sct_fmri_compute_tsnr

C o m p u t e t e m p o r a l S N R ( t S N R ) i n f M R I t i m e s e r i e s . Compute temporal SNR (tSNR) in fMRI time series.

usage: sct_fmri_compute_tsnr -i <file> [-m <file>] [-o <file>] [-qc <str>]
                             [-qc-dataset <str>] [-qc-subject <str>] [-h]
                             [-v <int>]

MANDATORY ARGUMENTS

-i

I n p u t f M R I d a t a . E x a m p l e : ` f m r i . n i i . g z ` Input fMRI data. Example: fmri.nii.gz

OPTIONAL ARGUMENTS

-m

B i n a r y ( o r w e i g h t e d ) m a s k w i t h i n w h i c h t S N R w i l l b e a v e r a g e d . E x a m p l e : ` f m r i _ m o c o _ m e a n _ s e g . n i i . g z ` Binary (or weighted) mask within which tSNR will be averaged. Example: fmri_moco_mean_seg.nii.gz

-o

t S N R d a t a o u t p u t f i l e . E x a m p l e : ` f m r i _ t s n r . n i i . g z ` tSNR data output file. Example: fmri_tsnr.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 . N o t e : T h e ` - m ` p a r a m e t e r i s r e q u i r e d t o g e n e r a t e t h e Q C r e p o r t , a s i t i s n e c e s s a r y t o c e n t e r t h e Q C o n t h e r e g i o n o f i n t e r e s t . The path where the quality control generated content will be saved. Note: The -m parameter is required to generate the QC report, as it is necessary to center the QC on the region of interest.

-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