DINIFTI(1)

📦 version 2.33.1, in debian bookworm, ubuntu jammy, ubuntu noble

✨ DINIFTI(1) ✨

okay bestie, welcome to the User Commands section, because today we're talking about dinifti — the little icon that could 💅

🎀 NAME 🎀

dinifti — converts DICOM files into the NIfTI format. no cap, that's the whole gig.

🦋 SYNOPSIS 🦋

dinifti [options] <DICOM input> <NIfTI output>

🌸 DESCRIPTION 🌸

so dinifti converts a single file or a whole bunch at once into the NIfTI data format. the DICOM input can be:

  • a single filename
  • a list of files
  • a directory

and if you hand it a directory, every single file in that directory gets converted. she's thorough like that. 💖

Images that belong to the same recording series get merged together appropriately into one 3d or 4d NIfTI file — which is honestly the slay of it all. to pull that off, dinifti gathers the number of time points and the number of slices per volume straight from the DICOM header. when that's literally impossible, dinifti will issue a warning (like, when it can only find 1 slice per volume and 1 time point — tragic). but don't worry, you have the option of running the program with the -s option and telling it the number of slices per volume yourself. main character energy: you take over. 👑

A number of items are retrieved from the Siemens Shadow set. here's the list of items, plus the default value if this is not Siemens:

  • Number of groups: 1
  • Number of channels: 1
  • Sagital, Coronal and Transverse position: From DICOM (0020,0032)

💅 OPTIONS 💅

  • -g — NIfTI files will be compressed. zip zip ✨
  • -f [a2|n2|n1] — sets the output file format. if you set it to a2, ANALYZE 7.5 file pairs (hdr/img) will be generated. setting n2 makes dinifti generate NIfTI image file pairs. and the default output format, n1, is single NIfTI files (header and image data combined in one file). one file, one vibe. 🫶
  • -d — if set, dinifti appends the series description from the DICOM header to the output file name(s).

and here's the tea: if two image series share a common description, dinifti will append as many characters as necessary to the second series description to create a unique filename. in that case a warning message is displayed that shows the old and the modified filename. 😭

  • --name="<format>" — formats the output file name(s) according to the <format> string, which has to be enclosed in quotes (").

the format is interpreted in the usual printf-like way. ordinary characters are directly copied, a percent sign is represented by %%, otherwise % indicates a conversion. the special character / is translated to ~ to avoid confusion with the directory separator. noted. ✍️

if --name is present, the -d flag will be ignored.

  • %I — Subject ID
  • %N — Subject name
  • %S — Relative series number
  • %D — Series description
  • %Y — Series date (YYYYMMDD)
  • %T — Series time (HHMM)
  • %A — Accession number
  • %C — Image comments

Example:

--name="%Y:%T- %A - %I -%D(%S)"
  • -s # — this option can be used to specify the number of slices in the volume, if dinifti fails to autodetect the correct value. sometimes you just gotta do it yourself bestie 🧚
  • -v, --verbose — enables verbose status messages. if any warning message occurs, this option can be helpful to determine which imageseries caused it. detective mode 🔍
  • -n, --noact — if set, dinifti performs all processing steps, but does not write NIfTI files at the end. this can be useful to quickly inspect the content of a DICOM directory (if ran together with --verbose). it's giving window shopping 🛍️
  • -h, --help — prints this help page and exits.
  • -V, --version — prints the version number and exits.

👑 AUTHOR 👑

dinifti is written by Valerio Luccio (valerio.luccio@nyu.edu).

🌈 SEE ALSO 🌈

💜 MAILING LIST 💜

🍓 LICENSE 🍓

The software is released under the standard BSD license: http://opensource.org/licenses/bsd-license.php

and that's the whole page, bestie — every flag, every default, every % conversion, untouched and iconic. go convert something. 💖✨

okay byeeee — this one's from Valerio Luccio, dated August 2006, and yes it really is DINIFTI(1). periodt. 💅🎀

📦 where this page comes from