Re: [Freesurfer] Overlay onto surf file

when you run mri_vol2surf you also pass a registration file with it. This allows vol2surf to compute the col, row, slice in the volume that maps to a given vertex. doug

On 07/03/2014 06:05 PM, Paul Quigley wrote:

Hi Bruce,

This will help me move in the right direction. I still need to figure out a way to find the closest voxel given (theta, phi) for every voxel on the surface, but this seems tractable. Thank you for your help.

Paul

On Thu, Jul 3, 2014 at 6:07 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:

Hi Paul

the 130K vector is a scalar for each vertex, so there is no
projection in
freeview - it was already done by mri_vol2surf. Using mri_vol2surf
you get
to pick your projection method (check out the help). To convert
from sphere
to volume, you simply find the vertex on the ?h.sphere.reg file
that is
closest to you given (theta, phi), then look up the x,y,z position
of that
vertex in the ?h.white or ?h.pial surface (or somewhere between
them if you
want, depending on how you want to do the projection). Make sense?

cheers
Bruce



On Thu, 3 Jul 2014, Paul
Quigley wrote:

> Hello,
>
> Could anyone give me some insight into how freeview projects an
overlay onto
> a surface? For example, I have an overlay generated though
mri_vol2surf for
> subject pq, call it stats.nii. Opening the nifti in MATLAB, I
see that the
> image it stores is a single, flat vector (had about 130,000
entries). I can
> overlay stats.nii onto a variety of surf files (e.g. sphere.lh,
> inflated.lh).
>
> So it seems clear that each surf file has its own method for
translating the
> indices in the vector to points on the surface... Is there any
way to
> extract this information from the surf file?
>
> Basically, my goal is to figure out how I can translate
coordinates on
> sphere.?h (theta, phi or x,y,z doesn't matter) to subscripts on
my T1.
>
> Any help would be greatly appreciated!
>
> Thank you,
> Paul
>
>
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