|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).
DESCRIPTION¶This tool reads a time series of 3D images and detects outliers.
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.
- --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).
- 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.
- --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]
- --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.
|Jan 25 2019||CMTK 3.3.1p1|