mia-3dmoti...a-nonrigid(1)

📦
version 2.4.7 · 3 versions
, in ubuntu jammy, ubuntu noble

💖 NAME 💖

okay so bestie, welcome to mia-3dmotioncompica-nonrigid 💅 — this page lives in the General Commands Manual and it is the main character of non-linear registration. Fr fr.

it does Non-linear registration of a series of 3D images. periodt. 🦋

✨ SYNOPSIS ✨

mia-3dmotioncompica-nonrigid -i <in-file> -o <out-file> [options]

🌸 DESCRIPTION 🌸

so mia-3dmotioncompica-nonrigid implements a 3D version of the motion compensation algorithm described in this paper, no cap 👑

Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis" Medical Image Analysis, 2012

🎀 OPTIONS 🎀

📁 File-IO

  • -i, --in-file=(required, input); io — the input images, and they have to be consecutively numbered files (nameXXXX.ext). for the supported file types, go peek at PLUGINS:3dimage/io 🫶
  • -o, --out-file=(output, required); io — the output image name, written as a C format string that includes a %04d so the file numbering actually works. supported file types again live at PLUGINS:3dimage/io 💖
  • --save-refs= — saves the reference images. the string you give becomes the file name base, the number pattern follows your input images, and the output format is always 'vista'.
  • --save-regs= — saves the intermediate registered images. same deal: your string = file name base, numbering follows the input images, output format is always 'vista'.
  • --save-coeffs= — saves the mixing matrix to a text file 📝
  • --save-features= — saves the feature images as PNG 🖼️

🆘 Help & Info

  • -V, --verbose=warning — how chatty the output is: 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 — prints the copyright info
  • -h, --help — prints this help
  • -?, --usage — prints a short help
  • --version — prints the version number and dips ✌️

🧠 ICA

  • --fastica=internal — which FastICA implementation gets used. for the supported plugins see PLUGINS:fastica/implementation
  • -C, --components=0 — ICA components; 0 means automatic estimation 🤖
  • --no-normalize — don't normalize the ICs
  • --no-meanstrip — don't strip the mean from the mixing curves
  • -k, --skip=0 — skip images at the beginning of the series, like when they're from other modalities, we don't want them 🚫
  • -m, --max-ica-iter=400 — maximum number of iterations in ICA

⚙️ 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)

📐 Registration

  • -O, --optimizer=gsl:opt=gd,step=0.1 — the optimizer used for minimization
  • -a, --start-c-rate=32 — start coefficient rate in spines; gets divided by --c-rate-divider with every pass
  • --c-rate-divider=4 — coefficient rate divider for each pass
  • -d, --start-divcurl=20 — start divcurl weight; gets divided by --divcurl-divider with every pass
  • --divcurl-divider=4 — divcurl weight scaling with each new pass
  • -w, --imagecost=image:weight=1,cost=ssd, — image cost
  • -l, --mg-levels=3 — multi-resolution levels
  • -P, --passes=3 — registration passes

🔌 PLUGINS: 3dimage/io 🔌

analyze

Analyze 7.5 image 📼

  • Recognized file extensions: .HDR, .hdr
  • Supported element types:
    • unsigned 8 bit, signed 16 bit, signed 32 bit, floating point 32 bit, floating point 64 bit

datapool

Virtual IO to and from the internal data pool 🫧

  • Recognized file extensions: .@

dicom

Dicom image series as 3D 🩻

  • Recognized file extensions: .DCM, .dcm
  • Supported element types:
    • signed 16 bit, unsigned 16 bit

hdf5

HDF5 3D image IO 📦

  • Recognized file extensions: .H5, .h5
  • Supported element types:
    • binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, signed 64 bit, unsigned 64 bit, floating point 32 bit, floating point 64 bit

inria

INRIA image 🎈

  • Recognized file extensions: .INR, .inr
  • Supported element types:
    • 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

mhd

MetaIO 3D image IO using the VTK implementation (experimental). 🧪

  • Recognized file extensions: .MHA, .MHD, .mha, .mhd
  • Supported element types:
    • 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

nifti

NIFTI-1 3D image IO. The orientation is transformed in the same way like it is done with 'dicomtonifti --no-reorder' from the vtk-dicom package. 🧭

  • Recognized file extensions: .NII, .nii
  • Supported element types:
    • signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, signed 64 bit, unsigned 64 bit, floating point 32 bit, floating point 64 bit

vff

VFF Sun raster format ☀️

  • Recognized file extensions: .VFF, .vff
  • Supported element types:
    • unsigned 8 bit, signed 16 bit

vista

Vista 3D 🌅

  • 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

vti

3D image VTK-XML in- and output (experimental). 🧪

  • Recognized file extensions: .VTI, .vti
  • Supported element types:
    • 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

vtk

3D VTK image legacy in- and output (experimental). 🧪

  • Recognized file extensions: .VTK, .VTKIMAGE, .vtk, .vtkimage
  • Supported element types:
    • 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 🧚

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 🌈

so say you wanna register the perfusion series that's sitting in images imagesXXXX.v, using 4-class ICA estimation. skip two images at the beginning, use at most 4 registration threads, an nlopt based optimizer, and otherwise just vibe with the default parameters. store the result in registeredXXXX.v. slay ✨

mia-3dmotioncompica-nonrigid -i images0000.v -o  registered%04d.v  -k 2
       -C 4 -t 4 -O
       nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300

👑 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'. ⚠️

k bye bestie, that's the whole page 💅 this was the mia-3dmotioncompica-nonrigid manual, version v2.4.7, straight out of USER COMMANDS 🎀 go register something gorgeous 🦋💖

📦 where this page comes from