mia-3dseri...-intensity(1)

💖 mia-3dseries-track-intensity — the manual, but make it cute 💖

okay so bestie, this is the manual page for mia-3dseries-track-intensity(1), living in the General Commands Manual section, and it is exactly what you need if you wanna stalk a pixel across a whole series of 3D images. no cap. 🎀

---

✨ NAME ✨

mia-3dseries-track-intensity — Track intensities of pixels in series of 3D images.

that's the whole vibe. you pick pixels, it watches them. it's giving surveillance but make it science. 🦋

---

🌸 SYNOPSIS 🌸

mia-3dseries-track-intensity -i <in-file> -o <out-file> [options]

---

💅 DESCRIPTION 💅

okay so mia-3dseries-track-intensity — this program tracks the intensity of a pixel at the given coordinates. that's it, that's the whole job. you tell it where in the volume you care about, and it follows that lil guy through the whole time series. lowkey obsessed with its dedication. 💖

---

🎀 OPTIONS 🎀

🍓 File-IO

• -i, --in-file=(input, required); io — the input perfusion data set. this is your main character input, and yes it is required, so don't ghost it. For supported file types see PLUGINS:3dimage/io (scroll down, I got you 👇)
• -o, --out-file=(output, required); string — file name for output intensity slopes. required too. no input, no output, no vibes. periodt.

🌈 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. legal era. ⚖️
• -h, --help — print this help
• -?, --usage — print a short help
• --version — print the version number and exit

🧚 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). so like, -1 means "girl, figure it out yourself". 💅

---

👑 PLUGINS: 3dimage/io 👑

these are all the file formats the IO layer is friends with. each one is a different little portal for your data to walk through. ✨

🔥 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 🍓

say you wanna evaluate the intensity-time curves at points <12,13,14> and <222,113,214>. then you literally just:

mia-3dseries-track-intensity -i images0000.v -o curves.txt '<12,13,14>'
       '<222,113,214>'

two pixels, one command, zero drama. ate. 💅✨

---

💜 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'.

bestie, note the ABSOLUTELY NO WARRANTY in all caps — that's not me being dramatic, that's the license being dramatic. respect it. 😭

---

and that's the whole page, fr fr. this one's from the USER COMMANDS corner of the manual, version v2.4.7, and the page itself is mia-3dseri...-intensity(1) (yes the name is truncated in the header, it's fine, it's iconic, iykyk). go track some pixels, you got this. 🫶👑🌈