Global Toolkit Options (these are shared by all CMTK tools)

--help

Write list of basic command line options to standard output.

--help-all

Write complete list of basic and advanced command line options to standard output.

--wiki

Write list of command line options to standard output in MediaWiki markup.

--man

Write man page source in 'nroff' markup to standard output.

--version

Write toolkit version to standard output.

--echo

Write the current command line to standard output.

--verbose-level <integer>

Set verbosity level.

--verbose, -v

Increment verbosity level by 1 (deprecated; supported for backward compatibility).

--threads <integer>

Set maximum number of parallel threads (for POSIX threads and OpenMP).

Input Options

--b0count <integer>

Number of b=0 images at the beginning of the image list. These are not included in the bad slice detection or masking, but are also written to the output directory for convenience. It is assumed that all b=0 images are at the beginning of the list of input images, but not at the end or in the middle. [Default: 0]

--slice-orientation

Define slice orientation of the diffusion images. Supported values: "axial", "sagittal", "coronal", "slice-x", "slice-y", "slice-z", where the default is "axial", or use one of the following:

Bad Slice Detection

--stdev <double>

Threshold for bad slice identification in units of intensity standard deviations over all corresponding slices from the remaining diffusion images. [Default: 3]

Output Options

--convert-to

Scalar data type for the output images. If your padding value is negative but your input data unsigned, for example, make sure to select a signed data type for the output. By default, the output data type is the same as the input type. Supported values: "char", "byte", "short", "ushort", "int", "uint", "float", "double", or use one of the following:

--padding-value <double>, -p <double>

Padding value to replace data of detected bad slices in output images. [Default: -1]

--bad-slice-statistics <string>, -s <string>

CSV file capturing the slice number and distance of bad slices. [Default: NONE]

--output-directory <string>, -o <string>

File system path for writing images with bad slices masked out (i.e., filled with a padding value). [Default: NONE]