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
