14 Nov
2016
14 Nov
'16
11:12 a.m.
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. 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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/