18 Nov
2016
18 Nov
'16
5:27 a.m.
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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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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