Re: [Freesurfer] Pial surface with point-to-point correspondance between subjects

[Alexandre Routier]

Okay, thanks for the answer, I'll have a look on this software.

Alexandre

2014-10-29 16:05 GMT+01:00 Bruce Fischl :

> no, but I think SUMA does. Check it out. I'll cc Ziad so he can chime in.
>
> cheers
> Bruce
> On
> Wed, 29 Oct 2014, Douglas N Greve wrote:
>
> > This is not something we support.
> >
> > On 10/29/2014 10:32 AM, Alexandre Routier wrote:
> >> What I wanted to say is that there is the exact number of points of
> >> the pial surface for each subject and if I look to the i-th vertex of
> >> the pial surface of a given subject, it should be located on the same
> >> area for another subject.
> >>
> >> Alexandre
> >>
> >> 2014-10-29 15:25 GMT+01:00 Douglas N Greve  >> >:
> >>
> >>
> >> I'm not sure what you mean by working with the pial surfaces with
> >> respect to point-to-point correspondence. Can you give more info?
> >> doug
> >>
> >> On 10/29/2014 06:29 AM, Alexandre Routier wrote:
> >>> Dear all,
> >>>
> >>> I would like to work with the pial surfaces of my database and more
> >>> particularly with a point-to-point correspondance between each
> >>> subject. But I didn't find how to do that, only for longitudinal
> >>> analysis of a single subject which I am not interested.
> >>>
> >>> Thanks in advance for you help,
> >>> Alexandre
> >>>
> >>>
> >>> ___
> >>> 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  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
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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@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
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Re: [Freesurfer] Pial surface with point-to-point correspondance between subjects

[Bruce Fischl]

no, but I think SUMA does. Check it out. I'll cc Ziad so he can chime in.

cheers
Bruce
On 
Wed, 29 Oct 2014, Douglas N Greve wrote:

> This is not something we support.
>
> On 10/29/2014 10:32 AM, Alexandre Routier wrote:
>> What I wanted to say is that there is the exact number of points of
>> the pial surface for each subject and if I look to the i-th vertex of
>> the pial surface of a given subject, it should be located on the same
>> area for another subject.
>>
>> Alexandre
>>
>> 2014-10-29 15:25 GMT+01:00 Douglas N Greve > >:
>>
>>
>> I'm not sure what you mean by working with the pial surfaces with
>> respect to point-to-point correspondence. Can you give more info?
>> doug
>>
>> On 10/29/2014 06:29 AM, Alexandre Routier wrote:
>>> Dear all,
>>>
>>> I would like to work with the pial surfaces of my database and more
>>> particularly with a point-to-point correspondance between each
>>> subject. But I didn't find how to do that, only for longitudinal
>>> analysis of a single subject which I am not interested.
>>>
>>> Thanks in advance for you help,
>>> Alexandre
>>>
>>>
>>> ___
>>> 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
>>
>>
>> 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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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] Pial surface with point-to-point correspondance between subjects

[Bruce Fischl]

you can just compute the jacobian of the ?h.sphere.reg for deformation. I'm 
not sure I understand how you would use an L2 metric. There are tools in 
AFNI/SUMA for converting a freesurfer surface to a standard mesh that you 
could use


cheers
Bruce


On Wed, 29 Oct 2014, Alexandre Routier wrote:


Hello Bruce,

I would like to build an atlas of subcortical structures and pial surface on
my population of study. But given the anatomical complexity of the pial
surface (and the number of points), I would like to use point-to-point
correspondence so as to have a L^2 metric (I use another metric for
subcortical structures).
I don't know if I am clear enough but since I estimate the template and the
variability between the template and the subjects, I would like to detect
information such as atrophy thanks to the deformation parameters.

Is there any solution?

Alexandre


2014-10-29 13:49 GMT+01:00 Bruce Fischl :
  Hi Alexandre

  can you tell us what you want to do with the point-to-point
  correspondence? We don't usually map surfaces into a common
  space since
  we want to have  uniform resolution/sampling in the individual
  coords.

  cheers
  Bruce


  On Wed, 29 Oct 2014, Alexandre Routier wrote:

  > Dear all,
  >
  > I would like to work with the pial surfaces of my database and
  more
  > particularly with a point-to-point correspondance between each
  subject. But
  > I didn't find how to do that, only for longitudinal analysis
  of a single
  > subject which I am not interested.
  >
  > Thanks in advance for you help,
  > Alexandre
  >
  >
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Re: [Freesurfer] Pial surface with point-to-point correspondance between subjects

[Alexandre Routier]

Oh, okay. I thought this kind of data could be obtained since it exists for
longitudinal analysis.

Thanks for your answer anyway!

