interle..._slices(1)

✨ interleaved_bad_slices ✨

okay bestie, so this one lives in section 1 of the manual (that's the "run it in your shell" section, iykyk) 💅 and it's a whole CMTK tool situation. Let's get into it.

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🌸 NAME 🌸

interleaved_bad_slices — find bad slices in a time series of interleaved images (like, say, a resting-state fMRI series) 💖

🦋 SYNOPSIS 🦋

interleaved_bad_slices ImagePaths

🌈 DESCRIPTION 🌈

So basically this tool reads a time series of 3D images and detects outliers. That's the whole vibe. It's giving "quality control but make it automatic." 👑

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🎀 OPTIONS 🎀

💜 Global Toolkit Options (these are shared by all CMTK tools)

Like, every CMTK tool has these. They're the group-chat regulars. 🫶

• --help — writes the list of basic command line options to standard output. baby's first flag 💖
• --help-all — writes the complete list of basic and advanced command line options to standard output. the deluxe edition ✨
• --wiki — writes the list of command line options to standard output in MediaWiki markup.
• --man — writes man page source in 'nroff' markup to standard output.
• --version — writes toolkit version to standard output.
• --echo — writes 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). ngl she's old but she's still here 🙈
• --threads <integer> — set maximum number of parallel threads (for POSIX threads and OpenMP). parallelize and slay 🔥

🦋 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 just use one of these instead:
  • --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 these instead:
  • --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] literally the "how bad is bad" dial 🚨

🌸 Output Options 🌸

• --bad-slices-thresh <none> — minimum number of detected bad slices before reporting a volume (only the number of detected bad slices is reported in this case, rather than each slice separately). [Default: 0] so like, set this and she stops yapping about every single slice and just gives you the count 🫶

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💖 AUTHORS 💖

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko. the whole squad, no cap 👑

⭐ LICENSE ⭐

http://www.fsf.org/licensing/licenses/gpl.html

💀 BUGS 💀

Report bugs at http://nitrc.org/projects/cmtk/ — please actually do it, not me side-eyeing the code silently 🙈

🌈 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. funding icons only 💅✨

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okay and for the cute sign-off: this whole page is CMTK 3.3.1p2, dated Jun 24 2026 🌸 and yeah, the manual name up top (interleaved_bad_slices, section 1) is the whole reason we're here. periodt. 💖