Dear Doug,
Thanks a lot for the fast reply. I got it to work with your tips. The missing
link for me was especially that I could get the vertices locations by using
read_surf over the mgz file. Instead of the fmri_info rotation matrix I can
also use the matrix from the nii-file, can't I? They are almost exactly equal.
Now I got the tal coordinates and try to convert them to indices in my nii
matrix. I now do that by add the origin of the nii scan to the found tal
coordinates (converted to mni or not). But this makes the brain end up too high
in the figure. Any idea how this can be? This is true irrespective of the
rotation matrix I take.
Thanks a lot in advance, it looks really promising,
kind regards,
Frank
----- Original Message -----
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: "Frank Leoné" <f.le...@donders.ru.nl>
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Monday, May 3, 2010 5:55:33 PM GMT +01:00 Amsterdam / Berlin / Bern /
Rome / Stockholm / Vienna
Subject: Re: [Freesurfer] Vertices to matrix coordinates
The coordinate system is not easy to explain in an email. There are
power point slides on our wiki about the geometry used. To get from
surface xyz to column, row, slice in the orig.mgz, first get a matrix
from the orig.mgz with
mri_info --tkrvox2ras orig.mgz
this will be 4x4, multiply the inverse of this matrix by the surface xyz
(adding a one to make it 4x1) to get the col, row, slice in the orig.
doug
f.le...@donders.ru.nl wrote:
> Hi all,
>
> I checked quite a number of previous posts, but still can't seem to figure
> out what the vertices numbers given by read_annotation in matlab stand for.
> My questions are:
>
> - In what reference frame are they?
> - How do I convert them to coordinates in my original structural image (an x
> * y * z matrix, based on a nii-file)?
>
> Thanks a lot in advance!
>
> kind regards,
>
> Frank
>
>
>
--
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
--
Frank T.M. Leoné, MSc
Graduate student | Donders Institute for Brain, Cognition and Behaviour
f.le...@donders.ru.nl | +31 24 36 12542 / +31 24 36 68388 | Room B.1.31 / Room
1.34
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