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PROGRAM:

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)
--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

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