mrbias(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

💖 mrbias(1) — MR Image Intensity Bias Field Correction 💖

okay bestie, sit down, hydrate, because we're about to talk about mrbias from The Computational Morphometry Toolkit (that's CMTK, and yes it's iconic). this is a section-1 manual page and it's about to become your new obsession 🎀

🌸 NAME 🌸

mrbias — MR Image Intensity Bias Field Correction 👑

✨ SYNOPSIS ✨

mrbias InputImage OutputImage

🦋 DESCRIPTION 🦋

so like. MR images have this whole intensity inhomogeneity artifact situation going on — the vibes are uneven, the brightness is doing whatever it wants 😭. mrbias fixes that. it corrects those intensity inhomogeneity artifacts using a bias field that gets estimated via entropy minimization. that's it, that's the whole glow-up. periodt 💅

🌈 OPTIONS 🌈

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

these are the universal faves — every CMTK tool has them, no cap.

  • --help — dumps the list of basic command line options to standard output ✨
  • --help-all — the director's cut: the complete list of basic and advanced command line options, straight to standard output 💖
  • --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 📜
  • --xml — writes the command line syntax specification in XML markup (this one's for Slicer integration) 🔌
  • --version — writes the toolkit version to standard output 🏷️
  • --echo — writes the current command line to standard output 📣
  • --verbose-level <integer> — sets the verbosity level 🔉
  • --verbose, -v — increments the verbosity level by 1. deprecated, bestie — it's only hanging around for backward compatibility 🙈
  • --threads <integer> — sets the maximum number of parallel threads (for POSIX threads and OpenMP) 🧵

🎀 Bias Field Parameterization 🎀

this is where you tell it how extra the bias field should be.

  • --degree-add <integer>, -A <integer> — polynomial degree for additive correction. [Default: 0]
  • --degree-mul <integer>, -M <integer> — polynomial degree for multiplicative correction. [Default: 2]
  • --incremental, -I — incrementally increase polynomial degrees 📈

🍓 Input Image Preprocessing 🍓

get your input image cute and ready before the main event.

  • --set-padding-value <double> — set the padding value for the input intensity image. pixels with this value get ignored, byeeeee 👋 [Default: disabled]
  • --mask <labelmap-path>, -m <labelmap-path> — binary mask image filename 🎭 [Default: NONE]
  • --thresh-min <float>, -t <float> — minimum intensity threshold for image foreground. [Default: disabled]
  • --thresh-max <float>, -T <float> — minimum intensity threshold for image foreground. [Default: disabled] (yes, it says "minimum" for both — that's literally what the page says, i'm just the messenger 🙈)
  • --thresh-auto — automatic minimum intensity threshold selection for image foreground, using an estimate of image noise level 🤖
  • --thresh-otsu-nbins <integer> — if this is a positive integer, use automatic minimum intensity threshold selection for image foreground by Otsu thresholding with the given number of histogram bins 📊 [Default: 0]

🧚 Entropy Estimation Settings 🧚

the math era. we love her.

  • --log-intensities, -L — use log intensities for entropy estimation 🪵
  • --sampling-density <float>, -s <float> — image sampling density, so you only use a subset of image pixels 🎯 [Default: disabled]
  • --num-bins <integer>, -n <integer> — number of histogram bins for entropy estimation 🗂️ [Default: 256]

⭐ Optimization Algorithm Settings ⭐

how hard it's gonna look for the answer.

  • --step-max <double> — maximum (initial) search step size 🔍 [Default: 1]
  • --step-min <double> — minimum (final) search step size 🐜 [Default: 0.1]

💜 Input and Output Options 💜

files in, files out, main character energy.

  • --import-bias-add <image-path> — import additive bias field (this disables optimization, fyi). [Default: NONE]
  • --import-bias-mul <image-path> — import multiplicative bias field (this also disables optimization). [Default: NONE]
  • --write-bias-add <image-path> — file name for output of the additive bias field. [Default: NONE]
  • --write-bias-mul <image-path> — file name for output of the multiplicative bias field. [Default: NONE]
  • --write-float, -F — write the output image with floating point pixel data 💾. if you don't pass this, the input data type is used.

🔥 Image/Transformation Database 🔥

  • --db <string> — path to the image/transformation database that should be updated with the newly created image 🗄️ [Default: NONE]

🌟 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/ — they want the feedback, bestie, tell them everything 🐛

🙌 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. iconic funding behavior, honestly 💖

and that's the whole page, bestie!! this was CMTK 3.3.1p2, dated Jun 24 2026, and it's still serving mrbias(1) realness. go correct some bias fields, you've got this 🦋✨💅

📦 where this page comes from