2014-10-29 15:35 GMT+01:00 Douglas N Greve :

> This is not something we support.
>
> On 10/29/2014 10:32 AM, Alexandre Routier wrote:
> > What I wanted to say is that there is the exact number of points of
> > the pial surface for each subject and if I look to the i-th vertex of
> > the pial surface of a given subject, it should be located on the same
> > area for another subject.
> >
> > Alexandre
> >
> > 2014-10-29 15:25 GMT+01:00 Douglas N Greve  > >:
> >
> >
> > I'm not sure what you mean by working with the pial surfaces with
> > respect to point-to-point correspondence. Can you give more info?
> > doug
> >
> > On 10/29/2014 06:29 AM, Alexandre Routier wrote:
> > > Dear all,
> > >
> > > I would like to work with the pial surfaces of my database and more
> > > particularly with a point-to-point correspondance between each
> > > subject. But I didn't find how to do that, only for longitudinal
> > > analysis of a single subject which I am not interested.
> > >
> > > Thanks in advance for you help,
> > > Alexandre
> > >
> > >
> > > ___
> > > 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  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/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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Re: [Freesurfer] Pial surface with point-to-point correspondance between subjects

[Douglas N Greve]

This is not something we support.

On 10/29/2014 10:32 AM, Alexandre Routier wrote:
> What I wanted to say is that there is the exact number of points of 
> the pial surface for each subject and if I look to the i-th vertex of 
> the pial surface of a given subject, it should be located on the same 
> area for another subject.
>
> Alexandre
>
> 2014-10-29 15:25 GMT+01:00 Douglas N Greve  >:
>
>
> I'm not sure what you mean by working with the pial surfaces with
> respect to point-to-point correspondence. Can you give more info?
> doug
>
> On 10/29/2014 06:29 AM, Alexandre Routier wrote:
> > Dear all,
> >
> > I would like to work with the pial surfaces of my database and more
> > particularly with a point-to-point correspondance between each
> > subject. But I didn't find how to do that, only for longitudinal
> > analysis of a single subject which I am not interested.
> >
> > Thanks in advance for you help,
> > Alexandre
> >
> >
> > ___
> > 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
>
>
> 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] Pial surface with point-to-point correspondance between subjects

[Alexandre Routier]

What I wanted to say is that there is the exact number of points of the
pial surface for each subject and if I look to the i-th vertex of the pial
surface of a given subject, it should be located on the same area for
another subject.

Alexandre

2014-10-29 15:25 GMT+01:00 Douglas N Greve :

>
> I'm not sure what you mean by working with the pial surfaces with
> respect to point-to-point correspondence. Can you give more info?
> doug
>
> On 10/29/2014 06:29 AM, Alexandre Routier wrote:
> > Dear all,
> >
> > I would like to work with the pial surfaces of my database and more
> > particularly with a point-to-point correspondance between each
> > subject. But I didn't find how to do that, only for longitudinal
> > analysis of a single subject which I am not interested.
> >
> > Thanks in advance for you help,
> > Alexandre
> >
> >
> > ___
> > 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
>
>
> 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] Pial surface with point-to-point correspondance between subjects

[Douglas N Greve]

I'm not sure what you mean by working with the pial surfaces with 
respect to point-to-point correspondence. Can you give more info?
doug

On 10/29/2014 06:29 AM, Alexandre Routier wrote:
> Dear all,
>
> I would like to work with the pial surfaces of my database and more 
> particularly with a point-to-point correspondance between each 
> subject. But I didn't find how to do that, only for longitudinal 
> analysis of a single subject which I am not interested.
>
> Thanks in advance for you help,
> Alexandre
>
>
> ___
> 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] Pial surface with point-to-point correspondance between subjects

[Alexandre Routier]

Hello Bruce,

I would like to build an atlas of subcortical structures and pial surface
on my population of study. But given the anatomical complexity of the pial
surface (and the number of points), I would like to use point-to-point
correspondence so as to have a L^2 metric (I use another metric for
subcortical structures).
I don't know if I am clear enough but since I estimate the template and the
variability between the template and the subjects, I would like to detect
information such as atrophy thanks to the deformation parameters.

Is there any solution?

Alexandre


2014-10-29 13:49 GMT+01:00 Bruce Fischl :

> Hi Alexandre
>
> can you tell us what you want to do with the point-to-point
> correspondence? We don't usually map surfaces into a common space since
> we want to have  uniform resolution/sampling in the individual coords.
>
> cheers
> Bruce
>
>
> On Wed, 29 Oct 2014, Alexandre Routier wrote:
>
> > Dear all,
> >
> > I would like to work with the pial surfaces of my database and more
> > particularly with a point-to-point correspondance between each subject.
> But
> > I didn't find how to do that, only for longitudinal analysis of a single
> > subject which I am not interested.
> >
> > Thanks in advance for you help,
> > Alexandre
> >
> >
> ___
> 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] Pial surface with point-to-point correspondance between subjects

[Bruce Fischl]

Hi Alexandre

can you tell us what you want to do with the point-to-point 
correspondence? We don't usually map surfaces into a common space since 
we want to have  uniform resolution/sampling in the individual coords.

cheers
Bruce


On Wed, 29 Oct 2014, Alexandre Routier wrote:

> Dear all,
> 
> I would like to work with the pial surfaces of my database and more
> particularly with a point-to-point correspondance between each subject. But
> I didn't find how to do that, only for longitudinal analysis of a single
> subject which I am not interested.
> 
> Thanks in advance for you help,
> Alexandre
> 
>
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[Freesurfer] Pial surface with point-to-point correspondance between subjects

[Alexandre Routier]

Dear all,

I would like to work with the pial surfaces of my database and more
particularly with a point-to-point correspondance between each subject. But
I didn't find how to do that, only for longitudinal analysis of a single
subject which I am not interested.

Thanks in advance for you help,
Alexandre
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