That is a file with the overlay info at each vertex. It looks like a
volume file because it is an mgz file, but that will have as many data
elements as there are surface vertices. Each element will have the value
of the overlay volume at the location of the surface vertex.
On 12/17/2024 11:53 AM, Pandey, Shraddha wrote:
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Hi,
Thank you for your response. I apologize if this is a basic question,
as I am new to FreeSurfer. Could you please elaborate on what
|overlay.lh.mgz| refers to?
Shraddha
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<dgr...@mgh.harvard.edu>
*Sent:* Tuesday, December 10, 2024 11:43 AM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* [External] Re: [Freesurfer] Subject: query about mri_vol2surf
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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:
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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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