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

       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.

CMTK 3.3.1p2                                       Feb 26 2025                         interleaved_bad_slices(1)

       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/

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

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

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

GlobalToolkitOptions(thesearesharedbyallCMTKtools)--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).

   InputOptions--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 [Thisisthedefault]--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 [Thisisthedefault]BadSliceDetection--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.  [Thisisthedefault]--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]OutputOptions--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]

interleaved_bad_slices ImagePaths