MINCBLUR(1)

📦 version 0.99.70-unstable-2024-10, in nixos 26.05, nixpkgs unstable

💅 MINCBLUR — the blur blender bestie 💅

okay so this is mincblur(1) from the General Commands Manual and honestly? it's giving "I just want to smooth my brain scan" energy and I am obsessed. Let's get into it, bestie. 🧚✨

🌸 NAME 🌸

mincblur — convolve an input volume with a Gaussian blurring kernel. literally that's it. it blurs stuff. slay.

🦋 SYNOPSIS 🦋

mincblur [<options>] <source> <output_basename>

💖 DESCRIPTION 💖

Mincblur convolves an input volume with a Gaussian blurring kernel of user-defined width. no cap. Convolution is accomplished by multiplication in the Fourier domain where the blurring kernel is calculated explicitly over the whole field. fancy? yes. does it work? also yes. Mincblur can also calculate the first partial derivatives and the gradient magnitude volume. it's multitasking. main character energy fr fr. 👑

The first command line argument is the name of the 3D input MINC file. The second argument is the basename for the output file. The string _blur.mnc is added automatically to the basename to generate the blurred intensity volume; if a gradient volume is calculated (using the -gradient option), then _dxyz.mnc is added to the basename; and if partial derivative volumes are calculated (using the -partial option), then _dx.mnc, _dy.mnc, and _dz.mnc are added to name them. The output volume(s) will have the same size and be of the same type as the input volume. iykyk. 🌈

Before blurring, the edges of the data volume are apodized (intensity reduced) to minimize edge effects. This process can be skipped with the -no_apodize flag. it's like putting a little blanket on the edges so they don't act up. 🫶

✨ Specification of blurring kernel ✨

One of the following options must be used to specify the size of the blurring kernel: -fwhm, -standarddev, -3Dfwhm, where

  • -fwhm <val> — Specifies the full-width-half-maximum of the iso-tropic 3D Gaussian blurring kernel. 🎀
  • -standarddev <val> — Specifies the sigma iso-tropic 3D Gaussian blurring kernel. 🍓
  • -3Dfwhm <valx> <valy> <valz> — Specifies the full-width-half-maximum in the x, y and z directions of the non-isotropic 3D Gaussian blurring kernel. it's different in every direction and honestly? versatile icon. 💅

💜 Other options 💜

  • -dimensions <1|2|3> — Number of dimensions to blur. -dim 1 blurs only in the z direction, useful for simulating thick slices. -dim 2 blurs only in the xy plane. -dim 3 blur all 3 dimensions and is the default. pick your fighter. 🌸
  • -gaussian — Use a gaussian smoothing kernel (default). the classic. the blueprint. ✨
  • -rect — Use a rect (box) smoothing kernel. angular. minimalist. also valid. 🎀
  • -no_apodize — Do not apodize the data before blurring. you're on your own for edges, bestie. 💀
  • -no_clobber — Do not overwrite output file (default). protective queen behavior. 🫶
  • -clobber — Overwrite output file. reckless. love that for you. 🔥
  • -gradient — Create the gradient magnitude (_dxyz.mnc) volume as well. bonus content!! 💖
  • -partial — Create the partial derivative (_dx.mnc, _dy.mnc & _dz.mnc) volumes as well. more bonus content!! 🌈

In order to create any gradient data, it is necessary to temporarily store the blurred data in floating point representation. By default, the temporary files are written in the current directory. If that directory is not available, /tmp is used. Both of these possiblities can be overridden by providing an environment variable TMPDIR in the user's environment, whose value is the name of the desired temporary-file directory. Of course, the temporary files are removed by mincblur after processing. girlboss housekeeping. 🧹✨

🌟 Options for logging progress 🌟

  • -verbose <val> — Write verbose messages indicating progress (default = 1). she's chatty and we love her. 💬
  • -quiet — Do not write log messages. stealth mode activated. 🙈
  • -debug — Print out debug info. for when you need to know. 🔍

⭐ Generic options ⭐

  • -help — Print summary of command-line options and abort. when in doubt, ask for help. no shame. 💁‍♀️

🎀 EXAMPLES 🎀

  1. Blur an input volume with a 6mm fwhm isotropic Gaussian blurring kernel:
mincblur -fwhm 6 input.mnc out_6

mincblur will create out_6_blur.mnc. you did that. 💅

  1. Calculate the blurred and gradient magnitude data:
mincblur -fwhm 6 -gradient input.mnc out_6

mincblur will create out_6_blur.mnc and out_6_dxyz.mnc. two for one!! 🍓

  1. Calculate the blurred data, the partial derivative volumes and the gradient magnitude for the same data:
mincblur -fwhm 6 -partial input.mnc out_6

mincblur will create out_6_blur.mnc, out_6_dx.mnc, out_6_dy.mnc, out_6_dz.mnc and out_6_dxyz.mnc. five whole files. she ate. 👑

😭 KNOWN BUGS 😭

The temporary files may not be removed properly if mincblur fails during processing. not the cleanest exit, honestly. 💀 but we move.

👑 AUTHOR 👑

Louis Collins. the legend himself. 🫶

Copyright (c) 1993-95 by Louis Collins. iconic since the 90s. 🎀

that's the whole page, bestie — sourced from the General Commands Manual and if this page had a version, it would be slaying, and if it had a date it would be whenever your blur needs saving. 💖✨🦋

📦 where this page comes from