Re: [Freesurfer] Longitudinal surface analysis of PET data

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 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>>>
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<mailto:matthieuvanhoutte@gmail.com>
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<mailto:matthieuvanhoutte@gmail.com>>
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<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
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<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>>
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<mailto:matthieuvanhoutte@gmail.com>
>     <mailto:matthieuvanhoutte@gmail.com
<mailto:matthieuvanhoutte@gmail.com>>>
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<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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>     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
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<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
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> 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
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 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