interleaved_bad_slices(1) 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

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.