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
> > > > >> _______________________________________________
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> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
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> > --
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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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