NAME

       interleaved_bad_slices  -  Find bad slices in a time series of interleaved images (e.g., a
       resting-state fMRI series).

SYNOPSIS

       interleaved_bad_slices ImagePaths

DESCRIPTION

       This tool reads a time series of 3D images and detects outliers.

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
       --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
       --metric
            Image-to-image similarity metric to compare neighbouring slices.   Supported  values:
            "ncc", "rms", where the default is "ncc", or use one of the following:

            --ncc
                 Normalized cross correlation.  [This is the default]

            --rms
                 Root of mean squared differences.

       --stdev-thresh <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
       --bad-slices-thresh <none>
            Minimum number of detected bad slices before  reporting  a  volume  (only  number  of
            detected  bad  slices  is  reported in this case, rather than each slice separately).
            [Default: 0]

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.