sct_detect_pmj¶

D e t e c t i o n o f t h e P o n t o - M e d u l l a r y J u n c t i o n ( P M J ) . T h i s m e t h o d i s b a s e d o n a m a c h i n e - l e a r n i n g a l g o r i t h m p u b l i s h e d i n ( G r o s e t a l . 2 0 1 8 , M e d i c a l I m a g e A n a l y s i s , h t t p s : / / d o i . o r g / 1 0 . 1 0 1 6 / j . m e d i a . 2 0 1 7 . 1 2 . 0 0 1 ) . T w o m o d e l s a r e a v a i l a b l e : o n e f o r T 1 w - l i k e a n d a n o t h e r f o r T 2 w - l i k e i m a g e s . I f t h e P M J i s d e t e c t e d f r o m t h e i n p u t i m a g e , a N I f T I m a s k i s o u t p u t ( “ * _ p m j . n i i . g z “ ) w i t h o n e v o x e l ( v a l u e = 5 0 ) l o c a t e d a t t h e p r e d i c t e d P M J p o s i t i o n . I f t h e P M J i s n o t d e t e c t e d , n o t h i n g i s o u t p u t . Detection of the Ponto-Medullary Junction (PMJ). This method is based on a machine-learning algorithm published in (Gros et al. 2018, Medical Image Analysis, https://doi.org/10.1016/j.media.2017.12.001). Two models are available: one for T1w-like and another for T2w-like images. If the PMJ is detected from the input image, a NIfTI mask is output (”*_pmj.nii.gz”) with one voxel (value=50) located at the predicted PMJ position. If the PMJ is not detected, nothing is output.

usage: sct_detect_pmj -i <file> -c {t1,t2} [-s <file>] [-ofolder <folder>]
                      [-o <file>] [-qc <str>] [-qc-dataset <str>]
                      [-qc-subject <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 1 , t 2 Possible choices: t1, t2

T y p e o f i m a g e c o n t r a s t , i f y o u r c o n t r a s t i s n o t i n t h e a v a i l a b l e o p t i o n s ( t 1 , t 2 ) , u s e t 1 ( c o r d b r i g h t / C S F d a r k ) o r t 2 ( c o r d d a r k / C S F b r i g h t ) Type of image contrast, if your contrast is not in the available options (t1, t2), use t1 (cord bright/ CSF dark) or t2 (cord dark / CSF bright)

OPTIONAL ARGUMENTS¶

-s: S C s e g m e n t a t i o n o r c e n t e r l i n e m a s k . P r o v i d e t h i s m a s k h e l p s t h e d e t e c t i o n o f t h e P M J b y i n d i c a t i n g t h e p o s i t i o n o f t h e S C i n t h e R i g h t - t o - L e f t d i r e c t i o n . E x a m p l e : ` t 2 _ s e g . n i i . g z ` SC segmentation or centerline mask. Provide this mask helps the detection of the PMJ by indicating the position of the SC in the Right-to-Left direction. Example: t2_seg.nii.gz
-ofolder: O u t p u t f o l d e r . E x a m p l e : ` M y _ O u t p u t _ F o l d e r ` Output folder. Example: My_Output_Folder
-o: O u t p u t f i l e n a m e . E x a m p l e : ` p m j . n i i . g z ` Output filename. Example: pmj.nii.gz
-qc: T h e p a t h w h e r e t h e q u a l i t y c o n t r o l g e n e r a t e d c o n t e n t w i l l b e s a v e d . The path where the quality control generated content will be saved.
-qc-dataset: I f p r o v i d e d , t h i s s t r i n g w i l l b e m e n t i o n e d i n t h e Q C r e p o r t a s t h e d a t a s e t t h e p r o c e s s w a s r u n o n . If provided, this string will be mentioned in the QC report as the dataset the process was run on.
-qc-subject: I f p r o v i d e d , t h i s s t r i n g w i l l b e m e n t i o n e d i n t h e Q C r e p o r t a s t h e s u b j e c t t h e p r o c e s s w a s r u n o n . If provided, this string will be mentioned in the QC report as the subject the process was run on.

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