dcm2niix

About

dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. This web page hosts the developmental source code - a compiled version for Linux, MacOS, and Windows of the most recent stable release is included with MRIcroGL. A full manual for this software is available in the form of a NITRC wiki.

The DICOM format is the standard image format generated by modern medical imaging devices. However, DICOM is very complicated and has been interpreted differently by different vendors. The NIfTI format is popular with scientists, it is very simple and explicit. However, this simplicity also imposes limitations (e.g. it demands equidistant slices). dcm2niix is also able to generate a BIDS JSON format sidecar which includes relevant information for brain scientists in a vendor agnostic and human readable form. The Neuroimaging DICOM and NIfTI Primer provides details.

JavaScript/WebAssembly

To view the WASM specific README, please click here. The rest of this README is for the dcm2niix CLI program.

License

This software is open source. The bulk of the code is covered by the BSD license. Some units are either public domain (nifti*.*, miniz.c) or use the MIT license (ujpeg.cpp). See the license.txt file for more details.

Dependencies

This software should run on macOS, Linux and Windows typically without requiring any other software. However, if you use dcm2niix to create gz-compressed images it will be faster if you have pigz installed. You can get a version of both dcm2niix and pigz compiled for your operating system by downloading MRIcroGL.

Image Conversion and Compression

DICOM provides many ways to store/compress image data, known as transfer syntaxes. The COMPILE.md file describes details on how to enable different options to provide support for more formats.

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