pydcm2niix 1.0.20220116

DCM2NIIX Python package

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]https://github.com/DataCurationNetwork/data-primers/blob/master/Neuroimaging%20DICOM%20and%20NIfTI%20Data%20Curation%20Primer/neuroimaging-dicom-and-nifti-data-curation-primer.md) provides details.

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.

• The base code includes support for raw, run-length encoded, and classic JPEG lossless decoding.
• Lossy JPEG is handled by the included NanoJPEG. This support is modular: you can compile for libjpeg-turbo or disable it altogether.
• JPEG-LS lossless support is optional, and can be provided by using CharLS.
• JPEG2000 lossy and lossless support is optional, and can be provided using OpenJPEG or Jasper.
• GZ compression (e.g. creating .nii.gz images) is optional, and can be provided using either the included miniz or the popular zlib. Of particular note, the Cloudflare zlib exploits modern hardware (available since 2008) for very rapid compression. Alternatively, you can compile dcm2niix without a gzip compressor. Regardless of how you compile dcm2niix, it can use the external program pigz for parallel compression.

Versions

See releases for recent release notes. See the VERSIONS.md file for details on earlier releases.

Contribute

dcm2niix is developed by the community for the community and everybody can become a part of the community.

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/output /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.

Install

There are a couple ways to install dcm2niix

• Github Releases provides the latest compiled executables. This is an excellent option for MacOS and Windows users. However, the provided Linux executable requires a recent version of Linux (e.g. Ubuntu 14.04 or later), so the provided Unix executable is not suitable for very old distributions. Specifically, it requires Glibc 2.19 (from 2014) or later. Users of older systems can compile their own copy of dcm2niix or download the compiled version included with MRIcroGL Glibc 2.12 (from 2011, see below).
• Run the following command to get the latest version for Linux, Macintosh or Windows:
  • curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_lnx.zip
  • curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_mac.zip
  • curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_mac_arm.pkg
  • curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_win.zip
• MRIcroGL (NITRC) or MRIcroGL (GitHub) includes dcm2niix that can be run from the command line or from the graphical user interface (select the Import menu item). The Linux version of dcm2niix is compiled on a holy build box, so it should run on any Linux distribution.
• If you have a MacOS computer with Homebrew or MacPorts you can run brew install dcm2niix or sudo port install dcm2niix, respectively.
• If you have Conda, conda install -c conda-forge dcm2niix on Linux, MacOS or Windows.
• If you have pip, python -m pip install pydcm2niix on Linux, MacOS or Windows.
• On Debian Linux computers you can run sudo apt-get install dcm2niix.

Build from source

It is often easier to download and install a precompiled version. However, you can also build from source.

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 or sudo port install cmake pkgconfig

Basic build:

git clone https://github.com/rordenlab/dcm2niix.git
cd dcm2niix
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.

In rare case if cmake fails with the message like "Generator: execution of make failed", it could be fixed by sudo ln -s `which make` /usr/bin/gmake.

Advanced build:

As noted in the Image Conversion and Compression Support section, the software provides many optional modules with enhanced features. A common choice might be to include support for JPEG2000, JPEG-LS (this option requires a c++14 compiler), as well as using the high performance Cloudflare zlib library (this option requires a CPU built after 2008). To build with these options simply request them when configuring cmake:

git clone https://github.com/rordenlab/dcm2niix.git
cd dcm2niix
mkdir build && cd build
cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -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.

Referencing

• Li X, Morgan PS, Ashburner J, Smith J, Rorden C (2016) The first step for neuroimaging data analysis: DICOM to NIfTI conversion. J Neurosci Methods. 264:47-56. doi: 10.1016/j.jneumeth.2016.03.001. PMID: 26945974

Alternatives

• BIDS-converter hosts Matlab and Python scripts for PET images, supporting DICOM and ECAT (ecat2nii) formats.
• dcm2nii is the predecessor of dcm2niix. It is deprecated for modern images, but does handle image formats that predate DICOM (proprietary Elscint, GE and Siemens formats).
• Python dcmstack DICOM to Nifti conversion with meta data preservation.
• dicm2nii is written in Matlab. The Matlab language makes this very scriptable.
• dicom2nifti uses the scriptable Python wrapper utilizes the high performance GDCMCONV executables.
• dicomtonifti leverages VTK.
• dinifti is focused on conversion of Siemens data.
• DWIConvert converts DICOM images to NRRD and NIfTI formats.
• mcverter has great support for various vendors.
• mri_convert is part of the popular FreeSurfer package. In my limited experience this tool works well for GE and Siemens data, but fails with Philips 4D datasets.
• MRtrix mrconvert is a useful general purpose image converter and handles DTI data well. It is an outstanding tool for modern Philips enhanced images.
• nanconvert uses the ITK library to convert DICOM from GE and proprietary Bruker to standard formats like DICOM.
• PET CT viewer for Fiji can load DICOM images and export as NIfTI.
• Plastimatch is a Swiss Army knife - it computes registration, image processing, statistics and it has a basic image format converter that can convert some DICOM images to NIfTI or NRRD.
• Simple Dicom Reader 2 (Sdr2) uses dcmtk to read DICOM images and convert them to the NIfTI format.
• SlicerHeart extension is specifically designed to help 3D Slicer support ultra sound (US) images stored as DICOM.
• spec2nii converts MR spectroscopy to NIFTI.
• SPM12 is one of the most popular tools in the field. It includes DICOM to NIfTI conversion. Being based on Matlab it is easy to script.

