dicom2nifti

Python library for converting dicom files to nifti

Author:	Arne Brys
Organization:	icometrix
Repository:	https://github.com/icometrix/dicom2nifti
API documentation:	http://dicom2nifti.readthedocs.io/en/latest

Using dicom2nifti

Installation

pip install dicom2nifti

Installation with pydicom >= 1.0.0

Should you have the need to use dicom2nifti in combination with pydicom 1.0.0 you have to install pydicom first from source before installing dicom2nifti. Once pydicom 1.0.0 is final and released on pypi this step will be obsolete.

pip install git+https://github.com/pydicom/pydicom.git
pip install dicom2nifti

Updating

pip install dicom2nifti --upgrade

Usage

Command line

dicom2nifti [--no-compression] [--no-reorientation] input_directory output_directory

for more information

dicom2nifti -h

From python

Converting a directory with dicom files to nifti files

import dicom2nifti

dicom2nifti.convert_directory(dicom_directory, output_folder)

Converting a directory with only 1 series to 1 nifti file

import dicom2nifti

dicom2nifti.dicom_series_to_nifti(original_dicom_directory, output_file, reorient_nifti=True)

Supported data

Most anatomical data for CT and MR should be supported as long as they are in classical dicom files.

Try avoiding "Implicit VR Endian" if possible as this makes converting non anatomical (i.e. DTI, fMRI, ...) much more difficult.

There is some vendor specific support, more specifically for 4D imaging like fMRI and DTI/DKI

GE MR

Anatomical data should all be support. 4D images like fMRI and DTI/DKI are supported.

Siemens MR

Anatomical data should all be support. 4D images like fMRI and DTI/DKI are supported.

Philips MR

For classic dicom files dicom2nifti support anatomical. For classic dicom files 4D images like fMRI and DTI/DKI are supported.

For "Philips Enhanced Dicom" there is no support for "Implicit VR Endian" transfer syntax. For the others we support anatomical and 4D images like fMRI and DTI/DKI.

Hitachi MR

Anatomical data should all be support. 4D images like fMRI and DTI/DKI are NOT supported. Anyone willing to share DTI and/or fMRI dicom form Hitachi scanners please contact us.

Unsupported data

If you encounter unsupported data you can help the development of dicom2nifti by providing a dataset. This dataset should be anonymised (but leave as much of the private fields as possible).