Provided by: cmtk_3.0.0-1ubuntu1_amd64
interleaved_bad_slices - Find bad slices in a time series of interleaved images (e.g., a resting-state fMRI series).
This tool reads a time series of 3D images and detects outliers.
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]
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/
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.