.TH interleaved_bad_slices "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
interleaved_bad_slices \- Find bad slices in a time series of interleaved images (e.g., a resting-state fMRI series).
.SH SYNOPSIS
\fBinterleaved_bad_slices\fR ImagePaths 
.SH DESCRIPTION
This tool reads a time series of 3D images and detects outliers.
.SH OPTIONS
.SS Global Toolkit Options (these are shared by all CMTK tools)
.TP 5
\fB\-\-help\fR
Write list of basic command line options to standard output.
.TP 5
\fB\-\-help-all\fR
Write complete list of basic and advanced command line options to standard output.
.TP 5
\fB\-\-wiki\fR
Write list of command line options to standard output in MediaWiki markup.
.TP 5
\fB\-\-man\fR
Write man page source in 'nroff' markup to standard output.
.TP 5
\fB\-\-version\fR
Write toolkit version to standard output.
.TP 5
\fB\-\-echo\fR
Write the current command line to standard output.
.TP 5
\fB\-\-verbose-level\fR \fI<integer>\fR
Set verbosity level.
.TP 5
\fB\-\-verbose\fR, \fB\-v\fR
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
.TP 5
\fB\-\-threads\fR \fI<integer>\fR
Set maximum number of parallel threads (for POSIX threads and OpenMP).
.SS Input Options
.TP 5
\fB\-\-slice-orientation\fR
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:
.RS 5
.TP 5
\fB\-\-axial\fR
Axial slices
\fB[This is the default]\fR
.TP 5
\fB\-\-sagittal\fR
Sagittal slices
.TP 5
\fB\-\-coronal\fR
Coronal slices
.TP 5
\fB\-\-slice-x\fR
X coordinate axis is slice direction
.TP 5
\fB\-\-slice-y\fR
Y coordinate axis is slice direction
.TP 5
\fB\-\-slice-z\fR
Z coordinate axis is slice direction
\fB[This is the default]\fR
.RE
.SS Bad Slice Detection
.TP 5
\fB\-\-metric\fR
Image-to-image similarity metric to compare neighbouring slices.
Supported values: "ncc", "rms", where the default is "ncc", or use one of the following:
.RS 5
.TP 5
\fB\-\-ncc\fR
Normalized cross correlation.
\fB[This is the default]\fR
.TP 5
\fB\-\-rms\fR
Root of mean squared differences.
.RE
.TP 5
\fB\-\-stdev-thresh\fR \fI<double>\fR
Threshold for bad slice identification in units of intensity standard deviations over all corresponding slices from the remaining diffusion images.
.B [Default: 3]
.SS Output Options
.TP 5
\fB\-\-bad-slices-thresh\fR \fI<none>\fR
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).
.B [Default: 0]
.SH AUTHORS
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
.SH LICENSE
http://www.fsf.org/licensing/licenses/gpl.html
.SH BUGS
Report bugs at http://nitrc.org/projects/cmtk/
.SH 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.