Freesurfer mri_vol2surf issue

Hi all

I have an issue trying to convert a volumetric (.nii) file into surface (.mgh)

The command line we have used :

bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg MNI152_T1_brain.dat --t1 --init-coreg

mri_vol2surf --file1.nii --reg MNI152_T1_brain.dat --hemi rh --o file1.mgh

The image is flipped between volumetric and surface
Someone has an idea about this issue ?
Thank you very much,
I would really appreciate any help,


Freesurfer’s mri_vol2surf have a pre-computed MNI-to-fsaverage registration matrix. Try to use something similar to:

mri_vol2surf --src file1.nii --out file1_surf.mgh --hemi rh --mni152reg

Victor M