mia-3dfluid(1)

🦋 mia-3dfluid 💅

okay bestie, welcome to the manual page for mia-3dfluid — a general commands manual entry, and honestly it's giving main character energy in the non-rigid registration department. sit down, grab a strawberry, we're doing this together 💖

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✨ NAME ✨

mia-3dfluid — fluid dynamic 3D registration. that's the whole vibe, no cap.

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🌊 SYNOPSIS 🌊

mia-3dfluid -i <in-image> -r <ref-image> -o <out-transformation>
[options]

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💫 DESCRIPTION 💫

so like, mia-3dfluid is the program you run when you want non-rigid registration based on fluid dynamics. the whole thing comes from this paper, and I'm putting it here verbatim because citations are sacred:

Wollny, G. and Kruggel, F., 'Computational cost of non-rigid registration algorithms based on fluid dynamics', IEEE Transactions on Medical Imaging, 11(8), pp. 946-952, 2002.

and the tea is: it uses SSD as the sole registration criterion. one criterion. that's it. iconic minimalism fr fr.

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🎀 OPTIONS 🎀

📁 File-IO 📁

• -i, --in-image=(input, required); io — the input image. literally the picture you're bringing to the party. For supported file types see PLUGINS:3dimage/io
• -r, --ref-image=(input, required); io — the reference image, aka the one everything gets registered to. your target, your north star ⭐ For supported file types see PLUGINS:3dimage/io
• -o, --out-transformation=(output, required); io — the output transformation, which contains the registering transformation field. this is where the ✨magic✨ gets written. For supported file types see PLUGINS:3dtransform/io
• -d, --out-image=(output); io — saves the deformed image. cute bonus, not required. For supported file types see PLUGINS:3dimage/io

🆘 Help & Info 🆘

• -V, --verbose=warning — verbosity of output. it prints messages of the given level and higher priorities. 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. respect the elders 💜
• -h, --help — print this help. you are here 🫶
• -?, --usage — print a short help. the snack-size version.
• --version — print the version number and exit. quick lil flex.

⚙️ Processing ⚙️

• --threads=-1 — Maxiumum 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). so like, don't oversubscribe your CPU babe, it will simply perish 😭

🔥 Registration parameters 🔥

• --disable-multigrid — disable multi-grid processing. turning off the fancy pyramid thing.
• --disable-fullres — disable processing on the full resolution image. goodbye full res, you were real.
• --lambda=1 — elasticy constant
• --mu=1 — elasticy constant
• -s, --start-size=16 — initial multigrided size
• -m, --method=sora — method for solving PDE. your choices:
  • sor ‐ successive overrelaxation
  • sora ‐ Gauss Southwell relexation
• --step=0.8 — Initial stepsize
• -p, --interpolator=bspline:d=3 — image interpolator kernel For supported plugins see PLUGINS:1d/splinekernel
• --relax=1 — overrelaxation factor vor method sor
• --maxiter=10 — maximum iterations
• --epsilon=0.01 — truncation condition
• --matter=4 — intensity above which real matter is assumed (experimental). ⚠️ yes, experimental, we said what we said.

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🧚 PLUGINS: 1d/splinekernel 🧚

bspline

B-spline kernel creation , supported parameters are:

• d = 3; int in [0, 5]
  • Spline degree.

omoms

OMoms-spline kernel creation, supported parameters are:

• d = 3; int in [3, 3]
  • Spline degree.

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🌈 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

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💜 PLUGINS: 3dtransform/io 💜

bbs

Binary (non-portable) serialized IO of 3D transformations

• Recognized file extensions: .bbs

datapool

Virtual IO to and from the internal data pool

• Recognized file extensions: .@

vista

Vista storage of 3D transformations

• Recognized file extensions: .v, .v3dt

xml

XML serialized IO of 3D transformations

• Recognized file extensions: .x3dt

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🍓 EXAMPLE 🍓

Register image test.v to image ref.v and write the deformation vector field regfield.v. Start registration at the smallest size above 16 pixel.

mia-3dfluid -i test.v -r ref.v -o regfield.v -s 16

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👑 AUTHOR(s) 👑

Gert Wollny — the legend themselves.

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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'.

ABSOLUTELY NO WARRANTY — like, we're not kidding, and we're not sorry. read the license bestie 💀

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and that's the whole thing, bestie 🫶 this page lives under USER COMMANDS, it's version v2.4.7, and the manpage name is, of course, mia-3dfluid(1). go register something and slay ✨💖