twitzelbos/nii2dcm

nii2dcm: NIfTI to DICOM creation with Python

nii2dcm

NIfTI to DICOM file creation with Python
Explore the docs »

View Repo · Report Bug · Request Feature

Overview

DICOM is the international standard used to store and display medical images in clinical institutions. It is a vast and complicated standard. The NIfTI file format is widely used within medical imaging research because it is a comparatively simple data format, generally stripped of identifiable patient data and with far fewer metadata fields.

Researchers often convert DICOM files to NIfTI files using tools such as dcm2niix. However, the reverse process is much harder.

nii2dcm is designed to convert a NIfTI file (.nii/.nii.gz) into a single-frame DICOM Series in one line, e.g.:

nii2dcm nifti-file.nii.gz dicom-output-directory

(back to top)

Getting Started

To install and run nii2dcm locally follow these steps.

Prerequisites

• Python (tested with v3.9)

Installation

Setup a Python virtual environment (recommended)

python -m venv nii2dcm-venv
source nii2dcm-venv/bin/activate

Install nii2dcm

pip install nii2dcm

Verify installation by displaying nii2dcm help information

nii2dcm -h

(back to top)

Usage

nii2dcm is designed to be pointed at a single .nii or .nii.gz and generate a single-frame DICOM dataset:

nii2dcm nifti-file.nii.gz dicom-output-directory

Currently, nii2dcm provides three Python classes in order to build different DICOM types. These are:

• Dicom – generic DICOM class
• DicomMRI – MRI DICOM class
• DicomMRISVR – 3D SVR MRI DICOM class

The created DICOM type can be specified with the -d or --dicom-type flag. For example, the following will output a 3D MRI SVR DICOM dataset

nii2dcm SVR-output.nii.gz path/to/output/dir/ -d SVR

(back to top)

Roadmap

This project is in its infancy! Expect 🐛🐜🪲

There are many things I would like to test and implement. Raise an Issue if you have ideas or suggestions.

(back to top)

Acknowledgments

• SVRTK @ KCL - the original motivation for this project
• Chris Rorden for dcm2niix - inspiration for the reverse process
• NHS Topol Digital Fellowships scheme - for the protected time to work on this

Links

Some useful, free image viewing software:

• ITK-Snap - fast, simple interface. Opens NIfTI and DICOM
• MITK Workbench - excellent for viewing multiple image datasets in the same geometric space. Opens NIfTI and DICOM
• 3D Slicer - comprehensive imaging software
• Horos - similar to a hospital clinical information system

(back to top)

Disclaimer

The Software has been developed for research purposes only and is not a clinical tool.

Licence

BSD 3-Clause License can be found here

(back to top)