Hello Everyone,

I've run the Freesurfer 6.0 and created the sub-brainstem structures (e.g., pons, midbrain, etc.). I would like to convert the brainstemSsLabels.v10.mgz results to a .nii file. However, unlike when I use mri_convert for aseg.mgz, I only get an image of the brainstem itself as a single intensity (or label) and not subparts (or labels for pons, midbrain, etc.). Is there a way to get the labels for all sub-brainstem parts included in the nii writeout, using mri_convert or another function in freesurfer?

Best,

Jon