NAME

       dwi_mask_bad_slices - Find bad slices in set of diffusion-weighted images.

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]

       --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]

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

BUGS

       Report bugs at http://nitrc.org/projects/cmtk/

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.