sct_smooth_spinalcord

Smooth the spinal cord along its centerline. Steps are:

  1. Spinal cord is straightened (using centerline),

  2. a Gaussian kernel is applied in the superior-inferior direction,

  3. then cord is de-straightened as originally.

usage: sct_smooth_spinalcord -i <file> -s <file> [-smooth <list>]
                             [-algo-fitting <str>] [-o <file>] [-h] [-v <int>]
                             [-r {0,1}]

MANDATORY ARGUMENTS

-i

Image to smooth. Example: data.nii.gz

-s

Spinal cord centerline or segmentation. Example: data_centerline.nii.gz

OPTIONAL ARGUMENTS

-smooth

Sigma (standard deviation) of the smoothing Gaussian kernel (in mm). For isotropic smoothing you only need to specify a value (e.g. 2). For anisotropic smoothing specify a value for each axis, separated with a comma. The order should follow axes Right-Left, Antero-Posterior, Superior-Inferior (e.g.: 1,1,3). For no smoothing, set value to 0.

Default: [0, 0, 3]

-algo-fitting

Possible choices: bspline, polyfit

Algorithm for curve fitting. For more information, see sct_straighten_spinalcord.

Default: 'bspline'

-o

Output filename. Example: smooth_sc.nii.gz. If not provided, the suffix _smooth will be added to the input file name.

MISC ARGUMENTS

-v

Possible choices: 0, 1, 2

Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode.

Default: 1

-r

Possible choices: 0, 1

Remove temporary files.

Default: 1