For mapping to the surface, each surface vertex has an xyz coordiate in
anatomical space. The registration file is used to convert this into the
column, row, slice in the overlay space. The value of the overlay volume
at the CRS is then assigned to that vertex. In your case, the coordinate
is adjusted by projecting it along the surface normal by a distance of
0.2 times the thickness at that vertex. The overlay could be
trilinearlly or cubically interpolated, but you don't have that in your
command line. If you want to see the input volume and the sampled
points, you can do something like
freeview mri/nu.mgz:overlay=overlay.mgz:reg=register.lta -f
surf/lh.white:overlay=overlay.lh.mgz
When viewing in the volume, select lh.white in the upper left, then go
to the lower left and check the "Use overlay color" to change the
surface color from yellow to the color of your overlay
On 12/6/2024 4:41 PM, Pandey, Shraddha wrote:
External Email - Use Caution
Hello FreeSurfer Experts,
I am using |mri_vol2surf| to map a volume onto a surface, with the
registration |.dat| file generated via |bbregister|. I would like to
understand how the input volume is being sampled to generate the
surface and how to visualize the sampled points.
mri_vol2surf --src "$input_volume" --out "$output_surface" --srcreg
"$output_reg_file" --hemi lh --projfrac 0.2
Specifically, how can I display the |input_volume| along with the
sampled points at a |projfrac| of 0.2 on Freeview?
Thank you in advance for your help!
Shraddha
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