sct_compute_mtsat

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> [-h] [-trmt <float>]
                         [-trpd <float>] [-trt1 <float>] [-famt <float>]
                         [-fapd <float>] [-fat1 <float>] [-b1map <file>]
                         [-omtsat <str>] [-ot1map <str>] [-v <int>]

MANDATORY ARGUMENTS

-mt

Image with MT_ON

-pd

Image PD weighted (typically, the MT_OFF)

-t1

Image T1-weighted

OPTIONAL ARGUMENTS

-trmt

TR [in s] for the MT image (MT on). By default, will be fetch from the json sidecar (if it exists).

-trpd

TR [in s] for proton density weighted image (MT off). By default, will be fetch from the json sidecar (if it exists).

-trt1

TR [in s] for T1-weighted image. By default, will be fetch from the json sidecar (if it exists).

-famt

Flip angle [in deg] for mt image. By default, will be fetch from the json sidecar (if it exists).

-fapd

Flip angle [in deg] for pd image. By default, will be fetch from the json sidecar (if it exists).

-fat1

Flip angle [in deg] for t1 image. By default, will be fetch from the json sidecar (if it exists).

-b1map

B1 map

-omtsat

Output file for MTsat

Default: “mtsat.nii.gz”

-ot1map

Output file for T1map

Default: “t1map.nii.gz”

-v

Possible choices: 0, 1, 2

Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode

Default: 1