Re: [Freesurfer] mri_surf2vol method one

2020-10-27 Thread Douglas N. Greve 
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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[Freesurfer] mri_surf2vol method one

2020-10-22 Thread Yixin Ma 
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.white rh.white.gii

mris_convert -n rh.white rh.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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Freesurfer@nmr.mgh.harvard.edu
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