Re: [Freesurfer] normal vector in gm

Hi Seok, Try using --projfac .01 in the surf2vol command. doug Seok Lew wrote: Thank you ! I successfully projected the pial surface normals in the volume. Now I wanted to project the normals in the inner gm boundary voxels (i.e. gm boundary voxels with wm). What I tried is scaling up

Re: [Freesurfer] normal vector in gm

Thank you ! I successfully projected the pial surface normals in the volume. Now I wanted to project the normals in the inner gm boundary voxels (i.e. gm boundary voxels with wm). What I tried is scaling up the wm surface by mris_convert -s 1.01 lh.white lh.white101 and then projected

[Freesurfer] normal vector in gm

Hello users, My colleagues and I are trying to create a gray matter electric conduction model where a preferable conduction direction is aligned with the normal direction induced from the pial and white surface normals. Freesurfer reconstruction already gives pial and white matter surface

Re: [Freesurfer] normal vector in gm

Try using mri_surf2surf with the --sval-nxyz. The output have 3-frame, one for each component in the normal. Then use mri_surf2vol to stuff this back into a volume. doug Seok Lew wrote: Hello users, My colleagues and I are trying to create a gray matter electric conduction model where a

Re: [Freesurfer] normal vector in gm

Thanks, first of all. I tried with the following scripts, but ended up with an error. I am not sure which format or file is required for the --volreg. # mri_surf2surf --s FS --hemi lh --sval-nxyz pial --tval ./ttt.mgz # mri_surf2vol --surfval ttt.mgz --hemi lh --volreg mri/transforms/

Re: [Freesurfer] normal vector in gm

That is the file created by registering your orig.mgz to the mni152 brain (assuming you are using the 152). You can create this registration file with the mni152reg script. doug Seok Lew wrote: Thanks, first of all. I tried with the following scripts, but ended up with an error. I am not