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 <mreu...@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 <
> matthieuvanhou...@gmail.com> wrote:
>
> Thank you !
>
> Best regards,
> Matthieu
>
> 2016-11-14 17:48 GMT+01:00 Douglas N Greve <gr...@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 <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
>> >     <mailto:mreu...@nmr.mgh.harvard.edu>
>> >     >     <mailto:mreu...@nmr.mgh.harvard.edu
>> >     <mailto:mreu...@nmr.mgh.harvard.edu>>
>> >     >     >     <mailto:mreu...@nmr.mgh.harvard.edu
>> >     <mailto:mreu...@nmr.mgh.harvard.edu>
>> >     >     <mailto:mreu...@nmr.mgh.harvard.edu
>> >     <mailto:mreu...@nmr.mgh.harvard.edu>>>
>> >     >     >     <mailto:mreu...@nmr.mgh.harvard.edu
>> >     <mailto:mreu...@nmr.mgh.harvard.edu>
>> >     >     <mailto:mreu...@nmr.mgh.harvard.edu
>> >     <mailto:mreu...@nmr.mgh.harvard.edu>>
>> >     >     >     <mailto:mreu...@nmr.mgh.harvard.edu
>> >     <mailto:mreu...@nmr.mgh.harvard.edu>
>> >     <mailto:mreu...@nmr.mgh.harvard.edu
>> >     <mailto:mreu...@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
>> >     >     >     >     <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>>>>>
>> >     >     >     >     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
>> >     >     > gr...@nmr.mgh.harvard.edu
>> >     <mailto:gr...@nmr.mgh.harvard.edu>
>> >     <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu
>> >>
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>> >     <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:
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>> >     <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
>> >     <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>>
>> >     >     >
>> >      <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
>> >     <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/>>
>> >     >     >
>> >      <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>>
>> >     >     <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>>
>> >     >     >
>> >     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:freesur...@nmr.mgh.har
>> vard.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/
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 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
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 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. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
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