cbedetti / dcm2niix

dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC

About

dcm2niix is a 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.

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.

Versions

See the VERSIONS.md file for details on releases.

Running

Command line usage is described in the NITRC wiki. The minimal command line call would be dcm2niix /path/to/dicom/folder. However, you may want to invoke additional options, for example the call dcm2niix -z y -f %p_%t_%s -o /path/ouput /path/to/dicom/folder will save data as gzip compressed, with the filename based on the protocol name (%p) acquisition time (%t) and DICOM series number (%s), with all files saved to the folder "output". For more help see help: dcm2niix -h.

See the BATCH.md file for instructions on using the batch processing version.

Build

Build command line version with cmake (Linux, MacOS, Windows)

cmake and pkg-config (optional) can be installed as follows:

Ubuntu: sudo apt-get install cmake pkg-config

MacOS: brew install cmake pkg-config

To build:

mkdir build && cd build
cmake ..
make

dcm2niix will be created in the bin subfolder. To install on the system run make install instead of make - this will copy the executable to your path so you do not have to provide the full path to the executable.

optional building with OpenJPEG:

Support for JPEG2000 using OpenJPEG is optional. To build with OpenJPEG change the cmake command to cmake -DUSE_OPENJPEG=ON ..:

mkdir build && cd build
cmake -DUSE_OPENJPEG=ON ..
make

optional batch processing version:

The batch processing binary dcm2niibatch is optional. To build dcm2niibatch as well change the cmake command to cmake -DBATCH_VERSION=ON ... This requires a compiler that supports c++11.

Building the command line version without cmake

If you have any problems with the cmake build script described above or want to customize the software see the COMPILE.md file for details on manual compilation.

Links

• Dcm2Bids uses dcm2niix to create BIDS datasets.
• bidskit uses dcm2niix to create BIDS datasets.
• DAC2BIDS uses dcm2niibatch to create BIDS datasets.
• heudiconv can use dcm2niix to create BIDS datasets.
• nipype can use dcm2niix to convert images.
• pydcm2niix is a Python module for working with dcm2niix.
• dcm2niir R wrapper for dcm2niix/dcm2nii.
• divest R interface to dcm2niix.
• sci-tran dcm2niix Flywheel Gear (docker).
• neuro_docker includes dcm2niix as part of a single, static Dockerfile.
• boutiques-dcm2niix is a dockerfile for installing and validating dcm2niix.
• neurodocker generates custom Dockerfiles given specific versions of neuroimaging software.
• dcm2niix_afni is a version of dcm2niix included with the AFNI distribution.
• MRIcroGL is available for MacOS, Linux and Windows and provides a graphical interface for dcm2niix. You can get compiled copies from the MRIcroGL NITRC web site.
• NeuroDebian provides up-to-date version of dcm2niix for Debian-based systems.