SYNOPSIS

dwi_mask_bad_slices DiffusionImagePaths

DESCRIPTION

This tool reads a set of 3D diffusion-weighted MR images and finds bad slices. A bad slice in a diffusion image is detected as one whose mean intensity is outside a specified interval around the mean of the means of all corresponding slices from the remaining diffusion images.

OPTIONS

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:

--axial

Axial slices [This is the default]

--sagittal

Sagittal slices

--coronal

Coronal slices

--slice-x

X coordinate axis is slice direction

--slice-y

Y coordinate axis is slice direction

--slice-z

Z coordinate axis is slice direction [This is the default]

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:

--char

8 bits, signed

--byte

8 bits, unsigned

--short

16 bits, signed

--ushort

16 bits, unsigned

--int

32 bits signed

--uint

32 bits unsigned

--float

32 bits floating point

--double

64 bits floating point

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

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

--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]

AUTHORS

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko

LICENSE

http://www.fsf.org/licensing/licenses/gpl.html

ACKNOWLEDGMENTS

CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium on Alcohol and Neurodevelopment in Adolescence (N-CANDA): Data Integration Component. From April 2009 through September 2011, CMTK development and maintenance was supported by the NIBIB under Grant EB008381.