sct_warp_template¶

T h i s f u n c t i o n w a r p s t h e t e m p l a t e a n d a l l a t l a s e s t o a d e s t i n a t i o n i m a g e . This function warps the template and all atlases to a destination image.

usage: sct_warp_template -d <file> -w <file> [-a <int>] [-s <int>]
                         [-ofolder <folder>] [-t <folder>] [-qc <folder>]
                         [-qc-dataset <str>] [-qc-subject <str>] [-histo <int>]
                         [-h] [-v <int>]

MANDATORY ARGUMENTS¶

-d: D e s t i n a t i o n i m a g e t h e t e m p l a t e w i l l b e w a r p e d t o . E x a m p l e : ` d w i _ m e a n . n i i . g z ` Destination image the template will be warped to. Example: dwi_mean.nii.gz
-w: W a r p i n g f i e l d . ` E x a m p l e : ` w a r p _ t e m p l a t e 2 d m r i . n i i . g z ` Warping field. Example: warp_template2dmri.nii.gz`

OPTIONAL ARGUMENTS¶

-a

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

W a r p a t l a s o f w h i t e m a t t e r . Warp atlas of white matter.

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

-s

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

W a r p s p i n a l l e v e l s . D E P R E C A T E D : A s o f S C T v 6 . 1 , p r o b a b i l i s t i c s p i n a l l e v e l s h a v e b e e n r e p l a c e d w i t h a s i n g l e i n t e g e r s p i n a l l e v e l f i l e , w h i c h c a n b e f o u n d i n s i d e o f t h e w a r p e d ‘ t e m p l a t e / ‘ f o l d e r . T h e ‘ - s ‘ o p t i o n i s n o l o n g e r n e e d e d . Warp spinal levels. DEPRECATED: As of SCT v6.1, probabilistic spinal levels have been replaced with a single integer spinal level file, which can be found inside of the warped ‘template/’ folder. The ‘-s’ option is no longer needed.

F o r m o r e i n f o r m a t i o n o n t h e r a t i o n a l e b e h i n d t h i s d e c i s i o n , p l e a s e r e f e r t o : For more information on the rationale behind this decision, please refer to:

h t t p s : / / g i t h u b . c o m / s p i n a l c o r d t o o l b o x / P A M 5 0 / i s s u e s / 1 6 https://github.com/spinalcordtoolbox/PAM50/issues/16
h t t p s : / / f o r u m . s p i n a l c o r d m r i . o r g / t / u p d a t i n g - s p i n a l - l e v e l s - f e e d b a c k - n e e d e d / 1 1 3 6 https://forum.spinalcordmri.org/t/updating-spinal-levels-feedback-needed/1136

D e f a u l t : ` ` 0 ` ` Default: 0

-ofolder

N a m e o f o u t p u t f o l d e r . Name of output folder.

D e f a u l t : ` ` ‘ l a b e l ‘ ` ` Default: 'label'

-t

P a t h t o t e m p l a t e . Path to template.

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 a t a / P A M 5 0 ‘ ` ` Default: '/home/docs/checkouts/readthedocs.org/user_builds/spinalcordtoolbox/checkouts/latest/data/PAM50'

-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.

-histo

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

W a r p h i s t o l o g y a t l a s f r o m D u v a l e t a l . N e u r o i m a g e 2 0 1 9 ( h t t p s : / / p u b m e d . n c b i . n l m . n i h . g o v / 3 0 3 2 6 2 9 6 / ) . Warp histology atlas from Duval et al. Neuroimage 2019 (https://pubmed.ncbi.nlm.nih.gov/30326296/).

D e f a u l t : ` ` 0 ` ` Default: 0

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