I tried to smooth my mean epi image in template space with:
sct_smooth_spinalcord -i mean_epi_norm.nii -s mean_epi_seg_norm.nii -smooth 2
and the result looks like that:
Also the smoothing function outputs that it straightens the spinal cord although my spinal cord is already straightened since it is in template space.
Am I doing something wrong or do I misunderstand the smoothing function?