sct_smooth_spinalcord¶
Smooth the spinal cord along its centerline. Steps are:
Spinal cord is straightened (using centerline),
a Gaussian kernel is applied in the superior-inferior direction,
then cord is de-straightened as originally.
usage: sct_smooth_spinalcord -i <file> -s <file> [-h] [-smooth <list>]
[-algo-fitting <str>] [-o <file>] [-r {0,1}]
[-v <int>]
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 to0
.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.- -r
Possible choices: 0, 1
Whether to remove temporary files. 0 = no, 1 = yes
Default: 1
- -v
Possible choices: 0, 1, 2
Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode
Default: 1