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.
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.
11-April-2017
- Updated cmake to make JPEG2000 support easier with improved Travis and AppVeyor support Ningfei Li.
- Supports Data/Time for images that report Data/Time (0008,002A) but not separate Date and Time (0008,0022 and 0008,0032).
- BIDS reports morning times correctly.
- Options -1..-9 to control gz compression level.
- Includes some PET details in the BIDS JSON sidecar.
- Better detection of image order for Philips 4D DICOM (reported by Jason McMorrow and Stephen Wilson).
7-Feb-2017
- Can be compiled to use either Philips Float or Display intensity intercept and slope values.
- Handle 3D Philips DICOM and PAR/REC files where images are not stored in a spatially contiguous order.
- Handle DICOM violations where icon is uncompressed but image data is compressed.
- Best guess matrix for 2D slices (similar to dcm2nii, SPM and MRIconvert).
- Linux (case sensitive filenames) now handles par/rec as well as PAR/REC.
- Images with unknown phase encoding do not generate BIDS entry.
- Unified printMessage/printWarning/printError aids embedding in other projects, such as divest.
1-Nov-2016
- AppVeyor Support (Ningfei Li & Chris Filo Gorgolewski)
- Swap 3rd/4th dimensions for GE sequential multi-phase acquisitions (Niels Janssen).
10-Oct-2016
- Restores/improves building for the Windows operating system using MinGW.
30-Sept-2016
- Save ImageType (0x0008,0x0008) to BIDS.
- Separate CT scans with different exposures.
- Fixed issues where some compilers would generate erratic filenames for zero-padded series (e.g. "-f %3s").
21-Sept-2016
- Reduce verbosity (reduce number of repeated warnings, less scary warnings for derived rather than raw images).
- Re-enable custom output directory "-o" option broken by 30-Apr-2016 version.
- Deal with mis-behaved GE CT images where slice direction across images is not consistent.
- Add new BIDS fields (field strength, manufacturer, etc).
- Philips PAR/REC conversion now reports inconsistent requested vs measured TR (due to prospect. motion corr.?).
- GE: Locations In Acquisition (0054, 0081) is inaccurate if slices are interpolated, use Images In Acquisition (0020,1002) if available.
- New filename options %d Series description (0008,103E), %z Sequence Name (0018,0024).
- New filename options %a antenna (coil) number, %e echo number.
- Initialize unused portions of NIfTI header to zero so multiple runs always produce identical results.
- Supports 3D lossless JPEG saved as multiple fragments.
5-May-2016
- Crop 3D T1 acquisitions (e.g. ./dcm2niix -x y ~/DICOM).
30-Apr-2016
- Convert multiple files/folders with single command line invocation (e.g. ./dcm2niix -b y ~/tst ~/tst2).
22-Apr-2016
- Detect Siemens Phase maps (phase image names end with "_ph").
- Use current working directory if file name not specified.
12-Apr-2016
- Provide override (command line option "-m y") to stack images of the same series even if they differ in study date/time, echo/coil number, or slice orientation. This mechanism allows users to concatenate images that break strict DICOM compliance.
22-Mar-2016
- Experimental support for DICOM datasets without DICOM file meta information.
12-Dec-2015
- Support PAR/REC FP values when possible (see PMC3998685).
11-Nov-2015
- Minor refinements.
12-June-2015
- Uses less memory (helpful for large datasets).
2-Feb-2015
- Support for Visual Studio.
- Remove dependency on zlib (now uses miniz).
1-Jan-2015
- Images separated based on TE (fieldmaps).
- Support for JPEG2000 using OpenJPEG or Jasper libraries.
- Support for JPEG using NanoJPEG library.
- Support for lossless JPEG using custom library.
24-Nov-2014
- Support for CT scans with gantry tilt and varying distance between slices.
11-Oct-2014
- Initial public release.
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.
Optional batch processing version:
Perform a batch conversion of multiple dicoms using the configurations specified in a yaml file.
dcm2niibatch batch_config.ymlThe configuration file should be in yaml format as shown in 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: fa3You can add as many files as you want to convert as long as this structure stays consistent. Note that a dash must separate each file.
mkdir build && cd build
cmake ..
makedcm2niix will be created in the bin subfolder. To install on the system run make install.
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 the following libraries:
- pkg-config
- yaml-cpp
- a compiler that supports c++11
e.g. the dependencies can be installed as follows:
Ubuntu 14.04
sudo apt-get install pkg-config libyaml-cpp-dev libyaml-cpp0.5 cmake libboost-dev
MacOS
brew install pkg-config yaml-cpp cmake