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.cpp#L373 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" <dgom...@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 -- Daniel Gomez, Ph.D. MR Physics and Instrumentation Group A. A. Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 USA dgom...@mgh.harvard.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
