sct_denoising_onlm¶

U t i l i t y f u n c t i o n t o d e n o i s e i m a g e s . R e t u r n t h e d e n o i s e d i m a g e a n d a l s o t h e d i f f e r e n c e b e t w e e n t h e i n p u t a n d t h e o u t p u t . T h e d e n o i s i n g a l g o r i t h m i s b a s e d o n t h e N o n - l o c a l m e a n s m e t h o d s ( P i e r r i c k C o u p e , J o s e M a n j o n , M o n t s e r r a t R o b l e s , L o u i s C o l l i n s . “ A d a p t i v e M u l t i r e s o l u t i o n N o n - L o c a l M e a n s F i l t e r f o r 3 D M R I m a g e D e n o i s i n g ” I E T I m a g e P r o c e s s i n g , I n s t i t u t i o n o f E n g i n e e r i n g a n d T e c h n o l o g y , 2 0 1 1 ) . T h e i m p l e m e n t a t i o n i s b a s e d o n D i p y ( h t t p s : / / d i p y . o r g / ) . Utility function to denoise images. Return the denoised image and also the difference between the input and the output. The denoising algorithm is based on the Non-local means methods (Pierrick Coupe, Jose Manjon, Montserrat Robles, Louis Collins. “Adaptive Multiresolution Non-Local Means Filter for 3D MR Image Denoising” IET Image Processing, Institution of Engineering and Technology, 2011). The implementation is based on Dipy (https://dipy.org/).

usage: sct_denoising_onlm -i <file> [-p {Rician,Gaussian}] [-d <int>]
                          [-std <float>] [-o <str>] [-h] [-v <int>] [-r {0,1}]

MANDATORY ARGUMENTS¶

-i: I n p u t N I F T I i m a g e t o b e d e n o i s e d . E x a m p l e : ` i m a g e _ i n p u t . n i i . g z ` Input NIFTI image to be denoised. Example: image_input.nii.gz

OPTIONAL ARGUMENTS¶

-p

P o s s i b l e c h o i c e s : R i c i a n , G a u s s i a n Possible choices: Rician, Gaussian

T y p e o f a s s u m e d n o i s e d i s t r i b u t i o n . Type of assumed noise distribution.

D e f a u l t : ` ` ‘ R i c i a n ‘ ` ` Default: 'Rician'

-d

T h r e s h o l d v a l u e f o r w h a t t o b e c o n s i d e r e d a s n o i s e . T h e s t a n d a r d d e v i a t i o n o f t h e n o i s e i s c a l c u l a t e d f o r v a l u e s b e l o w t h i s l i m i t . N o t r e l e v a n t i f ` - s t d ` v a l u e i s p r e c i s e d . Threshold value for what to be considered as noise. The standard deviation of the noise is calculated for values below this limit. Not relevant if -std value is precised.

D e f a u l t : ` ` 8 0 ` ` Default: 80

-std

S t a n d a r d d e v i a t i o n o f t h e n o i s e . I f n o t s p e c i f i e d , i t i s c a l c u l a t e d u s i n g a b a c k g r o u n d o f p o i n t o f v a l u e s b e l o w t h e t h r e s h o l d v a l u e ( p a r a m e t e r ` - d ` ) . Standard deviation of the noise. If not specified, it is calculated using a background of point of values below the threshold value (parameter -d).

-o

N a m e o f t h e o u t p u t N I F T I i m a g e . Name of the output NIFTI image.

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