sct_dice_coefficient¶

C o m p u t e t h e D i c e C o e f f i c i e n t . N . B . : i n d e x i n g ( i n b o t h t i m e a n d s p a c e ) s t a r t s w i t h 0 n o t 1 ! I n p u t t i n g ` - 1 ` f o r a s i z e w i l l s e t i t t o t h e f u l l i m a g e e x t e n t f o r t h a t d i m e n s i o n . Compute the Dice Coefficient. N.B.: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension.

usage: sct_dice_coefficient -i <file> -d <file> [-2d-slices {0,1,2}] [-b <list>]
                            [-bmax {0,1}] [-bzmax {0,1}] [-bin {0,1}] [-o <str>]
                            [-h] [-v <int>] [-r {0,1}]

MANDATORY ARGUMENTS¶

-i: F i r s t i n p u t i m a g e . E x a m p l e : ` t 2 _ s e g . n i i . g z ` First input image. Example: t2_seg.nii.gz
-d: S e c o n d i n p u t i m a g e . E x a m p l e : ` t 2 _ m a n u a l _ s e g . n i i . g z ` Second input image. Example: t2_manual_seg.nii.gz

OPTIONAL ARGUMENTS¶

-2d-slices

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

C o m p u t e D C o n 2 D s l i c e s i n t h e s p e c i f i e d d i m e n s i o n Compute DC on 2D slices in the specified dimension

-b

B o u n d i n g b o x w i t h t h e c o o r d i n a t e s o f t h e o r i g i n a n d t h e s i z e o f t h e b o x a s f o l l o w : x _ o r i g i n , x _ s i z e , y _ o r i g i n , y _ s i z e , z _ o r i g i n , z _ s i z e . E x a m p l e : 5 , 1 0 , 5 , 1 0 , 1 0 , 1 5 Bounding box with the coordinates of the origin and the size of the box as follow: x_origin,x_size,y_origin,y_size,z_origin,z_size. Example: 5,10,5,10,10,15

-bmax

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

U s e m a x i m u m b o u n d i n g b o x o f t h e i m a g e s u n i o n t o c o m p u t e D C . Use maximum bounding box of the images union to compute DC.

-bzmax

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

U s e m a x i m u m b o u n d i n g b o x o f t h e i m a g e s u n i o n i n t h e “ Z “ d i r e c t i o n t o c o m p u t e D C . Use maximum bounding box of the images union in the “Z” direction to compute DC.

-bin

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

B i n a r i z e i m a g e b e f o r e c o m p u t i n g D C . ( P u t n o n - z e r o - v o x e l s t o 1 ) Binarize image before computing DC. (Put non-zero-voxels to 1)

-o

O u t p u t f i l e w i t h D C r e s u l t s ( . t x t ) . E x a m p l e : ` d i c e _ c o e f f . t x t ` Output file with DC results (.txt). Example: dice_coeff.txt

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