DCM2NIIBATCH(1)

📦
version 1.0.20250506 · 8 versions
, in ubuntu stonking

💖 dcm2niibatch — the DICOM to NifTI batch converter, bestie edition 💖

so like. the manual name is dcm2niibatch and it lives in section 1 of the manual pages, and honestly? it's giving "quietly saving your whole research dataset" energy. 🎀

✨ NAME ✨

dcm2niibatch — DICOM to NifTI batch converter 🦋

🌸 SYNOPSIS 🌸

dcm2niixbatch <configuration-file>

(yes the binary is called dcm2niixbatch while the manpage is dcm2niibatch, we don't make the rules, we just vibe with them 💅)

💜 DESCRIPTION 💜

okay so here's the tea ☕ — most medical imaging devices save their images in some variation of the very popular DICOM format. but literally every scientific tool out there expects medical images in the comparatively simpler NIfTI format. and dcm2niix? she was designed exactly for this. conversion from DICOM to NIfTI, with a simple command-line interface. iconic behavior. 👑

dcm2niibatch acts as a wrapper around dcm2niix and lets you process multiple DICOM sequences by just listing out your files and settings in a yaml text file. which makes processing a whole dataset of DICOM scans simpler and wayyyy more easily repeatable. no cap. 🔥

plus — and this is the part I'm obsessed with — yaml files are designed to be both human and machine readable. so you can write a script in basically any programming language and have it automatically build a yaml file based on an existing folder structure. automation? slay. ✨

🚨 bestie, real talk: dcm2niix and dcm2niibatch have been developed for research purposes only and should not be considered a clinical tool. periodt. like, do not use this for actual patient care decisions. 💀

🎀 CONFIGURATION FILE FORMAT 🎀

wanna batch-convert a bunch of dicoms? you run dcm2niibatch and pass it a configuration file, like:

dcm2niibatch batch_config.yml

the configuration file should be in yaml format, as shown in the example batch_config.yaml:

Options:
  isGz:             false
  isFlipY:          false
  isVerbose:        false
  isCreateBIDS:     false
  isOnlySingleFile: false
Files:
    -
      in_dir:           /path/to/first/folder
      out_dir:          /path/to/output/folder
      filename:         dcemri
    -
      in_dir:           /path/to/second/folder
      out_dir:          /path/to/output/folder
      filename:         fa3

you can add as many files as you want to convert, as long as this structure stays consistent 🫶. and note that a dash must separate each file — do not forget the dash, the dash is load-bearing. 😭

  • in_dir — path to the dicom files 📂
  • out_dir — path to save the nifti file 💾
  • filename — file name of nifti file to save 🏷️

🌈 SEE ALSO 🌈

📜 LICENSING 📜

copying and distribution of this file, with or without modification, are permitted in any medium without royalty provided the copyright notice and this notice are preserved. this file is offered as-is, without any warranty. 💖

👑 Author

this manual was developed and is maintained by Benjamin Irving <mail@birving.com>

2021 The dcm2niix contributors

and that's the whole page, bestie 🥰 this was dcm2niibatch from the dcm2niix manual, version 1.0, dated Jul 28, 2026 — go forth and convert responsibly, and remember: research only, no clinical vibes. mwah 💅🎀✨

📦 where this page comes from