The surface coordinates are in "tkregister" coordinates whereas freeview
is giving you scanner coordinates.
See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems for how
to convert between them
On 3/25/2021 7:14 AM, Shizuka Hayashi wrote:
External Email - Use Caution
Dear Freesurfer team,
I have a question about the inconsistency between the vertex read from
read_surf and vertex shown in Freeview.
I have a volume from the hippocampal subfield pipeline and I converted
it to surface mesh using
mri_tessellate mri/lh.hippoAmygLabels-T1.long.v21.mgz -an
surf/lh.hippoAmygLabels-T1.long.v21.surf.
Then I smoothed the surface using mris_smooth
surf/lh.hippoAmygLabels-T1.long.v21.surf
surf/lh.hippoAmygLabels-T1.long.v21.surf
Now I want to get the corresponding voxel of
lh.hippoAmygLabels-T1.long.v21.mgz with the vertex. In Freeview, for
example, the vertex 0 is [5.17, -19.5, 4.83]. I know how to convert
this vertex to the corresponding voxel.
However, when I read the surf/lh.hippoAmygLabels-T1.long.v21.surf from
Matlab using read_surf, the first vertex ( vertex(1,:,:)) is equal to
[165.4900,217.3600,-159.7300].
Are there any ways to solve the issue?
Thank you.
Regards,
Shizuka
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