Links

The following tools exploit dcm2niix

• abcd-dicom2bids selectively downloads high quality ABCD datasets.
• autobids automates dcm2bids which uses dcm2niix.
• BiDirect_BIDS_Converter for conversion from DICOM to the BIDS standard.
• BIDScoin is a DICOM to BIDS converter with a GUI and thorough documentation.
• BIDS Toolbox is a web service for the creation and manipulation of BIDS datasets, using dcm2niix for importing DICOM data.
• birc-bids provides a Docker/Singularity container with various BIDS conversion utilities.
• BOLD5000_autoencoder uses dcm2niix to pipe imaging data into an unsupervised machine learning algorithm.
• brainnetome DiffusionKit uses dcm2niix to convert images.
• Brain imAgiNg Analysis iN Arcana (Banana) is a collection of brain imaging analysis workflows, it uses dcm2niix for format conversions.
• BraTS-Preprocessor uses dcm2niix to import files for Brain Tumor Segmentation.
• bidsify is a Python project that uses dcm2niix to convert DICOM and Philips PAR/REC images to the BIDS standard.
• bidskit uses dcm2niix to create BIDS datasets.
• BioImage Suite Web Project is a JavaScript project that uses dcm2niix for its DICOM conversion module.
• boutiques-dcm2niix is a dockerfile for installing and validating dcm2niix.
• clinica is a software platform for clinical neuroimaging studies that uses dcm2niix to convert DICOM images.
• clpipe uses dcm2bids for DICOM import.
• conversion is a Python library that can convert dcm2niix created NIfTI files to the popular NRRD format (including DWI gradient tables). Note, recent versions of dcm2niix can directly convert DICOM images to NRRD.
• DAC2BIDS uses dcm2niibatch to create BIDS datasets.
• Dcm2Bids uses dcm2niix to create BIDS datasets. Here is a tutorial describing usage.
• dcm2niir R wrapper for dcm2niix/dcm2nii.
• dcm2niixpy Python package of dcm2niix.
• dcm2niix_afni is a version of dcm2niix included with the AFNI distribution.
• dcm2niiXL is a shell script and tuned compilation of dcm2niix designed for accelerated conversion of extra large datasets.
• dcmwrangle a Python interactive and static tool for organizing dicoms.
• DeepDicomSort can recognize different scan types.
• DICOM2BIDS is a Python 2 script for creating BIDS files.
• dicom2bids includes python modules for converting dicom files to nifti in a bids-compatible file structure that use dcm2niix.
• dicom2nifti_batch is a Matlab script for automating dcm2niix.
• DICOM-to-NIfTI-GUI is a Python script that provides a graphical wrapper for dcm2niix.
• divest R interface to dcm2niix.
• ExploreASL uses dcm2niix to import images.
• ezBIDS is a web service for converting directory full of DICOM images into BIDS without users having to learn python nor custom configuration file.
• fmrif tools uses dcm2niix for its oxy2bids tool.
• fMRIprep.dcm2niix is designed to convert DICOM format to the NIfTI format.
• fsleyes is a powerful Python-based image viewer. It uses dcm2niix to handle DICOM files through its fslpy libraries.
• Functional Real-Time Interactive Endogenous Neuromodulation and Decoding (FRIEND) Engine uses dcm2niix.
• heudiconv can use dcm2niix to create BIDS datasets. Data acquired using the reproin convention can be easily converted to BIDS.
• kipettools uses dcm2niix to load PET data.
• LEAD-DBS uses dcm2niix for DICOM import.
• lin4neuro releases such as the English l4n-18.04.4-amd64-20200801-en.ova include MRIcroGL and dcm2niix pre-installed. This allows user with VirtualBox or VMWarePlayer to use these tools (and many other neuroimaging tools) in a graphical virtual machine.
• 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.
• neurodocker includes dcm2niix as a lean, minimal install Dockerfile.
• neuro_docker includes dcm2niix as part of a single, static Dockerfile.
• NeuroDebian provides up-to-date version of dcm2niix for Debian-based systems.
• neurodocker generates custom Dockerfiles given specific versions of neuroimaging software.
• NeuroElf can use dcm2niix to convert DICOM images.
• Neuroinformatics Database (NiDB) is designed to store, retrieve, analyze, and share neuroimaging data. It uses dcm2niix for image QA and handling some formats.
• NiftyPET provides PET image reconstruction and analysis, and uses dcm2niix to handle DICOM images.
• nipype can use dcm2niix to convert images.
• py2bids dcm2niix dicom to bids conversion wrapper.
• pyBIDSconv provides a graphical format for converting DICOM images to the BIDS format. It includes clever default heuristics for identifying Siemens scans.
• pydcm2niix is a Python module for working with dcm2niix.
• pydra-dcm2niix is a contains Pydra task interface for dcm2niix.
• qsm Quantitative Susceptibility Mapping software.
• reproin is a setup for automatic generation of shareable, version-controlled BIDS datasets from MR scanners.
• Retina_OCT_dcm2nii converts optical coherence tomography (OCT) data to NIfTI.
• sci-tran dcm2niix Flywheel Gear (docker).
• shimming-toolbox enabled static and real-time shimming, using dcm2niix to import DICOM data.
• The SlicerDcm2nii extension is one method to import DICOM data into Slicer.
• tar2bids converts DICOM tarball(s) to BIDS using heudiconv which invokes dcm2niix.
• TORTOISE is used for processing diffusion MRI data, and uses dcm2niix to import DICOM images.
• TractoR (Tracto­graphy with R) uses dcm2niix for image conversion.