---
name: "cmtk-interleaved_bad_slices"
section: "1"
platform: "linux"
package: "cmtk"
version: "3.3.1p2+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cmtk-interleaved_bad_slices"
---

# cmtk-interleaved\_bad\_slices(1)

Find bad slices in a time series of interleaved images (e.g., a resting-state fMRI series).

## 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

## 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.