We have not used .w files in years. Try converting the .w file to .mgz
using mri_surf2surf (or even better, don't save them as .w files)
On 10/22/2020 4:03 PM, Yixin Ma wrote:
External Email - Use Caution
Hi Freesurfer experts,
I'm trying to write the normals of the GM/WM meshes to the entire ribbon.
We usually do it by:
1) Generate normal files from rh.white and lh.white
mris_convert rh.whiterh.white.gii
mris_convert -nrh.whiterh.white.normals.asc
2) Use matlab 'read_normals' function to read the normals and write
individual directions xyz as a paint format file.
g = gifti([path 'Analysis/' exam '/' subject '/surf/rh.white.gii']);
norm = read_normals(g,[path 'Analysis/' exam '/' subject
'/surf/rh.white.normals.asc']);
write_wfile([path 'Analysis/' exam '/' subject
'/surf/rh_normx.w'],norm(:,1));
write_wfile([path 'Analysis/' exam '/' subject
'/surf/rh_normy.w'],norm(:,2));
write_wfile([path 'Analysis/' exam '/' subject
'/surf/rh_normz.w'],norm(:,3));
3) Use mri_surf2vol method two to paint the normals into the ribbon.
But the problem is that method two gives me lots of holes in the ribbon.
I'm wondering if it's possible to use mri_surf2vol method one to paint
the normals into the ribbon because method one does not leave holes in
the ribbon. However, it seems like the overlay does not accept paint
file format (rh_normx.w). The overlay in method one accepts
rh.thickness as an input, as shown in the example on the website. I'm
wondering how to convert the painting files to have the same format as
rh.thickness?
Thank you in advance,
Yixin
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