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


  • 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-rays penetrate skin and create image of internal structures

Software to visualize medical data


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


  • 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


  • manually-segmented MRI scans of glioblastomas