Problems with sct_smooth_spinalcord

Hi Julien,

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?


Hi Alexandra,

Since the spinal cord is already straightened in the template space, you could do (e.g. for 3mm smoothing along Z):

sct_maths -i IMAGE -smooth 0,0,3


Ok, I seeā€¦ I thought that smooth_spinalcord would smooth the image only withing the segmented area. My mistake.
With your suggested approach the result looks fine.
Thanks for the clarification!