Executables¶

Synthesis Quality¶

create quality metric plots for all nifti images in directory

usage: synth-quality [-h] -s SYNTH_DIR [SYNTH_DIR ...] -t TRUTH_DIR
                     [-na NORM_ALGS [NORM_ALGS ...]]
                     [-sa SYNTH_ALGS [SYNTH_ALGS ...]] [-o OUTPUT_DIR]
                     [-m MASK_DIR] [-ot OUTPUT_TYPE] [-v] [--mean]

Required¶

`-s, --synth-dir`
	path to directory of synthesized images
`-t, --truth-dir`
	path to corresponding truth images

Optional¶

`-na, --norm-algs`
	normalizaiton algorithms, must be provided if multiple directories provided
`-sa, --synth-algs`
	synthesis algorithms, must be provided if multiple directories provided
`-o, --output-dir`
	directory to output the quality metric plots
`-m, --mask-dir`	optional directory of labels for images
`-ot, --output-type`
	type of output image to save (e.g., png, pdf, etc.) Default: “png”
`-v, --verbosity`
	increase output verbosity (e.g., -vv is more than -v) Default: 0
`--mean`	plot the mean of the quality metrics for the directory Default: False

Directory Viewer¶

create profile views of every nifti image in a directory

usage: directory-view [-h] -i IMG_DIR [-o OUTPUT_DIR] [-l LABEL_DIR]
                      [-f FIGSIZE [FIGSIZE ...]] [-ot OUTPUT_TYPE] [-a AXIS]
                      [-s SLICES [SLICES ...]] [--trim] [-v]

Required¶

-i, --img-dir

path to directory with images to be processed

Optional¶

`-o, --output-dir`
	directory to output the corresponding views
`-l, --label-dir`
	optional directory of labels for images
`-f, --figsize`	size of output image (two integers) Default: (8, 8)
`-ot, --output-type`
	type of output image to save (e.g., png, pdf, etc.) Default: “png”
`-a, --axis`	axis on which to take a slice Default: 0
`-s, --slices`	if provided (relative slices), plot these slices instead of ortho view
`--trim`	trim output image of blank/white space outside the plot Default: False
`-v, --verbosity`
	increase output verbosity (e.g., -vv is more than -v) Default: 0