Dear Freesurfer’s experts, > > > >> > > > >> I would like to use the longitudinal mixed-effects > model for > > > surface PET analysis. Although I could find allthe
> process to > > > follow the longitudinal analysis of cortical thickness, I > > couldn’t > > > resolve the steps/commands to apply successivelyto
> coregistered > > > PET data on T1 MRI. > > > >> > > > >> Could you precise me the process and commandsto
> use for PET > > > longitudinal analysis ? > > > >> > > > >> Many thanks in advance ! > > > >> > > > >> Best regards, > > > >> Matthieu > > > >> ______________________________
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3:33 p.m.
New subject: Longitudinal surface analysis of PET data
Hi Mathieu,
1. if you happen to have a PET/MR scanner, I would assume that coordinates between PET and MRI are pre-aligned, so the difference is only small motion. In that case a registration (to remove the small motion) between PET and the MRI first is optimal. In that case I would make use of that and register first to the cross sectional data, then concatenate with the transform to the longitudinal for analysis.
2. you would just use the data from the long directory as the target for the registration (instead of the one from the cross directory), because that’s the registration you will need at the end. And you are right, the long time point T1 will not be deformed, only rigidly transformed to the base space.
Best, Martin
On Nov 18, 2016, at 11:27 AM, Matthieu Vanhoutte matthieuvanhoutte@gmail.com wrote:
Hi Martin,
Thank you for clarifications !
What do you mean by "If, for some reason, the pet and MR (cross) are already very close in space" ?
How could it be possible to directly register to the long time point ? Since I use a rigid registration, the long time point T1 will not have been deformed (affine or non linear) ?
Best regards, Matthieu
2016-11-18 11:18 GMT+01:00 Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu>: Hi Matthieu,
to clarify, you can directly register to the long time point.
If, for some reason, the pet and MR (cross) are already very close in space, it may make sense to first register to that, then concatenate that transform with the one from cross to long and then map the PET there. Don’t map it twice, instead concatenate the transforms. mri_concatenate_lta will do that.
You find the transforms from base to each time point in the long mri/transforms directory and probably also in the base/mri/transforms dir.
Best, Martin
On Nov 14, 2016, at 5:49 PM, Matthieu Vanhoutte <matthieuvanhoutte@gmail.com mailto:matthieuvanhoutte@gmail.com> wrote:
Thank you !
Best regards, Matthieu
2016-11-14 17:48 GMT+01:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>: Rigid.
On 11/14/2016 11:43 AM, Matthieu Vanhoutte wrote:
Still using rigid-body registration on --long subject directory ?
Or is affine registration in this case needed ?
Best regards, Matthieu
2016-11-14 17:12 GMT+01:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>:
I would just register the pet to the closest (in time) anatomical On 11/14/2016 07:20 AM, Matthieu Vanhoutte wrote: > Dear Freesurfer's experts, > > I come back to you concerning questions of registrations. > > Since during the longitudinal process each --long subject directory > has been registered onto the common --base template, shouldn't I: > > 1) Register PET data onto the subject cross-sectional directory > (native data) with rigid-body transformation > 2) Then take into account the registration between --cross and --long > directory subject and apply the registration to the PET first > registered onto native space ? In this case, how and where is this > transformation has been saved ? > > Best regards, > Matthieu > > 2016-09-30 23:05 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>: > > Yes > > > On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote: > > > > Hi Douglas, > > > > Does the surface of the closest MRI time point mean the surface > of the > > -long subject time point directory rather than cross-sectional > subject > > time point directory ? > > > > Best regards, > > Matthieu > > > > > > Le 30 sept. 2016 9:14 PM, "Douglas N Greve" > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> a écrit : > > > > There is no such long process for PET. The idea is that you > > process the > > MRI in a longitudinal way, then sample the PET data onto the > > surface of > > the closest MRI time point. Then proceed in a way similar to the > > thickness analysis > > > > > > On 09/29/2016 11:08 AM, Matthieu Vanhoutte wrote: > > > Dear Freesurfer's experts, > > > > > > Could you answer me about my last question with no > response in the > > > mail below ? > > > > > > When using cortical thickness in longitudinal analysis > with LME, we > > > used lh.thickness or rh.thickness from -long subject > directories. > > > These data followed particular processing steps including > > > registrations in order to use them with more precision in > > longitudinal > > > studies, didn't they ? > > > > > > My problem is that I would like to perform longitudinal > study on PET > > > data images with LME. So I wonder if I just have to > resample onto > > > -long cortical subject surface ? Do I need to follow the > same steps > > > than cortical thickness from cross-sectional to -long subject > > > directories ? If this is the case, which commands should I > use to > > > mimic cortical thickness longitudinal data ? > > > > > > Many thanks in advance for helping ! > > > > > > Best regards, > > > Matthieu > > > > > > 2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte > > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>>>>: > > > > > > Hi Martin, > > > > > > Thanks for your answer. However, it seems to me that > cortical > > > thickness follow a particular process with the > recon-all -long > > > process, isn’t it ? Is there any resample onto average > time > > > subject then other operation following ? > > > > > > Best regards, > > > Matthieu > > > > > > > Le 18 sept. 2016 à 16:26, Martin Reuter > > > <mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>>>>> > > > a écrit : > > > > > > > > Hi Matthieu, > > > > > > > > I never used PET data, but once you manage to > resample you pet > > > data onto the surface, you will have a file similar to the > > > thickness file for each subjects. Instead of thickness > it holds > > > you PET information. From that point on everything > should be > > > identical to the thickness analysis. > > > > > > > > So this is really more a question how to get your > PET data > > > sampled onto the surface. If no one else replies, > write that > > into > > > the subject line and repost. > > > > > > > > Best, Martin > > > > > > > > > > > >> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte > > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>>>> > > > wrote: > > > >> > > > >> Dear Freesurfer’s experts, > > > >> > > > >> I would like to use the longitudinal mixed-effects > model for > > > surface PET analysis. Although I could find all the > process to > > > follow the longitudinal analysis of cortical thickness, I > > couldn’t > > > resolve the steps/commands to apply successively to > coregistered > > > PET data on T1 MRI. > > > >> > > > >> Could you precise me the process and commands to > use for PET > > > longitudinal analysis ? > > > >> > > > >> Many thanks in advance ! > > > >> > > > >> Best regards, > > > >> Matthieu > > > >> _______________________________________________ > > > >> Freesurfer mailing list > > > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > 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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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>>> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>>> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>>> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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<mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422
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19 Nov
19 Nov
7:16 a.m.
New subject: Longitudinal surface analysis of PET data
Hi Martin,
Thank you for these detailed explanations.
Best, Matthieu
Le 18 nov. 2016 à 21:33, Martin Reuter mreuter@nmr.mgh.harvard.edu a écrit :
Hi Mathieu,
if you happen to have a PET/MR scanner, I would assume that coordinates between PET and MRI are pre-aligned, so the difference is only small motion. In that case a registration (to remove the small motion) between PET and the MRI first is optimal. In that case I would make use of that and register first to the cross sectional data, then concatenate with the transform to the longitudinal for analysis.
you would just use the data from the long directory as the target for the registration (instead of the one from the cross directory), because that’s the registration you will need at the end. And you are right, the long time point T1 will not be deformed, only rigidly transformed to the base space.
Best, Martin
On Nov 18, 2016, at 11:27 AM, Matthieu Vanhoutte <matthieuvanhoutte@gmail.com mailto:matthieuvanhoutte@gmail.com> wrote:
Hi Martin,
Thank you for clarifications !
What do you mean by "If, for some reason, the pet and MR (cross) are already very close in space" ?
How could it be possible to directly register to the long time point ? Since I use a rigid registration, the long time point T1 will not have been deformed (affine or non linear) ?
Best regards, Matthieu
2016-11-18 11:18 GMT+01:00 Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu>: Hi Matthieu,
to clarify, you can directly register to the long time point.
If, for some reason, the pet and MR (cross) are already very close in space, it may make sense to first register to that, then concatenate that transform with the one from cross to long and then map the PET there. Don’t map it twice, instead concatenate the transforms. mri_concatenate_lta will do that.
You find the transforms from base to each time point in the long mri/transforms directory and probably also in the base/mri/transforms dir.
Best, Martin
On Nov 14, 2016, at 5:49 PM, Matthieu Vanhoutte <matthieuvanhoutte@gmail.com mailto:matthieuvanhoutte@gmail.com> wrote:
Thank you !
Best regards, Matthieu
2016-11-14 17:48 GMT+01:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>: Rigid.
