mia-3dforce(1)

💖 mia-3dforce 💖

okay bestie, gather round, because we're reading a General Commands Manual page today and the star of the show is mia-3dforce — a section 1 user command, periodt. ✨

---

🌸 NAME 🌸

mia-3dforce — evaluate the registration force between two 3D images. that's it, that's the whole job description, and she does it beautifully. 💅

---

🦋 SYNOPSIS 🦋

mia-3dforce -i <src-file> -r <ref-file> -o <out-file> [options]

---

✨ DESCRIPTION ✨

so like, mia-3dforce is the program you run when you want to create an image made up of the pixel-wise norm of the gradient of whatever cost function you picked. that's the whole vibe. you give it images, it gives you a force-norm image back. iconic behavior, no notes. 🔥

---

🎀 OPTIONS 🎀

• -i, --src-file=(input, required); io — the input image. 🫶
  • for which file types are supported, go peek at PLUGINS:3dimage/io.
• -r, --ref-file=(input, required); io — output force norm image.
  • for which file types are supported, go peek at PLUGINS:3dimage/io.
• -o, --out-file=(output, required); io — reference image.
  • for which file types are supported, go peek at PLUGINS:3dimage/io.
• -c, --cost=ssd — which cost function to use. 💜
  • for which plugins are available, go peek at PLUGINS:3dimage/cost.

🧚 Help & Info 🧚

• -V, --verbose=warning — how chatty the output is: it prints messages of the given level and everything with a higher priority. the supported priorities, starting at the lowest level, are:
  1. trace ‐ Function call trace
  2. debug ‐ Debug output
  3. info ‐ Low level messages
  4. message ‐ Normal messages
  5. warning ‐ Warnings
  6. fail ‐ Report test failures
  7. error ‐ Report errors
  8. 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. 🚪

⚙️ 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 your machine. (-1: automatic estimation). bestie please don't set this to 9000, your laptop will simply pass away. 💀

---

🔌 PLUGINS: 1d/splinekernel 🔌

bspline

B-spline kernel creation. the supported parameters are:

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

omoms

OMoms-spline kernel creation. the supported parameters are:

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

---

🔌 PLUGINS: 3dimage/cost 🔌

lncc

local normalized cross correlation with masking support. the supported parameters are:

• w = 5; uint in [1, 256] — half width of the window used for evaluating the localized cross correlation.

mi

Spline parzen based mutual information. the supported parameters are:

• cut = 0; float in [0, 40] — Percentage of pixels to cut at high and low intensities to remove outliers.
• mbins = 64; uint in [1, 256] — Number of histogram bins used for the moving image.
• mkernel = [bspline:d=3]; factory — Spline kernel for moving image parzen histogram. for supported plug-ins see PLUGINS:1d/splinekernel.
• rbins = 64; uint in [1, 256] — Number of histogram bins used for the reference image.
• rkernel = [bspline:d=0]; factory — Spline kernel for reference image parzen histogram. for supported plug-ins see PLUGINS:1d/splinekernel.

ncc

normalized cross correlation.

• (no parameters) — she's low maintenance, we love that. 💖

ngf

This function evaluates the image similarity based on normalized gradient fields. Given normalized gradient fields $ _S$ of the src image and $ _R$ of the ref image various evaluators are implemented. the supported parameters are:

• eval = ds; dict — plugin subtype (sq, ds, dot, cross). the supported values are:
  • ds ‐ square of scaled difference
  • dot ‐ scalar product kernel
  • cross ‐ cross product kernel

ssd

3D image cost: sum of squared differences. the supported parameters are:

• autothresh = 0; float in [0, 1000] — Use automatic masking of the moving image by only taking intensity values into account that are larger than the given threshold.
• norm = 0; bool — Set whether the metric should be normalized by the number of image pixels.

ssd-automask

3D image cost: sum of squared differences, with automasking based on given thresholds. the supported parameters are:

• rthresh = 0; double — Threshold intensity value for reference image.
• sthresh = 0; double — Threshold intensity value for source image.

---

🔌 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

---

🌈 EXAMPLE 🌈

Evaluate the weighted sum of SSD between src.v and ref.v, and store the result in forcenorm.v. 🍓

mia-3dforce -i src.v -r ref.v -c ssd -o forcenorm.v

---

👑 AUTHOR(s) 👑

Gert Wollny

---

📜 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.

---

and that's the whole page bestie, every last flag accounted for, no crumbs left behind. 💅✨

okay love u, bye!! 💖 — this was the USER COMMANDS page for mia-3dforce, v2.4.7, section 1. slay. 🎀🦋