There is a minor bug/typo in mri_surf2vol that was leading to registration issues if the "--fillribbon" flag is used, like in my case.
https://github.com/freesurfer/freesurfer/blob/dev/mri_surf2vol/mri_surf2vol.... The call to MRIcopyHeader(OutVol,VtxVol); has to happen after the closing of the if/else statement, otherwise the if branch (fillribbon) won't be covered and the output vtxvol file will have a wrong header.
Regards, Daniel
"Gomez, Daniel" dgomez1@mgh.harvard.edu writes:
Dear FS users,
I’m trying to get surface indices from surfaces generated with recon-all into a volume in native functional/EPI space. I’m using mri_surf2vol for that, though if there is a better alternative solution, I’m happy to take it.
My issue is that the output index volume (vtxvol) I get from mri_surf2vol does not seem to ever be properly aligned/registered with the target space.
Here's the command I run (I'm interesting in vtxvol.nii.gz)
mri_surf2vol --reg anat2epi.dat --hemi lh --vtxvol vtxvol.nii.gz --fillribbon --outvol foo.nii.gz --template epi.nii.gz --mkmask
Upon further investigation, I learn I can’t get the projection to work properly even if I try projecting the surface onto the native anatomical space. As in:
mri_surf2vol --hemi lh --vtxvol vtxvol.nii.gz --fillribbon --outvol foo.nii.gz --template ../mri/orig.mgz --mkmask --identity sub-01
Given the output vtxvol doesn't even have the same dimensions as the template specified in the command line, it makes me think I’m doing something wrong:
nib-ls vtxvol.nii.gz ../mri/orig.mgz
vtxvol.nii.gz float32 [320, 320, 320] 1.00x1.00x1.00 sform ../mri/orig.mgz uint8 [320, 320, 320] 0.75x0.75x0.75
What is the proper way to get vertex indices in EPI space?
Thank you,
Daniel