sct_analyze_texture¶

E x t r a c t i o n o f g r a y l e v e l c o - o c c u r e n c e m a t r i x ( G L C M ) t e x t u r e f e a t u r e s f r o m a n i m a g e w i t h i n a g i v e n m a s k . T h e t e x t u r e s f e a t u r e s a r e t h o s e d e f i n e d i n t h e s c k i t - i m a g e i m p l e m e n t a t i o n : h t t p s : / / s c i k i t - i m a g e . o r g / d o c s / d e v / a p i / s k i m a g e . f e a t u r e . h t m l # g r a y c o p r o p s . T h i s f u n c t i o n o u t p u t s o n e n i f t i f i l e p e r t e x t u r e m e t r i c ( c o n t r a s t , d i s s i m i l a r i t y , h o m o g e n e i t y , e n e r g y , c o r r e l a t i o n , A S M ) a n d p e r o r i e n t a t i o n c a l l e d f n a m e I n p u t _ f e a t u r e _ d i s t a n c e _ a n g l e . n i i . g z . A l s o , a f i l e a v e r a g i n g e a c h m e t r i c a c r o s s t h e a n g l e s , c a l l e d f n a m e I n p u t _ f e a t u r e _ d i s t a n c e _ m e a n . n i i . g z , i s o u t p u t . Extraction of gray level co-occurence matrix (GLCM) texture features from an image within a given mask. The textures features are those defined in the sckit-image implementation: https://scikit-image.org/docs/dev/api/skimage.feature.html#graycoprops. This function outputs one nifti file per texture metric (contrast,dissimilarity,homogeneity,energy,correlation,ASM) and per orientation called fnameInput_feature_distance_angle.nii.gz. Also, a file averaging each metric across the angles, called fnameInput_feature_distance_mean.nii.gz, is output.

usage: sct_analyze_texture -i <file> -m <file> [-feature <str>]
                           [-distance <int>] [-angle <list>] [-dim {ax,sag,cor}]
                           [-ofolder <folder>] [-h] [-v <int>] [-r {0,1}]

MANDATORY ARGUMENTS¶

-i: I m a g e t o a n a l y z e . E x a m p l e : ` t 2 . n i i . g z ` Image to analyze. Example: t2.nii.gz
-m: I m a g e m a s k . E x a m p l e : ` t 2 _ s e g . n i i . g z ` Image mask. Example: t2_seg.nii.gz

OPTIONAL ARGUMENTS¶

-feature

L i s t o f G L C M t e x t u r e f e a t u r e s ( s e p a r a t e a r g u m e n t s w i t h ` , ` ) . List of GLCM texture features (separate arguments with ,).

D e f a u l t : ` ` ‘ c o n t r a s t , d i s s i m i l a r i t y , h o m o g e n e i t y , e n e r g y , c o r r e l a t i o n , A S M ‘ ` ` Default: 'contrast,dissimilarity,homogeneity,energy,correlation,ASM'

-distance

D i s t a n c e o f f s e t f o r G L C M c o m p u t a t i o n , i n p i x e l ( s u g g e s t e d d i s t a n c e v a l u e s b e t w e e n 1 a n d 5 ) . Distance offset for GLCM computation, in pixel (suggested distance values between 1 and 5).

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

-angle

L i s t o f a n g l e s f o r G L C M c o m p u t a t i o n , s e p a r a t e a r g u m e n t s w i t h ` , ` , i n d e g r e e s ( s u g g e s t e d d i s t a n c e v a l u e s b e t w e e n 0 a n d 1 7 9 ) . List of angles for GLCM computation, separate arguments with ,, in degrees (suggested distance values between 0 and 179).

D e f a u l t : ` ` ‘ 0 , 4 5 , 9 0 , 1 3 5 ‘ ` ` Default: '0,45,90,135'

-dim

P o s s i b l e c h o i c e s : a x , s a g , c o r Possible choices: ax, sag, cor

C o m p u t e t h e t e x t u r e o n t h e a x i a l ( a x ) , s a g i t t a l ( s a g ) o r c o r o n a l ( c o r ) s l i c e s . Compute the texture on the axial (ax), sagittal (sag) or coronal (cor) slices.

D e f a u l t : ` ` ‘ a x ‘ ` ` Default: 'ax'

-ofolder

O u t p u t f o l d e r . Output folder.

D e f a u l t : ` ` ‘ . / t e x t u r e ‘ ` ` Default: './texture'

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