sct_dmri_compute_dti

C o m p u t e D i f f u s i o n T e n s o r I m a g e s ( D T I ) u s i n g d i p y . Compute Diffusion Tensor Images (DTI) using dipy.

usage: sct_dmri_compute_dti -i <file> -bval <file> -bvec <file>
                            [-method {standard,restore}] [-evecs {0,1}]
                            [-m <file>] [-o <str>] [-h] [-v <int>]

MANDATORY ARGUMENTS

-i

I n p u t 4 d f i l e . E x a m p l e : ` d m r i . n i i . g z ` Input 4d file. Example: dmri.nii.gz

-bval

B v a l s f i l e . E x a m p l e : ` b v a l s . t x t ` Bvals file. Example: bvals.txt

-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

-method

P o s s i b l e c h o i c e s : s t a n d a r d , r e s t o r e Possible choices: standard, restore

T y p e o f m e t h o d t o c a l c u l a t e t h e d i f f u s i o n t e n s o r : Type of method to calculate the diffusion tensor:

  • ` s t a n d a r d : ` S t a n d a r d e q u a t i o n [ B a s s e r , B i o p h y s J 1 9 9 4 ] standard: Standard equation [Basser, Biophys J 1994]

  • ` r e s t o r e ` : R o b u s t f i t t i n g w i t h o u t l i e r d e t e c t i o n [ C h a n g , M R M 2 0 0 5 ] restore: Robust fitting with outlier detection [Chang, MRM 2005]

D e f a u l t : ` ` ‘ s t a n d a r d ‘ ` ` Default: 'standard'

-evecs

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

O u t p u t t e n s o r e i g e n v e c t o r s a n d e i g e n v a l u e s . Output tensor eigenvectors and eigenvalues.

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

-m

M a s k u s e d t o c o m p u t e D T I i n f o r f a s t e r p r o c e s s i n g . E x a m p l e : ` m a s k . n i i . g z ` Mask used to compute DTI in for faster processing. Example: mask.nii.gz

-o

O u t p u t p r e f i x . Output prefix.

D e f a u l t : ` ` ‘ d t i _ ‘ ` ` Default: 'dti_'

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