Re: [Freesurfer] MNI to RAS surface coordinates

yes

On 06/12/2012 08:17 AM, Yolanda Vives wrote:

Thank you for your answer. Just one more question, is the "fsaverage" already in MNI305 space? In this case, the RAS coordinates from tksurfer/QDEC are already MNI?

Regards, Yolanda

2012/6/7 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>

Here are instructions to go from a surface RAS to the mni305 RAS, so
just invert them.
doug


I have an RAS point on the surface (tkrR tkrA tkrS) ("Vertex RAS" from
tksurfer) and want to compute the MNI305 RAS that corresponds to this
point:

MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]'
  TalXFM: subject/orig/transforms/talairach.xfm
  Norig: mri_info --vox2ras orig.mgz
  Torig: mri_info --vox2ras-tkr orig.mgz

Test: click on a point in tksurfer. Use "Vertex RAS" to compute
MNI305RAS. Compare MNI305RAS to "Vertex MNI Talairach". Also, hit Save
Point in tksurfer. In tkmedit, Goto Saved Point, compare MNI305RAS to
"MNI Coordinates". Note: you may need to use the "Volume RAS" from
tkmedit in the computation above to get an exact match.



On 06/06/2012 09:43 AM, Yolanda Vives wrote:
> Dear Freesurfer experts,
>
> How can I transform from MNI coordinates to RAS surface coordinates?
>
> Regards,
> Yolanda
>
>
> 2012/6/5 Yolanda Vives <yvives@pic.es <mailto:yvives@pic.es>
<mailto:yvives@pic.es <mailto:yvives@pic.es>>>
>
>     Dear Freesurfer experts,
>
>     I have performed a VBM analysis with SPM, using some VOIs. Now I
>     would like to compare the volumetric results obtained with SPM
>     with those of cortical thickness obtained with Freesurfer in the
>     same VOIs (approximately).
>
>     For this purpose, I would like to transform the MNI
coordinates of
>     my SPM VOIs into RAS surface coordinates of fsaverage, to draw a
>     label of more or less the same size of the SPM VOI and to
propage
>     it to all the subjects in order to obtain an average cortical
>     thickness of this label (VOI) for each subject.
>
>     1) Would this procedure be correct?
>
>     2) How could I transform my MNI coordinates into RAS surface
>     coordinates?
>
>     Thank you in advance,
>     Yolanda
>
>
>
>
> --
> Yolanda Vives
> PIC (Port d'Informació Científica)
> Campus UAB, Edificio D
> E-08193 Bellaterra, Barcelona
> Telf. +34 93 586 8232 <tel:%2B34%2093%20586%208232>
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>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
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-- Yolanda Vives PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Telf. +34 93 586 8232 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html