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Medical Image Formats#

Introduction#

A medical image is a digital representation of the internal structure or function of an anatomic region, typically presented as an array of picture elements called pixels (2D) or voxels (3D). This representation is a discrete mapping of numerical values to positions in space.

Medical Image Metadata#

Medical images often come with metadata, which provides additional information about the image. This metadata is usually stored at the beginning of the image file as a "header."

Common Metadata Fields#

  • Image dimensions: Width, height, depth
  • Voxel size: Spacing between voxels
  • Origin: Location of the first voxel
  • Orientation: Direction of x, y, and z axes
  • Pixel depth: Bytes used to represent each voxel intensity
  • Data type: Integer, floating-point, etc.

add diagram showing a sample header with key metadata fields

Pixel Data#

The pixel data in a medical image file represents the actual image values, stored in a format specific to the image file.

  • In fixed-size header formats, pixel data follows the header directly.
  • In other formats, a marker or tag indicates the start of pixel data.

Pixel Data Size#

\[ \text{Pixel Data Size} = \text{Rows} \times \text{Columns} \times \text{Pixel Depth (Bytes)} \times \text{Number of Frames} \]

Image File Size#

\[ \text{Image File Size} = \text{Header Size} + \text{Pixel Data Size} \]
Example Calculation:

For a DICOM image with the following parameters:

Parameter Value
Rows 512
Columns 512
Pixel Depth 2 bytes (16-bit image)
Number of Frames 32 (32 slices)
\[ \text{Pixel Data Size} = 512 \times 512 \times 2 \times 32 = 16,777,216 \text{ bytes (or 16 MB)} \]

Assuming the header size for this DICOM file is 1,024 bytes:

\[ \text{Image File Size} = 1,024 \text{ bytes} + 16,777,216 \text{ bytes} = 16,778,240 \text{ bytes (or 16.01 MB)} \]

Medical Image File Formats#

Categories of Medical Image Formats#

  1. Standardization Formats: Standardize images from diagnostic modalities.

    • Example: DICOM

  2. Post-Processing Formats: Facilitate and strengthen post-processing analysis.

    • Examples: Analyze, NIfTI, MINC

Configurations for Storing Medical Images#

  • Single File: Contains both metadata and image data, with metadata stored at the beginning.

    • Examples: DICOM, MINC, NIfTI

  • Two Files: Metadata and image data stored separately.

    • Example: Analyze (.hdr and .img)

add diagram comparing single file vs. two-file configurations