reformatx(1)

📦
version 3.3.1p2 · 7 versions
, in ubuntu stonking

🎀 NAME 🎀

okay bestie, meet reformatx 💖 — she's a Volume reformatter and she eats every single time. 🦋

✨ SYNOPSIS ✨

the vibes come in three flavors, so pick your fighter:

reformatx [options] --floating floatingImg target x0 [x1 ...]

or…

reformatx [options] target [x0 x1 ...] {-j,--jacobian} xx0 [xx1 ...]

or… WHERE x0 ... xN and xx0 ... xxN is [{-i,--inverse}] transformation##. 🫶

⚠️ plot twist alert: if the first transformation in the sequence is inverted, then --inverse must be preceded by --, i.e., use -- --inverse xform.path. no skipping this, bestie, she's strict about it. 😭

💅 DESCRIPTION 💅

so like, reformatx is the extended volume reformatter tool, and her whole thing is computing reformatted images and Jacobian maps from arbitrary sequences of concatenated transformations. that's it, that's the girl. iconic. 👑

🌈 OPTIONS 🌈

👑 Global Toolkit Options (these are shared by all CMTK tools)

like, the communal wardrobe, every CMTK tool borrows from it:

  • --help — writes the list of basic command line options to standard output.
  • --help-all — writes the complete list of basic and advanced command line options to standard output.
  • --wiki — writes the list of command line options to standard output in MediaWiki markup.
  • --man — writes man page source in nroff markup to standard output.
  • --version — writes the toolkit version to standard output.
  • --echo — writes the current command line to standard output.
  • --verbose-level <integer> — sets the verbosity level.
  • --verbose, -v — increments the verbosity level by 1 (deprecated; supported for backward compatibility — she still answers the phone, but like, she's retired).
  • --threads <integer> — sets the maximum number of parallel threads (for POSIX threads and OpenMP). 🧚 go parallel bestie
  • --outputtype — scalar data type for the output image. Supported values: "char", "byte", "short", "ushort", "int", "uint", "float", "double", or use one of the following:
    • --char — 8 bits, signed
    • --byte — 8 bits, unsigned
    • --short — 16 bits, signed
    • --ushort — 16 bits, unsigned
    • --int — 32 bits signed
    • --uint — 32 bits unsigned
    • --float — 32 bits floating point
    • --double — 64 bits floating point
  • --pad-out <double>, -P <double> — padding value for the output image [Default: 0]

🎀 Options for Plain Reformatting

  • --interpolation — image interpolation method. Supported values: "linear", "nn", "cubic", "pv", "sinc-cosine", "sinc-hamming", where the default is "linear", or use one of the following:
    • --linear — trilinear interpolation [This is the default]
    • --nn — Nearest neighbor interpolation
    • --cubic — Tricubic interpolation
    • --pv — Partial volume interpolation
    • --sinc-cosine — Sinc interpolation with cosine window
    • --sinc-hamming — Sinc interpolation with Hamming window
  • --sinc-window-radius <integer> — window radius for Sinc interpolation [Default: 3]
  • --preserve-mass — mass-preserving reformatting: multiply every reformatted value with the Jacobian determinant of the applied transformation. 🍓 she's thorough like that

🦋 Options for Jacobian Map Reformatting

  • --jacobian-correct-global — correct Jacobian maps for global scale.
  • --no-jacobian-correct-global — do not correct Jacobian maps for global scale. [This is the default] 💀

🌸 Input Options

  • --target-grid <string> — define target grid for reformating as Nx,Ny,Nz:dX,dY,dZ[:Ox,Oy,Oz] (dims:pixel:offset)
  • --mask, -m — use target pixel data as binary mask.
  • --crop <string> — crop target image: x0,y0,z0,x1,y1,z2
  • --target-offset <string>, -O <string> — override target image offset and set to x,y,z mm
  • --target-offset-pixels <string> — override target image offset and set to dx,dy,dz pixels
  • --floating <string>, -F <string> — format and path of floating image. [Default: NONE]
  • --pad-floating <double> — padding value for the floating image [Default: disabled]

💜 Output Options

  • --outfile <string>, -o <string> — format and path of output image. [Default: reformat.nii ]

🌟 Image/Transformation Database

  • --db <string> — path to image/transformation database that should be updated with the newly created image. [Default: NONE]

🫶 AUTHORS 🫶

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko. 👑 the whole friend group showed up and they all ate.

📜 LICENSE 📜

http://www.fsf.org/licensing/licenses/gpl.html

go read it bestie, it's giving legal realness. 💅

💀 BUGS 💀

Report bugs at http://nitrc.org/projects/cmtk/ — she wants the tea, fr fr. 🐛

✨ ACKNOWLEDGMENTS ✨

CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium on Alcohol and Neurodevelopment in Adolescence (N-CANDA): Data Integration Component. From April 2009 through September 2011, CMTK development and maintenance was supported by the NIBIB under Grant EB008381. 🌈 thank you funders, you're the real main characters.

okay that's the whole page bestie, you're fully caught up 💖 this was reformatx(1) from CMTK 3.3.1p2, dated Jun 24 2026 — go reformat something and slay. 🎀✨

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