Re: [Freesurfer] Longitudinal surface analysis of PET data

2016-11-18 Thread Matthieu Vanhoutte 
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 :

> 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 :
>
>> 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 > > >:
>> >
>> > 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
>> > 
>> > > > > >>:
>> > >
>> > > 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"
>> > > > > 
>> > > >>
>> > > > > > 
>> > > > > > > > >
>> > > > 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
>>

Re: [Freesurfer] Longitudinal surface analysis of PET data

2016-11-18 Thread Martin Reuter 
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  
> wrote:
> 
> Thank you !
> 
> Best regards,
> Matthieu
> 
> 2016-11-14 17:48 GMT+01:00 Douglas N Greve  >:
> 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  > 
> > >>:
> >
> > 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
> >  
> > >
> > > 
> >  > >
> > > 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"
> > > 
> > >
> >  
> > >>
> > > >  > 
> > >
> > >  > 
> >  >  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

Re: [Freesurfer] Longitudinal surface analysis of PET data

2016-11-14 Thread Matthieu Vanhoutte 
Thank you !

Best regards,
Matthieu

2016-11-14 17:48 GMT+01:00 Douglas N Greve :

> 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  > >:
> >
> > 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
> > 
> > >  > >>:
> > >
> > > 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"
> > >  > 
> >  >>
> > > >  > 
> > >  >  > > >
> > > > 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
> > > > >  > 
> > >  > >
> > > >  > 
> > >  > >>
> > > >

Re: [Freesurfer] Longitudinal surface analysis of PET data

2016-11-14 Thread Douglas N Greve 
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  >:
>
> 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
> 
> >  >>:
> >
> > 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"
> >  
> >
> > >  
> >   > >
> > > 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
> > > >  
> >  >
> > >  
> >  >>
> > >  
> >  >
> > >  
>  :
> > > >
> >

Re: [Freesurfer] Longitudinal surface analysis of PET data

2016-11-14 Thread Matthieu Vanhoutte 
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 :

> 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  > >:
> >
> > 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"
> > 
> > >  > >> 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
> > > >  > 
> > >  > >
> > >  > 
> > >  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
> > > >  > 
> > >  > >
> > >  > 
> > >  harvard.edu
> > > > a écrit :
> > > > >
> > > > > Hi Matthieu,
> > > > >
> > > > > I never used PET data, but once you manage to
> > resample you pet
> > > >

Re: [Freesurfer] Longitudinal surface analysis of PET data

2016-11-14 Thread Douglas N Greve 
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  >:
>
> 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"
> 
> >  >> 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
> > >  
> >  >
> >  
> >   > >
> > > 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
> > >  
> >  >
> >  
> >   > > 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

Re: [Freesurfer] Longitudinal surface analysis of PET data

2016-11-14 Thread Matthieu Vanhoutte 
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 :

> 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"  > > 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
> > >  > 
> >  > >>:
> > >
> > > 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
> > >  > 
> >  > >>
> > > 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
> > >  > 
> >  > >>
> > > 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

Re: [Freesurfer] Longitudinal surface analysis of PET data

2016-09-30 Thread Douglas N Greve 
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"  > 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
> >  
>  >>:
> >
> > 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
> >  
>  >>
> > 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
> >  
>  >>
> > 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
> > >> ___
> > >> 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
>

Re: [Freesurfer] Longitudinal surface analysis of PET data

2016-09-30 Thread Matthieu Vanhoutte 
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"  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
> > >:
> >
> > 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
> > >
> > 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
> > >
> > 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
> > >> ___
> > >> 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 error
> > > but does not contain patient information, please contact the
> > sender and properly
> > > dispose of the e-mail.
> >
> >
> >
> >
> > ___
> > 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
>

Re: [Freesurfer] Longitudinal surface analysis of PET data

2016-09-30 Thread Douglas N Greve 
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 
> >:
>
> 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
> >
> 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
> >
> 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
> >> ___
> >> 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 error
> > but does not contain patient information, please contact the
> sender and properly
> > dispose of the e-mail.
>
>
>
>
> ___
> 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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Re: [Freesurfer] Longitudinal surface analysis of PET data

2016-09-29 Thread Matthieu Vanhoutte 
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 :

> 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  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> 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
> >> ___
> >> 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 error
> > but does not contain patient information, please contact the sender and
> properly
> > dispose of the e-mail.
>
>
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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 error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Longitudinal surface analysis of PET data

2016-09-18 Thread Matthieu Vanhoutte 
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  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 
>>  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
>> ___
>> 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 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.


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Re: [Freesurfer] Longitudinal surface analysis of PET data

2016-09-18 Thread Martin Reuter 
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  
> 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
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 


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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 error
but does not contain patient information, please contact the sender and properly
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