mia-2dmyocard-icaseries(1)

mia-2dmyocard-icaseries 💖

okay bestie, welcome to the General Commands Manual entry for mia-2dmyocard-icaseries(1), and omg you're gonna love this one. it's giving math girlie does cardiology. 🫶

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✨ NAME ✨

mia-2dmyocard-icaseries — Run an ICA analysis on a series of 2D images 🧠💅

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✨ SYNOPSIS ✨

mia-2dmyocard-icaseries -i <in-file> [options]

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✨ DESCRIPTION ✨

so basically, mia-2dmyocard-icaseries runs an ICA (independent component analysis, iykyk) on a series of myocardial perfusion images that you hand over inside a segmentation set. the whole point? it cooks up synthetic references that you can then use for motion correction via image registration. slay. 🔥

no cap though — if your actual goal is a full motion compensation, bestie, please go run mia-2dmyoica-nonrigid instead. this program is essentially the same thing minus the registration bits. it's the vibe without the commitment. 🙈

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✨ OPTIONS ✨

🌸 File-IO

• -i, --in-file=(required, input); string — the input perfusion data set. yes it's required, yes you must give it, no exceptions boo. 💖
• -r, --references=(output); string — file name base for the reference images. the image type and the numbering scheme get borrowed straight from your input images, cute right. ✨
• -c, --save-cropped=(output); string — saves the cropped version of the original set to this file. the image files use the stem of the name as the file name base. 🎀
• --save-feature=(output); string — saves the feature images that come out of the ICA, plus some intermediate images used for the RV-LV segmentation, to PNG files using the given file name base. it also saves the coefficients of the initial best and the final IC mixing matrix. obsessed. 🌈

🌸 Help & Info

• -V, --verbose=warning — verbosity of output. 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

🌸 ICA

• --fastica=internal — the FastICA implementation to be used. for supported plugins see PLUGINS:fastica/implementation. 👑
• -C, --components=0 — ICA components. 0 means automatic estimation, so it just figures it out for you. main character energy tbh.
• --normalize — normalized ICs ✨
• --no-meanstrip — don't strip the mean from the mixing curves
• -s, --segscale=1.4 — segment and scale the crop box around the LV. 0 means no segmentation at all.
• -k, --skip=0 — skip images at the beginning of the series, since they're of other modalities. lowkey a lifesaver.
• -m, --max-ica-iter=400 — maximum number of iterations in ICA
• -E, --segmethod=features — Segmentation method:
  • delta-feature — difference of the feature images
  • delta-peak — difference of the peak enhancement images
  • features — feature images

🌸 Processing

• --threads=-1 — maximum number of threads to use for processing. this number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation). 💅

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✨ PLUGINS: fastica/implementation ✨

• internal — This is the MIA implementation of the FastICA algorithm.
  • (no parameters)
• itpp — This is the IT++ implementation of the FastICA algorithm.
  • (no parameters)

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✨ EXAMPLE ✨

evaluate the synthetic references from set segment.set and save them to refXXXX.??? by using five independent components, and skipping 2 images. per default a bounding box around the LV will be segmented and scaled by 1.4, and the cropped images will be saved to cropXXXX.??? and a segmentation set cropped.set is created. the image file type ??? is deducted from the input images in segment.set. 🦋

mia-2dmyocard-icaseries -i segment.set -r ref -o ref -k 2 -C 5

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✨ AUTHOR(s) ✨

Gert Wollny 👑

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✨ COPYRIGHT ✨

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, that's the whole thing. go make some synthetic references, bestie. 🎀

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okay that's the page!! this was USER COMMANDS, version v2.4.7, and yeah mia-2dmyocard-icaseries(1) ate and left no crumbs. periodt. 💖✨🌈🫶