sct_deepseg_lesion

M S l e s i o n S e g m e n t a t i o n u s i n g c o n v o l u t i o n a l n e t w o r k s . R e f e r e n c e : G r o s C e t a l . A u t o m a t i c s e g m e n t a t i o n o f t h e s p i n a l c o r d a n d i n t r a m e d u l l a r y m u l t i p l e s c l e r o s i s l e s i o n s w i t h c o n v o l u t i o n a l n e u r a l n e t w o r k s . N e u r o i m a g e . 2 0 1 8 O c t 6 ; 1 8 4 : 9 0 1 - 9 1 5 . MS lesion Segmentation using convolutional networks. Reference: Gros C et al. Automatic segmentation of the spinal cord and intramedullary multiple sclerosis lesions with convolutional neural networks. Neuroimage. 2018 Oct 6;184:901-915.

usage: sct_deepseg_lesion -i <file> -c {t2,t2_ax,t2s}
                          [-centerline {svm,cnn,viewer,file}]
                          [-file_centerline <str>] [-brain {0,1}]
                          [-ofolder <str>] [-h] [-v <int>] [-r {0,1}]

MANDATORY ARGUMENTS

-i

I n p u t i m a g e . E x a m p l e : ` t 2 . n i i . g z ` Input image. Example: t2.nii.gz

-c

P o s s i b l e c h o i c e s : t 2 , t 2 _ a x , t 2 s Possible choices: t2, t2_ax, t2s

T y p e o f i m a g e c o n t r a s t . Type of image contrast.

  • ` t 2 ` : T 2 w s c a n w i t h i s o t r o p i c o r a n i s o t r o p i c r e s o l u t i o n . t2: T2w scan with isotropic or anisotropic resolution.

  • ` t 2 _ a x ` : T 2 w s c a n w i t h a x i a l o r i e n t a t i o n a n d t h i c k s l i c e s . t2_ax: T2w scan with axial orientation and thick slices.

  • ` t 2 s ` : T 2 * w s c a n w i t h a x i a l o r i e n t a t i o n a n d t h i c k s l i c e s . t2s: T2*w scan with axial orientation and thick slices.

OPTIONAL ARGUMENTS

-centerline

P o s s i b l e c h o i c e s : s v m , c n n , v i e w e r , f i l e Possible choices: svm, cnn, viewer, file

M e t h o d u s e d f o r e x t r a c t i n g t h e c e n t e r l i n e : Method used for extracting the centerline:

  • ` s v m ` : A u t o m a t i c d e t e c t i o n u s i n g S u p p o r t V e c t o r M a c h i n e a l g o r i t h m . svm: Automatic detection using Support Vector Machine algorithm.

  • ` c n n ` : A u t o m a t i c d e t e c t i o n u s i n g C o n v o l u t i o n a l N e u r a l N e t w o r k . cnn: Automatic detection using Convolutional Neural Network.

  • ` v i e w e r ` : S e m i - a u t o m a t i c d e t e c t i o n u s i n g m a n u a l s e l e c t i o n o f a f e w p o i n t s w i t h a n i n t e r a c t i v e v i e w e r f o l l o w e d b y r e g u l a r i z a t i o n . viewer: Semi-automatic detection using manual selection of a few points with an interactive viewer followed by regularization.

  • ` f i l e ` : U s e a n e x i s t i n g c e n t e r l i n e ( u s e w i t h f l a g ` - f i l e _ c e n t e r l i n e ` ) file: Use an existing centerline (use with flag -file_centerline)

D e f a u l t : ` ` ‘ s v m ‘ ` ` Default: 'svm'

-file_centerline

I n p u t c e n t e r l i n e f i l e ( t o u s e w i t h f l a g ` - c e n t e r l i n e ` f i l e ) . E x a m p l e : ` t 2 _ c e n t e r l i n e _ m a n u a l . n i i . g z ` Input centerline file (to use with flag -centerline file). Example: t2_centerline_manual.nii.gz

-brain

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

I n d i c a t e i f t h e i n p u t i m a g e c o n t a i n s b r a i n s e c t i o n s ( t o s p e e d u p s e g m e n t a t i o n ) . T h i s f l a g i s o n l y e f f e c t i v e w i t h ` - c e n t e r l i n e c n n ` . Indicate if the input image contains brain sections (to speed up segmentation). This flag is only effective with -centerline cnn.

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

-ofolder

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

D e f a u l t : ` ` ‘ / h o m e / d o c s / c h e c k o u t s / r e a d t h e d o c s . o r g / u s e r _ b u i l d s / s p i n a l c o r d t o o l b o x / c h e c k o u t s / l a t e s t / d o c u m e n t a t i o n / s o u r c e ‘ ` ` Default: '/home/docs/checkouts/readthedocs.org/user_builds/spinalcordtoolbox/checkouts/latest/documentation/source'

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