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¶
- --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).
- --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
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.