Provided by: cmtk_3.3.1-1.2build1_amd64
dwi_mask_bad_slices - Find bad slices in set of diffusion-weighted images.
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.
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]
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
Report bugs at http://nitrc.org/projects/cmtk/
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.