mia-2dmyocard-ica(1)

📦
version 2.4.7 · 3 versions
, in debian bookworm, ubuntu noble

💖 mia-2dmyocard-ica — run an ICA analysis on a series of 2D images 💖

okay bestie, so you know how your myocardial perfusion images are just vibing there, all wobbly and un-registered? yeah. this little tool right here (it lives in the General Commands Manual, section 1, iykyk) runs an ICA on a whole series of 2D images so you can build synthetic references that you then use for motion correction via image registration. it's giving ✨ preprocessing icon ✨.

🎀 SYNOPSIS 🎀

mia-2dmyocard-ica -i <in-base> [options]

that's it. that's the whole vibe. one required flag and then you go feral with the options.

🌸 DESCRIPTION 🌸

okay so listen. mia-2dmyocard-ica is the program you use to run an ICA on a series of myocardial perfusion images, and the whole point is to create synthetic references that can be used for motion correction by image registration. slay.

but here's the tea 🫖 — if your actual goal is a full motion compensation, then honestly bestie, it's better to make a segmentation set and use mia-2dmyoica-nonrigid instead. and if your input data is given by means of a segmentation set, then you can also use mia-2dmyocard-icaseries. options on options, we love to see it.

so what is this one for then? this program is essentially used to test different options on how to run the ICA for reference image creation. it's the experimental bestie, the tester, the "let me try something" girlie. periodt. 💅

✨ OPTIONS ✨

🦋 Main Character Options

  • -i, --in-base=(required, input); io — the input file name, and it follows the pattern nameXXXX.ext where X=numbers. for supported file types, go peek at PLUGINS:2dimage/io below 👇
  • --coefs= — output the mixing coefficients to this file. cute, let's keep receipts.
  • -o, --out-base=(output); string — the output file name base.
  • -t, --type=exr — the output file type.

Supported values are: -, @, BMP, DCM, EXR, JPEG, JPG, PNG, RAW, TIF, TIFF, V, VISTA, bmp, dcm, exr, jpeg, jpg, png, raw, tif, tiff, v, vista, `` (yes, lowercase versions count, they're all valid, no cap).

  • -k, --skip=2 — skip images at the beginning of the series. bye girlies, you're not invited.
  • -e, --end=60 — the last image in the series.
  • -C, --components=0 — the number of components. and 0 means "estimate it automatically", which is very main character energy of it. 👑
  • -m, --strip-mean — strip the mean image from the series.
  • -f, --save-features= — save the feature image.
  • -p, --strip-periodic — strip only the periodic component.
  • --fastica=internal — which FastICA implementation to use. for supported plugins, check PLUGINS:fastica/implementation below 👇
  • -x, --max-ica-iterations=0 — the max ICA solver iterations.
  • -n, --ica-normalize — ica_normalize the feature images.
  • --all-features= — save all feature images to this location. all of them. every single one. no crumbs. 🔥
  • -L, --LV-crop-amp=0 — the LV crop mask amplification, where 0.0 = don't crop. so if you leave it at zero, we're not cropping anything, bestie.

💜 Help & Info

  • -V, --verbose=warning — verbosity of output; it prints messages of the given level and higher priorities. the supported priorities, starting at the lowest level, are:
    • trace ‐ Function call trace
    • debug ‐ Debug output
    • info ‐ Low level messages
    • message ‐ Normal messages
    • warning ‐ Warnings
    • fail ‐ Report test failures
    • error ‐ Report errors
    • fatal ‐ Report only fatal errors
  • --copyright — print copyright information.
  • -h, --help — print this help.
  • -?, --usage — print a short help.
  • --version — print the version number and exit. (a goodbye girlie.)

🌈 Processing

  • --threads=-1 — the maximum number of threads to use for processing. this number should be lower than or equal to the number of logical processor cores in the machine. (-1: automatic estimation). so basically -1 = "figure it out yourself, queen."

🧚 PLUGINS: 2dimage/io 🧚

these are all the file formats your images can show up in, and what they support. read carefully, bestie, some of these are read-only or ignore your colour table:

  • bmp — BMP 2D-image input/output support. the plug-in supports reading and writing of binary images and 8-bit gray scale images. read-only support is provided for 4-bit gray scale images. the colour table is ignored and the pixel values are taken as literal gray scale values.

Recognized file extensions: .BMP, .bmp

Supported element types:

  • binary data, unsigned 8 bit
  • datapool — virtual IO to and from the internal data pool.

Recognized file extensions: .@

  • dicom — 2D image io for DICOM.

Recognized file extensions: .DCM, .dcm

Supported element types:

  • signed 16 bit, unsigned 16 bit
  • exr — a 2dimage io plugin for OpenEXR images.

Recognized file extensions: .EXR, .exr

Supported element types:

  • unsigned 32 bit, floating point 32 bit
  • jpg — a 2dimage io plugin for jpeg gray scale images.

Recognized file extensions: .JPEG, .JPG, .jpeg, .jpg

Supported element types:

  • unsigned 8 bit
  • png — a 2dimage io plugin for png images.

Recognized file extensions: .PNG, .png

Supported element types:

  • binary data, unsigned 8 bit, unsigned 16 bit
  • raw — RAW 2D-image output support.

Recognized file extensions: .RAW, .raw

Supported element types:

  • binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit
  • tif — TIFF 2D-image input/output support.

Recognized file extensions: .TIF, .TIFF, .tif, .tiff

Supported element types:

  • binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit
  • vista — a 2dimage io plugin for vista images.

Recognized file extensions: .-, .V, .VISTA, .v, .vista

Supported element types:

  • binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit

🎀 PLUGINS: fastica/implementation 🎀

your two FastICA options, bestie. pick your fighter:

  • internal — this is the MIA implementation of the FastICA algorithm.

(no parameters)

  • itpp — this is the IT++ implementation of the FastICA algorithm.

(no parameters)

⭐ EXAMPLE ⭐

okay here's the moment you've been waiting for. the goal: evaluate the synthetic references from images imageXXXX.exr and save them to refXXXX.exr by using five independent components, mean stripping, normalizing, and skipping 2 images. watch her work:

mia-2dmyocard-ica -i imageXXXX.exr -o ref -k 2 -C 5 -m -n

ate and left no crumbs. 💅

👑 AUTHOR(s) 👑

Gert Wollny

This software is Copyright (c) 1999‐2015 Leipzig, Germany and Madrid, Spain. It comes with ABSOLUTELY NO WARRANTY and you may redistribute it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 (or later). For more information run the program with the option --copyright.

fr fr, no warranty. like, none. so don't come for anybody if it goes sideways. 💀

and that's the whole page, bestie! this one shipped as part of the v2.4.7 user commands collection, dated with that v2.4.7 energy — so go run your ICA, make those synthetic references, and remember: it's mia-2dmyocard-ica(1), not to be confused with her cousins. mwah! 🫶🌸✨

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