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
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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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:
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 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> 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
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.
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>:
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>> 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>> 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> >> 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> > > > 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> . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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>:
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>> 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>> 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> >> 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> > > > 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> . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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>>>: > > 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 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>>> > 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>> > >> 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 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>> . 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>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Martin Reuter -
Matthieu Vanhoutte