Theoretical Background
What are NIFTI and DICOM Formats?
NIFTI (Neuroimaging Informatics Technology Initiative) is a file format commonly used in the field of medical imaging. It’s popular in research environments and is known for its capability to store a rich set of metadata along with the imaging data.
DICOM (Digital Imaging and Communications in Medicine) is a standard commonly used for transmitting, storing, and sharing medical images. Unlike NIFTI, DICOM is widely used in clinical settings.
Why Convert?
- Compatibility: Many medical imaging software do not support the NIFTI format but will support DICOM.
- Metadata: DICOM can carry a vast amount of metadata which is useful in clinical settings.
- Standardization: DICOM is the standard format in medical imaging making it essential for sharing data across different platforms and systems.
Conversion Complexity
Converting a NIFTI file to a DICOM series involves:
- Reading the NIFTI file and extracting the imaging data.
- Rescaling image intensities.
- Mapping the metadata from the NIFTI file to DICOM tags.
- Writing each slice of the 3D image as a separate DICOM file with appropriate metadata.
Module Documentation: NiftiToDicomConverter
Overview
NiftiToDicomConverter is a Python class designed for converting NIFTI files to DICOM format. It can convert a single or multiple NIFTI files and saves each slice of the 3D image as a separate DICOM file.
Class Initialization
from pycad.converters import NiftiToDicomConverter
converter = NiftiToDicomConverter()No parameters are needed for initialization.
You can check the tutorial here: https://github.com/amine0110/pycad/blob/main/tutorials/nifti2dicom.py
Methods
writeSlices(series_tag_values, new_img, i, out_dir)
Parameters:
series_tag_values: List of tuples containing DICOM metadata tags and their corresponding values.new_img: SimpleITK Image object representing the 3D image to be written.i: Index of the current slice to be written.out_dir: Directory where the DICOM files will be saved.
Description:
This is an internal helper function and is generally not called directly by the user. It takes a slice of a 3D image and writes it as a DICOM file. The metadata for the DICOM file is taken from series_tag_values.
nifti2dicom_1file(in_dir, out_dir)
Parameters:
in_dir: File path of the input NIFTI file.
out_dir: Directory where the DICOM files will be saved.
Description:
Converts a single NIFTI file into a series of DICOM files. Each slice of the 3D image is saved as a separate DICOM file in the directory specified by out_dir.
nifti2dicom_mfiles(nifti_dir, out_dir)
Parameters:
nifti_dir: Directory containing multiple NIFTI files.
out_dir: Directory where the DICOM files will be saved.
Description:
Converts multiple NIFTI files into DICOM series. The method iteratively calls nifti2dicom_1file for each NIFTI file in the directory specified by nifti_dir. Each converted DICOM series is saved in a separate folder under out_dir.
