mrs_tools

The command-line tool for manipulation of NIfTI-MRS files.

usage: mrs_tools [-h] [-v] {info,vis,merge,split,reorder,conjugate} ...

NIfTI-MRS (Magnetic Resonance Spectroscopy) tools

optional arguments:

-h, --help

show this help message and exit

-v, --version

show program’s version number and exit

subcommands:

Available tools

{info, vis, merge, split, reorder, conjugate}

info

Information about the NIfTI-MRS file.

usage: mrs_tools info [-h] FILE or list of FILEs [FILE or list of FILEs ...]`

positional arguments:

FILE or list of FILEs

NIfTI MRS file(s)

optional arguments:

-h, --help

show this help message and exit

vis

Quick visualisation of a NIfTI-MRS file or FSL-MRS basis set.

usage: mrs_tools vis [-h] [--ppmlim LOW HIGH] [--mask MASK] [--save SAVE] [--display_dim DISPLAY_DIM] [--no_mean] FILE or DIR

positional arguments:

FILE or DIR

NIfTI file or directory of basis sets

optional arguments:

-h, --help

show this help message and exit

--ppmlim LOW-HIGH

limit the fit to a freq range (default=(.2,4.2))

--mask MASK

Mask for MRSI

--save SAVE

Save fig to path

--display_dim

DISPLAY_DIM. A NIFTI-MRS tag. Do not average across this dimension.

--no_mean

Do not plot the mean signal line in the case of multiple spectra.

merge

Merge NIfTI-MRS along higher dimensions.

usage: mrs_tools merge [-h] --files FILES [FILES ...] --dim DIM [--newaxis] [--output OUTPUT][--filename FILENAME]

optional arguments:

-h, --help

show this help message and exit

--newaxis

Join files along a new axis (tag specified by –dim).

--output OUTPUT

output folder (defaults to current directory)

--filename FILENAME

Override output file name.

required arguments:

–files FILES [FILES …]

List of files to merge

--dim DIM

NIFTI-MRS dimension tag to merge across.

split

Split NIfTI-MRS along higher dimensions.

usage: mrs_tools split [-h] --file FILE --dim DIM (--indices INDICES [INDICES ...] | --index INDEX) [--output OUTPUT] [--filename FILENAME]

optional arguments:

-h, --help

show this help message and exit

–indices INDICES [INDICES …]

List of indices to extract into second file. All indices are zero-indexed.

--index INDEX

Index to split at (split after index, zero-indexed).

--output OUTPUT

output folder (defaults to current directory)

--filename FILENAME

Override output file names.

required arguments:

--file FILE

File to split

--dim DIM

NIFTI-MRS dimension tag to split across.

reorder

Reorder higher dimensions of NIfTI-MRS.

usage: mrs_tools reorder [-h] --file FILE --dim_order DIM_ORDER [DIM_ORDER ...] [--output OUTPUT] [--filename FILENAME]

optional arguments:

-h, --help

show this help message and exit

--output OUTPUT

output folder (defaults to current directory)

--filename FILENAME

Override output file names.

required arguments:

--file FILE

File to reorder

–dim_order DIM_ORDER [DIM_ORDER …]

NIFTI-MRS dimension tags in desired order. Enter as strings (min:1, max:3). Can create singleton dimension at end.

reshape

Reshapes the higher dimensions of a NIfTI-MRS file.

usage: mrs_tools reshape [-h] --file FILE --shape SHAPE [SHAPE ...] [--d5 D5] [--d6 D6] [--d7 D7] [--output OUTPUT] [--filename FILENAME]

optional arguments:

-h, --help

show this help message and exit

--d5 D5

5th dimension tag (e.g. DIM_DYN).

--d6 D6

6th dimension tag (e.g. DIM_DYN).

--d7 D7

7th dimension tag (e.g. DIM_DYN).

--output OUTPUT

output folder (defaults to current directory)

--filename FILENAME

Override output file names.

required arguments:

--file FILE

File to reshape

–shape SHAPE [SHAPE …]

Numpy-like target shape.Enter as integers, -1 is used for any. Only enter shape for higher (5th-7th) dimensions.

conjugate

Conjugate data to correct phase/frequency convention in a NIfTI-MRS file.

usage: mrs_tools conjugate [-h] --file FILE [--output OUTPUT] [--filename FILENAME]

optional arguments:

-h, --help

show this help message and exit

--output OUTPUT

output folder (defaults to current directory)

--filename FILENAME

Override output file names.

required arguments:

--file FILE

File to conjugate