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 <gr...@nmr.mgh.harvard.edu 
> <mailto:gr...@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
>     <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>     > <mailto:gr...@nmr.mgh.harvard.edu
>     <mailto:gr...@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"
>     >     <gr...@nmr.mgh.harvard.edu
>     <mailto:gr...@nmr.mgh.harvard.edu>
>     <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
>     >     > <mailto:gr...@nmr.mgh.harvard.edu
>     <mailto:gr...@nmr.mgh.harvard.edu>
>     >     <mailto:gr...@nmr.mgh.harvard.edu
>     <mailto:gr...@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
>     >     >     > <matthieuvanhou...@gmail.com
>     <mailto:matthieuvanhou...@gmail.com>
>     >     <mailto:matthieuvanhou...@gmail.com
>     <mailto:matthieuvanhou...@gmail.com>>
>     >     >     <mailto:matthieuvanhou...@gmail.com
>     <mailto:matthieuvanhou...@gmail.com>
>     >     <mailto:matthieuvanhou...@gmail.com
>     <mailto:matthieuvanhou...@gmail.com>>>
>     >     >     <mailto:matthieuvanhou...@gmail.com
>     <mailto:matthieuvanhou...@gmail.com>
>     >     <mailto:matthieuvanhou...@gmail.com
>     <mailto:matthieuvanhou...@gmail.com>>
>     >     >     <mailto:matthieuvanhou...@gmail.com
>     <mailto:matthieuvanhou...@gmail.com>
>     <mailto:matthieuvanhou...@gmail.com
>     <mailto:matthieuvanhou...@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
>     >     >     >     <mreu...@nmr.mgh.harvard.edu
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>     <mailto:mreu...@nmr.mgh.harvard.edu>>>
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>     >     >     >     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
>     >     >     >     <matthieuvanhou...@gmail.com
>     <mailto:matthieuvanhou...@gmail.com>
>     >     <mailto:matthieuvanhou...@gmail.com
>     <mailto:matthieuvanhou...@gmail.com>>
>     >     >     <mailto:matthieuvanhou...@gmail.com
>     <mailto:matthieuvanhou...@gmail.com>
>     >     <mailto:matthieuvanhou...@gmail.com
>     <mailto:matthieuvanhou...@gmail.com>>>
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>     <mailto:matthieuvanhou...@gmail.com>
>     >     <mailto:matthieuvanhou...@gmail.com
>     <mailto:matthieuvanhou...@gmail.com>>
>     >     >     <mailto:matthieuvanhou...@gmail.com
>     <mailto:matthieuvanhou...@gmail.com>
>     <mailto:matthieuvanhou...@gmail.com
>     <mailto:matthieuvanhou...@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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>     <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
>     > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>     <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@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
>     gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>     Phone Number: 617-724-2358
>     Fax: 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

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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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