Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

[Douglas N Greve]

By default they are in talairach. But you can get mni305 by adding 
--nofixmni to the surfcluster command line

On 08/02/2016 03:36 PM, Sabin Khadka wrote:
> Hi Doug, Thanks. Are these coordinates in talairach or MNI space? From 
> previous post you mentioned these are in mni305 space but if I look at 
> the log file it say TalX, TalY, TalZ. I am a little confused.
>
> And how can I convert these coordinates to MNI152 space?
>
> thanks for your help.
>
> Cheers,
> Sabin Khadka
>
> On Mon, Aug 1, 2016 at 9:24 PM, Douglas Greve 
> > wrote:
>
> ps. you can always just load the xyz in the label into matlab and
> compute the centroid
>
>
> On 8/1/16 10:23 AM, Sabin Khadka wrote:
>> Anyone?
>>
>> Cheers,
>> Sabin Khadka
>>
>> On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka
>> > wrote:
>>
>> Hi Doug, I tried to pick up from the thread below to get MNI
>> coordinates of each destrieux parcellation region.
>>
>>
>> 
>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html
>>
>> I created label files from
>> mri_annotation2label --subject fsaverage --hemi lh(/rh)
>> --annotation aparc.a2009s --outdir label_destrieux   # which
>> works fine
>>
>> And I tried to get the coordinates of each labels using
>>
>> mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness
>> --clabel  --sum  --centroid --thmin
>> 0 --hemi lh --subject fsaverage
>>
>> But, all left labels would produce the same coordinates and
>> so does right labels. (I've attached few example files here
>> with). Also, it says TalX, TalY, TalZ are these coordinates
>> in MNI or Talairach?
>>
>> Thanks for help.
>>
>>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

[Douglas Greve]

ps. you can always just load the xyz in the label into matlab and 
compute the centroid



On 8/1/16 10:23 AM, Sabin Khadka wrote:

Anyone?

Cheers,
Sabin Khadka

On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka 
> wrote:


Hi Doug, I tried to pick up from the thread below to get MNI
coordinates of each destrieux parcellation region.


https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html

I created label files from
mri_annotation2label --subject fsaverage --hemi lh(/rh)
--annotation aparc.a2009s --outdir label_destrieux   # which works
fine

And I tried to get the coordinates of each labels using

mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness
--clabel  --sum  --centroid --thmin 0
--hemi lh --subject fsaverage

But, all left labels would produce the same coordinates and so
does right labels. (I've attached few example files here with).
Also, it says TalX, TalY, TalZ are these coordinates in MNI or
Talairach?

Thanks for help.




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Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

[Douglas Greve]

Try setting thmin to something small but non-zero (eg, 10e-6)


On 8/1/16 10:23 AM, Sabin Khadka wrote:

Anyone?

Cheers,
Sabin Khadka

On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka 
> wrote:


Hi Doug, I tried to pick up from the thread below to get MNI
coordinates of each destrieux parcellation region.


https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html

I created label files from
mri_annotation2label --subject fsaverage --hemi lh(/rh)
--annotation aparc.a2009s --outdir label_destrieux   # which works
fine

And I tried to get the coordinates of each labels using

mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness
--clabel  --sum  --centroid --thmin 0
--hemi lh --subject fsaverage

But, all left labels would produce the same coordinates and so
does right labels. (I've attached few example files here with).
Also, it says TalX, TalY, TalZ are these coordinates in MNI or
Talairach?

Thanks for help.




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Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

[Sabin Khadka]

Anyone?

Cheers,
Sabin Khadka

On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka 
wrote:

> Hi Doug, I tried to pick up from the thread below to get MNI coordinates
> of each destrieux parcellation region.
>
>
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html
>
> I created label files from
> mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation
> aparc.a2009s --outdir label_destrieux   # which works fine
>
> And I tried to get the coordinates of each labels using
>
> mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel
>  --sum  --centroid --thmin 0
> --hemi lh --subject fsaverage
>
> But, all left labels would produce the same coordinates and so does right
> labels. (I've attached few example files here with). Also, it says TalX,
> TalY, TalZ are these coordinates in MNI or Talairach?
>
> Thanks for help.
>
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[Freesurfer] MNI coordinates of all the vertices of fsaverage

[Sabin Khadka]

Hi Doug, I tried to pick up from the thread below to get MNI coordinates of
each destrieux parcellation region.


https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html

I created label files from
mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation
aparc.a2009s --outdir label_destrieux   # which works fine

And I tried to get the coordinates of each labels using

mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel
 --sum  --centroid --thmin 0
--hemi lh --subject fsaverage

But, all left labels would produce the same coordinates and so does right
labels. (I've attached few example files here with). Also, it says TalX,
TalY, TalZ are these coordinates in MNI or Talairach?

Thanks for help.


rh_G_S_Ant
Description: Binary data


rh_S_suborbital
Description: Binary data


lh_S_suborbital
Description: Binary data


lh_G_S_Ant
Description: Binary data
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Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

[Yolanda Vives]

Thank you Doug, I think that my question was not precise enough. I would
like to know which function I can use to obtain a vector with the number of
vertices and the corresponding MNI coordinates.

Regards,
Yolanda

2012/6/19 Douglas N Greve gr...@nmr.mgh.harvard.edu

 For fsaverage, the coordinates are the MNI305 coordinates.
 doug

 On 06/19/2012 08:48 AM, Yolanda Vives wrote:
  Dear Freesurfer experts,
 
  How could I know the MNI coordinates of the 163.842 vertices of the
  left hemisphere of fsaverage?
 
  Best regards,
  Yolanda
 
 
 
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 --
 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
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 is
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 e-mail
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 HelpLine at
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Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

[Douglas N Greve]

Hi Yolanda, you can run
mris_convert lh.white lh.white.asc
to produce a text file of the vertices and their coordinates. We also 
have a matlab function to read in surfaces.
doug

On 06/20/2012 02:44 AM, Yolanda Vives wrote:
 Thank you Doug, I think that my question was not precise enough. I 
 would like to know which function I can use to obtain a vector with 
 the number of vertices and the corresponding MNI coordinates.

 Regards,
 Yolanda

 2012/6/19 Douglas N Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu

 For fsaverage, the coordinates are the MNI305 coordinates.
 doug

 On 06/19/2012 08:48 AM, Yolanda Vives wrote:
  Dear Freesurfer experts,
 
  How could I know the MNI coordinates of the 163.842 vertices of the
  left hemisphere of fsaverage?
 
  Best regards,
  Yolanda
 
 
 
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 mailto:Freesurfer@nmr.mgh.harvard.edu
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 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 tel:617-724-2358
 Fax: 617-726-7422 tel:617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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-- 
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
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[Freesurfer] MNI coordinates of all the vertices of fsaverage

[Yolanda Vives]

Dear Freesurfer experts,

How could I know the MNI coordinates of the 163.842 vertices of the left
hemisphere of fsaverage?

Best regards,
Yolanda
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Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

[Douglas N Greve]

For fsaverage, the coordinates are the MNI305 coordinates.
doug

On 06/19/2012 08:48 AM, Yolanda Vives wrote:
 Dear Freesurfer experts,

 How could I know the MNI coordinates of the 163.842 vertices of the 
 left hemisphere of fsaverage?

 Best regards,
 Yolanda



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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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