On 11/14/2016 11:43 AM, Matthieu Vanhoutte wrote:
Still using rigid-body registration on --long subject directory ?
Or is affine registration in this case needed ?
Best regards, Matthieu
2016-11-14 17:12 GMT+01:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>:
I would just register the pet to the closest (in time) anatomical On 11/14/2016 07:20 AM, Matthieu Vanhoutte wrote: > Dear Freesurfer's experts, > > I come back to you concerning questions of registrations. > > Since during the longitudinal process each --long subject directory > has been registered onto the common --base template, shouldn't I: > > 1) Register PET data onto the subject cross-sectional directory > (native data) with rigid-body transformation > 2) Then take into account the registration between --cross and --long > directory subject and apply the registration to the PET first > registered onto native space ? In this case, how and where is this > transformation has been saved ? > > Best regards, > Matthieu > > 2016-09-30 23:05 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>: > > Yes > > > On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote: > > > > Hi Douglas, > > > > Does the surface of the closest MRI time point mean the surface > of the > > -long subject time point directory rather than cross-sectional > subject > > time point directory ? > > > > Best regards, > > Matthieu > > > > > > Le 30 sept. 2016 9:14 PM, "Douglas N Greve" > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> a écrit : > > > > There is no such long process for PET. The idea is that you > > process the > > MRI in a longitudinal way, then sample the PET data onto the > > surface of > > the closest MRI time point. Then proceed in a way similar to the > > thickness analysis > > > > > > On 09/29/2016 11:08 AM, Matthieu Vanhoutte wrote: > > > Dear Freesurfer's experts, > > > > > > Could you answer me about my last question with no > response in the > > > mail below ? > > > > > > When using cortical thickness in longitudinal analysis > with LME, we > > > used lh.thickness or rh.thickness from -long subject > directories. > > > These data followed particular processing steps including > > > registrations in order to use them with more precision in > > longitudinal > > > studies, didn't they ? > > > > > > My problem is that I would like to perform longitudinal > study on PET > > > data images with LME. So I wonder if I just have to > resample onto > > > -long cortical subject surface ? Do I need to follow the > same steps > > > than cortical thickness from cross-sectional to -long subject > > > directories ? If this is the case, which commands should I > use to > > > mimic cortical thickness longitudinal data ? > > > > > > Many thanks in advance for helping ! > > > > > > Best regards, > > > Matthieu > > > > > > 2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte > > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>>>>: > > > > > > Hi Martin, > > > > > > Thanks for your answer. However, it seems to me that > cortical > > > thickness follow a particular process with the > recon-all -long > > > process, isn’t it ? Is there any resample onto average > time > > > subject then other operation following ? > > > > > > Best regards, > > > Matthieu > > > > > > > Le 18 sept. 2016 à 16:26, Martin Reuter > > > <mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>> > > <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> <mailto:mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>>>>>> > > > a écrit : > > > > > > > > Hi Matthieu, > > > > > > > > I never used PET data, but once you manage to > resample you pet > > > data onto the surface, you will have a file similar to the > > > thickness file for each subjects. Instead of thickness > it holds > > > you PET information. From that point on everything > should be > > > identical to the thickness analysis. > > > > > > > > So this is really more a question how to get your > PET data > > > sampled onto the surface. If no one else replies, > write that > > into > > > the subject line and repost. > > > > > > > > Best, Martin > > > > > > > > > > > >> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte > > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> > > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>>>> > > > wrote: > > > >> > > > >> Dear Freesurfer’s experts, > > > >> > > > >> I would like to use the longitudinal mixed-effects > model for > > > surface PET analysis. Although I could find all the > process to > > > follow the longitudinal analysis of cortical thickness, I > > couldn’t > > > resolve the steps/commands to apply successively to > coregistered > > > PET data on T1 MRI. > > > >> > > > >> Could you precise me the process and commands to > use for PET > > > longitudinal analysis ? > > > >> > > > >> Many thanks in advance ! > > > >> > > > >> Best regards, > > > >> Matthieu > > > >> _______________________________________________ > > > >> Freesurfer mailing list > > > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > 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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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>>> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>>> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>>> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
3482
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freesurfer@nmr.mgh.harvard.edu
8 comments
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participants (3)
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Douglas N Greve -
Martin Reuter -
Matthieu Vanhoutte