Medical Imaging file formats

By Shreya D'Souza

What is a medical image?

A medical image represents the internal structure or function of an anatomic region in the form of pixels or voxels (value on a regular grid in a three-dimensional space).

Analyze .img .hdr

Fixed-length: 348 byte binary format

Nifti .nii

Fixed-length: 352 byte binary formata (348 byte in the case of data stored as .img and .hdr)

Minc .mnc

Extensible binary format

Dicom .dicom

Variable length binary format

Medical Imaging Modalities

Ultrasound

  • High-frequency sound waves transmitted from the probe to body via a conducting gel

  • Waves bounce back when they hit the different structures within the body - used to create an image for diagnosis.

CT (Computed Tomography)

  • Form of X-ray that creates a 3D picture for diagnosis: produce cross-sectional images of the body

  • X-ray source and a detector then rotate around the patient producing a narrow ‘fan-shaped’ beam of X-rays that passes through a section of the patient’s body

  • Different snapshots collated into one or multiple images of the internal organs and issues.

PET (Positron Emission Tomography)

  • Nuclear medical imaging

  • Uses small amounts of radioactive materials, a special camera and a computer to evaluate organ and tissue functions

  • Tracer is given through a vein (IV).

MRI (Magnetic Resonance Imaging)

  • Uses magnetic field and radio waves to generate images of body

  • Protons aligned in magnetic field

  • Scanner uses magnetic field to align proton spins, followed by a radio frequency being applied to flip spins of protons before they return to original alignments

  • Protons in different body tissues return to normal spins at different rates

    • MRI can distinguish between different tissue types

X-Ray

  • X-rays penetrate skin and create image of internal structures

Software to visualize medical data

Slicer

  • open source software platform for medical image informatics, image processing, and three-dimensional visualization

TomViz

  • cross platform, open source application for the processing, visualization, and analysis of 3D tomographic data

Sources of medical data

The Cancer Imaging Archive

  • large archive of medical images of cancer accessible for public download

  • sorted by collection

  • MRI/CT/digital histopathology

BraTS

  • manually-segmented MRI scans of glioblastomas