sct_smooth_spinalcord

S m o o t h t h e s p i n a l c o r d a l o n g i t s c e n t e r l i n e . S t e p s a r e : Smooth the spinal cord along its centerline. Steps are:

  1. S p i n a l c o r d i s s t r a i g h t e n e d ( u s i n g c e n t e r l i n e ) , Spinal cord is straightened (using centerline),

  2. a G a u s s i a n k e r n e l i s a p p l i e d i n t h e s u p e r i o r - i n f e r i o r d i r e c t i o n , a Gaussian kernel is applied in the superior-inferior direction,

  3. t h e n c o r d i s d e - s t r a i g h t e n e d a s o r i g i n a l l y . 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

I m a g e t o s m o o t h . E x a m p l e : ` d a t a . n i i . g z ` Image to smooth. Example: data.nii.gz

-s

S p i n a l c o r d c e n t e r l i n e o r s e g m e n t a t i o n . E x a m p l e : ` d a t a _ c e n t e r l i n e . n i i . g z ` Spinal cord centerline or segmentation. Example: data_centerline.nii.gz

OPTIONAL ARGUMENTS

-smooth

S i g m a ( s t a n d a r d d e v i a t i o n ) o f t h e s m o o t h i n g G a u s s i a n k e r n e l ( i n m m ) . F o r i s o t r o p i c s m o o t h i n g y o u o n l y n e e d t o s p e c i f y a v a l u e ( e . g . ` 2 ` ) . F o r a n i s o t r o p i c s m o o t h i n g s p e c i f y a v a l u e f o r e a c h a x i s , s e p a r a t e d w i t h a c o m m a . T h e o r d e r s h o u l d f o l l o w a x e s R i g h t - L e f t , A n t e r o - P o s t e r i o r , S u p e r i o r - I n f e r i o r ( e . g . : ` 1 , 1 , 3 ` ) . F o r n o s m o o t h i n g , s e t v a l u e t o ` 0 ` . 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.

D e f a u l t : ` ` [ 0 , 0 , 3 ] ` ` Default: [0, 0, 3]

-algo-fitting

P o s s i b l e c h o i c e s : b s p l i n e , p o l y f i t Possible choices: bspline, polyfit

A l g o r i t h m f o r c u r v e f i t t i n g . F o r m o r e i n f o r m a t i o n , s e e ` s c t _ s t r a i g h t e n _ s p i n a l c o r d ` . Algorithm for curve fitting. For more information, see sct_straighten_spinalcord.

D e f a u l t : ` ` ‘ b s p l i n e ‘ ` ` Default: 'bspline'

-o

O u t p u t f i l e n a m e . E x a m p l e : ` s m o o t h _ s c . n i i . g z ` . I f n o t p r o v i d e d , t h e s u f f i x ` _ s m o o t h ` w i l l b e a d d e d t o t h e i n p u t f i l e n a m e . Output filename. Example: smooth_sc.nii.gz. If not provided, the suffix _smooth will be added to the input file name.

MISC ARGUMENTS

-v

P o s s i b l e c h o i c e s : 0 , 1 , 2 Possible choices: 0, 1, 2

V e r b o s i t y . 0 : D i s p l a y o n l y e r r o r s / w a r n i n g s , 1 : E r r o r s / w a r n i n g s + i n f o m e s s a g e s , 2 : D e b u g m o d e . Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode.

D e f a u l t : ` ` 1 ` ` Default: 1

-r

P o s s i b l e c h o i c e s : 0 , 1 Possible choices: 0, 1

R e m o v e t e m p o r a r y f i l e s . Remove temporary files.

D e f a u l t : ` ` 1 ` ` Default: 1