sct_create_mask¶

C r e a t e m a s k a l o n g z d i r e c t i o n . Create mask along z direction.

usage: sct_create_mask -i <file> -p <str> [-size <str>]
                       [-f {cylinder,box,gaussian}] [-o <str>] [-h] [-v <int>]
                       [-r {0,1}]

MANDATORY ARGUMENTS¶

-i

I m a g e t o c r e a t e m a s k o n . O n l y u s e d t o g e t h e a d e r . M u s t b e 3 D . E x a m p l e : ` d a t a . n i i . g z ` Image to create mask on. Only used to get header. Must be 3D. Example: data.nii.gz

-p

P r o c e s s t o g e n e r a t e m a s k . Process to generate mask.

` c o o r d , X x Y ` : C e n t e r m a s k a t t h e X , Y c o o r d i n a t e s . E x a m p l e : ` c o o r d , 2 0 x 1 5 ` coord,XxY: Center mask at the X,Y coordinates. Example: coord,20x15
` p o i n t , F I L E ` : C e n t e r m a s k a t t h e X , Y c o o r d i n a t e s o f t h e l a b e l d e f i n e d i n i n p u t v o l u m e F I L E . E x a m p l e : ` p o i n t , l a b e l . n i i . g z ` point,FILE: Center mask at the X,Y coordinates of the label defined in input volume FILE. Example: point,label.nii.gz
` c e n t e r ` : C e n t e r m a s k i n t h e m i d d l e o f t h e F O V ` [ n x / 2 , n y / 2 ] ` . center: Center mask in the middle of the FOV [nx/2, ny/2].
` c e n t e r l i n e , F I L E ` : A t e a c h s l i c e , t h e m a s k i s c e n t e r e d a t t h e s p i n a l c o r d c e n t e r l i n e , d e f i n e d b y t h e i n p u t s e g m e n t a t i o n F I L E . E x a m p l e : ` c e n t e r l i n e , t 2 _ s e g . n i i . g z ` centerline,FILE: At each slice, the mask is centered at the spinal cord centerline, defined by the input segmentation FILE. Example: centerline,t2_seg.nii.gz

D e f a u l t : ` ` ‘ c e n t e r ‘ ` ` Default: 'center'

OPTIONAL ARGUMENTS¶

-size

D i a m e t e r o f t h e m a s k i n t h e a x i a l p l a n e , g i v e n i n p i x e l ( E x a m p l e : ` 3 5 ` ) o r i n m i l l i m e t e r ( E x a m p l e : ` 3 5 m m ` ) . I f s h a p e = g a u s s i a n , s i z e i n s t e a d c o r r e s p o n d s t o “ s i g m a “ ( E x a m p l e : ` 4 5 ` ) . Diameter of the mask in the axial plane, given in pixel (Example: 35) or in millimeter (Example: 35mm). If shape=gaussian, size instead corresponds to “sigma” (Example: 45).

D e f a u l t : ` ` ‘ 4 1 ‘ ` ` Default: '41'

-f

P o s s i b l e c h o i c e s : c y l i n d e r , b o x , g a u s s i a n Possible choices: cylinder, box, gaussian

S h a p e o f t h e m a s k Shape of the mask

D e f a u l t : ` ` ‘ c y l i n d e r ‘ ` ` Default: 'cylinder'

-o

N a m e o f o u t p u t m a s k , E x a m p l e : ` d a t a . n i i . g z ` Name of output mask, Example: data.nii.gz

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