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.

Versions

24-July-2017

• Compiles with recent releases of OpenJPEG for JPEG2000 support.

23-June-2017

• Ensure slice timing always encoded for Siemens EPI
• Integrates validation
• JSON fix (InstitutionName -> InstitutionAddress)

21-June-2017

• Read DICOM header in 1Mb segments rather than loading whole file : reduces ram usage and faster for systems with slow io.
• Report TotalReadoutTime.
• Fix JPEG2000 support in Superbuild.

28-May-2017

• Remove all derived images from Philips DTI series.
• Provide some Siemens EPI sequence details.

28-April-2017

• Experimental ECAT support.
• 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).
• Include StudyInstanceUID and SeriesInstanceUID in filename.

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.

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.

Optional batch processing version:

Perform a batch conversion of multiple dicoms using the configurations specified in a yaml file.

dcm2niibatch batch_config.yml

The 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:         fa3

You 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.

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.

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

See the COMPILE.md file for details on manual compilation.