sct_compute_mtsat

C o m p u t e M T s a t a n d T 1 m a p . R e f e r e n c e : H e l m s G , D a t h e H , K a l l e n b e r g K , D e c h e n t P . H i g h - r e s o l u t i o n m a p s o f m a g n e t i z a t i o n t r a n s f e r w i t h i n h e r e n t c o r r e c t i o n f o r R F i n h o m o g e n e i t y a n d T 1 r e l a x a t i o n o b t a i n e d f r o m 3 D F L A S H M R I . M a g n R e s o n M e d 2 0 0 8 ; 6 0 ( 6 ) : 1 3 9 6 - 1 4 0 7 . Compute MTsat and T1map. Reference: Helms G, Dathe H, Kallenberg K, Dechent P. High-resolution maps of magnetization transfer with inherent correction for RF inhomogeneity and T1 relaxation obtained from 3D FLASH MRI. Magn Reson Med 2008;60(6):1396-1407.

usage: sct_compute_mtsat -mt <file> -pd <file> -t1 <file> [-trmt <float>]
                         [-trpd <float>] [-trt1 <float>] [-famt <float>]
                         [-fapd <float>] [-fat1 <float>] [-b1map <file>]
                         [-omtsat <str>] [-ot1map <str>] [-h] [-v <int>]

MANDATORY ARGUMENTS

-mt

I m a g e w i t h M T _ O N Image with MT_ON

-pd

I m a g e P D w e i g h t e d ( t y p i c a l l y , t h e M T _ O F F ) Image PD weighted (typically, the MT_OFF)

-t1

I m a g e T 1 - w e i g h t e d Image T1-weighted

JSON SIDECAR OVERRIDES

A n y a r g u m e n t s w i t h i n t h i s g r o u p w i l l o v e r r i d e t h e i r c o r r e s p o n d i n g v a l u e s i n t h e J S O N s i d e - c a r f i l e s o f t h e M R I s e q u e n c e s y o u h a v e p r o v i d e d . O t h e r w i s e , a l l v a l u e s w i l l b e f e t c h e d f r o m t h e a s s o c i a t e d J S O N s i d e c a r , a s s u m i n g i t e x i s t s . I f n o t , y o u s h o u l d p r o v i d e t h e c o r r e s p o n d i n g m e t r i c s u s i n g t h e s e a r g u m e n t s . Any arguments within this group will override their corresponding values in the JSON side-car files of the MRI sequences you have provided. Otherwise, all values will be fetched from the associated JSON sidecar, assuming it exists. If not, you should provide the corresponding metrics using these arguments.

-trmt

T R [ i n s ] f o r t h e M T i m a g e ( M T o n ) . TR [in s] for the MT image (MT on).

-trpd

T R [ i n s ] f o r p r o t o n d e n s i t y w e i g h t e d i m a g e ( M T o f f ) . TR [in s] for proton density weighted image (MT off).

-trt1

T R [ i n s ] f o r t h e T 1 - w e i g h t e d i m a g e . TR [in s] for the T1-weighted image.

-famt

F l i p a n g l e [ i n d e g ] f o r t h e M T - w e i g h t e d i m a g e . Flip angle [in deg] for the MT-weighted image.

-fapd

F l i p a n g l e [ i n d e g ] f o r t h e P D - w e i g h t e d i m a g e . Flip angle [in deg] for the PD-weighted image.

-fat1

F l i p a n g l e [ i n d e g ] f o r t h e T 1 - w e i g h t e d i m a g e . Flip angle [in deg] for the T1-weighted image.

OPTIONAL ARGUMENTS

-b1map

B 1 m a p B1 map

-omtsat

O u t p u t f i l e f o r M T s a t Output file for MTsat

D e f a u l t : ` ` ‘ m t s a t . n i i . g z ‘ ` ` Default: 'mtsat.nii.gz'

-ot1map

O u t p u t f i l e f o r T 1 m a p Output file for T1map

D e f a u l t : ` ` ‘ t 1 m a p . n i i . g z ‘ ` ` Default: 't1map.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