Mesh2voxel, bad coordinate

Dear All,

I am trying to convert freesurfer surfaces to partial volum with mesh2voxel

I try with the lh.pial surface which I converted to vtk with meshconvert (or mris_convert from freesurfer)

then when using:
mesh2voxel surfac.vtk T1.nii pve_result.nii

the output is shifted compare to the original T1 (whereas it was correct with freeview)

I tried the 4 option -transform for the meshconvert function, but wihtout success : I optained empty results, except with I do not use the -transform argument. In this case I get a shifted pve volume.

Any hints to get a perfect match ?

Many thanks

For those who are interested, we found the problem:
It seems that freesurfer surfaces does not take into consideration the nifti volume affine and the mm position of the vertex are expressed in a coordinate system where the 0,0,0 mm is at the volume center.
So changing the nifti affine of the volume, leads to a good match.

This was more a freesurfer issue, sorry for the spam on mrtrix forum

1 Like

Glad you figured it out, and thanks for keeping us updated!

With 3.0.0, meshconvert now includes a fifth option for the -transform argument, “fs2real”, which utilises the T1w image to determine the appropriate transformation from FreeSurfer’s internal representation to MRtrix3’s preferred real-space coordinate system. I expect this is the functionality that you actually need.