you are right! Just fixed it. thanks
On 2/18/2022 2:15 PM, Gomez, Daniel wrote: > 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 > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
