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interleaved_bad_slices(1) The Computational Morphometry Toolkit interleaved_bad_slices(1)

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)

Write list of basic command line options to standard output.
Write complete list of basic and advanced command line options to standard output.
Write list of command line options to standard output in MediaWiki markup.
Write man page source in 'nroff' markup to standard output.
Write toolkit version to standard output.
Write the current command line to standard output.
Set verbosity level.
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
Set maximum number of parallel threads (for POSIX threads and OpenMP).

Input Options

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 slices [This is the default]
Sagittal slices
Coronal slices
X coordinate axis is slice direction
Y coordinate axis is slice direction
Z coordinate axis is slice direction [This is the default]

Bad Slice Detection

Image-to-image similarity metric to compare neighbouring slices. Supported values: "ncc", "rms", where the default is "ncc", or use one of the following:
Normalized cross correlation. [This is the default]
Root of mean squared differences.
Threshold for bad slice identification in units of intensity standard deviations over all corresponding slices from the remaining diffusion images. [Default: 3]

Output Options

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.

Jun 6 2022 CMTK 3.3.1p2