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.