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

MANDATORY ARGUMENTS

-mt

Image with MT_ON

-pd

Image PD weighted (typically, the MT_OFF)

-t1

Image T1-weighted

JSON SIDECAR OVERRIDES

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

TR [in s] for the MT image (MT on).

-trpd

TR [in s] for proton density weighted image (MT off).

-trt1

TR [in s] for the T1-weighted image.

-famt

Flip angle [in deg] for the MT-weighted image.

-fapd

Flip angle [in deg] for the PD-weighted image.

-fat1

Flip angle [in deg] for the T1-weighted image.

OPTIONAL ARGUMENTS

-b1map

B1 map

-omtsat

Output file for MTsat

Default: “mtsat.nii.gz”

-ot1map

Output file for T1map

Default: “t1map.nii.gz”

MISC ARGUMENTS

-v

Possible choices: 0, 1, 2

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

Default: 1

-profile-time

Enables time-based profiling of the program, dumping the results to the specified file.

If no file is specified, human-readable results are placed into a ‘time_profiling_results.txt’ document in the current directory (’/home/docs/checkouts/readthedocs.org/user_builds/spinalcordtoolbox/checkouts/stable/documentation/source’). If the specified file is a .prof file, the file will instead be in binary format, ready for use with common post-profiler utilities (such as snakeviz).

-trace-memory

Enables memory tracing of the program.

When active, a measure of the peak memory (in KiB) will be output to the file peak_memory.txt. Optionally, developers can also modify the SCT code to add additional snapshot_memory() calls. These calls will ‘snapshot’ the memory usage at that moment, saving the memory trace at that point into a second file (memory_snapshots.txt).

By default, both outputs will be placed in the current directory (’/home/docs/checkouts/readthedocs.org/user_builds/spinalcordtoolbox/checkouts/stable/documentation/source’). Optionally, you may provide an alternative directory (-trace-memory <dir_name>), in which case all files will be placed in that directory instead. Note that this WILL incur an overhead to runtime, so it is generally advised that you do not run this in conjunction with the time profiler or in time-sensitive contexts.