[Freesurfer] mri_convert mnc to nii

Hi freesurfers, I want to convert minc files to nii to work with them in ITK-SNAP segmentation software. I have used mri_convert binary, but the orientation on the nii images is completely wonky. Any advice in terms of how to use the --in_orientation argument --out_orientation argument flags?

Re: [Freesurfer] mri_convert mnc to nii

Hi Fidel How do you know it is wrong? Have you looked at the minc and the nifti in freeview? Cheers Bruce On Aug 15, 2015, at 10:19 PM, Schumman Resonance schumm...@gmail.com wrote: Hi freesurfers, I want to convert minc files to nii to work with them in ITK-SNAP segmentation