sct_dmri_separate_b0_and_dwi¶

S e p a r a t e b = 0 a n d D W i m a g e s f r o m d i f f u s i o n d a t a s e t . T h e o u t p u t f i l e s w i l l h a v e a s u f f i x ( _ b 0 a n d _ d w i ) a p p e n d e d t o t h e i n p u t f i l e n a m e . Separate b=0 and DW images from diffusion dataset. The output files will have a suffix (_b0 and _dwi) appended to the input file name.

usage: sct_dmri_separate_b0_and_dwi -i <file> -bvec <file> [-a {0,1}]
                                    [-bval <file>] [-bvalmin <float>]
                                    [-ofolder <folder>] [-h] [-v <int>]
                                    [-r {0,1}]

MANDATORY ARGUMENTS¶

-i: D i f f u s i o n d a t a . E x a m p l e : ` d m r i . n i i . g z ` Diffusion data. Example: dmri.nii.gz
-bvec: B v e c s f i l e . E x a m p l e : ` b v e c s . t x t ` Bvecs file. Example: bvecs.txt

OPTIONAL ARGUMENTS¶

-a

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

A v e r a g e b = 0 a n d D W I d a t a . 0 = n o , 1 = y e s Average b=0 and DWI data. 0 = no, 1 = yes

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

-bval

b v a l s f i l e . U s e d t o i d e n t i f y l o w b - v a l u e s ( i n c a s e d i f f e r e n t f r o m 0 ) . E x a m p l e : ` b v a l s . t x t ` bvals file. Used to identify low b-values (in case different from 0). Example: bvals.txt

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

-bvalmin

B - v a l u e t h r e s h o l d ( i n s / m m 2 ) b e l o w w h i c h d a t a i s c o n s i d e r e d a s b = 0 . E x a m p l e : ` 5 0 . 0 ` B-value threshold (in s/mm2) below which data is considered as b=0. Example: 50.0

-ofolder

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

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

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