Digital Medical Imaging Fundamentals & Medical Image File Formats

Digital Image

A two dimensional (2D) function

VOXEL (volume element)

If the digital image f(x,y,z) is 3-D, then the picture element is called a ...

4-D (fourth dimension is t)

As f(x,y,z) is collected though time t, the collection becomes ... image set

Matrix

a rectangular arrangement of numbers in rows and columns

Matrix element or entry

Each number in a matrix is referred to as a ...

2x3 matrix

Matrix with 2 rows and 3 columns.

Digitized

Image is obtained through a digitizer

Digital images

Image is generated digitally

8-bit to 12-bit

The pixel (voxel) value (gray level) can range from:

Gray levels

Represent physical, chemical, & physiological properties of the state of anatomical structures or physiological processes when the image was captured

Digitizer

Represents the optical density of the small square area of the film

computed tomography (CT)

Represents the relative linear attenuation coefficient of the tissue

1000 Hounsfield units

Hounsfeild unit of bone

-1000 Hounsfield Units

Hounsfield unit of air

MRI

Corresponds to the MR signal response of the tissue

UTZ

Echo signal of the ___ beam when it penetrates the tissues

M x N bits, gray level range

Size of the image is the product of _________ where 2k represents the ____ ____ ____

M=N

Sectional images of a 3D volume

512 x 512

512

1024 x 1024

1k

2048 x 2048

2k

Spatial resolution, density resolution, signal-to-noise ratio

Quality of a digital image is measured by three parameters:

Image file format

Provide a standardized way to store the information describing an image in a computer file

Projection or planar imaging

One or more images representing the projection of an anatomical volume onto an image plane

Tomographic or multi-slice 2D imaging

A series of images representing thin slices through a volume

volume or 3D

A set of data from a volume

4D

Medical acquisition of the same tomographic or volume image over time to produce a dynamic series of acquisitions

File format

Describes how the image data are organized inside the image

file and how the pixel data should be interpreted by a software

for the correct loading and visualization.

Analyze, Nifti, Minc, DICOM

4 major file formats used in medical imaging:

Medical image

representation of the internal structure or function of an Anatomic region in the form of an array of picture elements called pixels or voxels

Imaging modality, acquisition protocol,, reconstruction, post-processing

Numerical value of a pixel depends on:

Pixel depth

Number of bits used to encode the information of each pixel

Color depth (pixel depth)

The amount of information per pixel

Monochrome

1 bit of information per pixel

Grey-scale

8 bits of information per pixel

Color (RGB)

8 or 16 bits of information per pixel

True color (RGB)

24 or 32 bits of information per pixel

Photometric interpretation

This specifies the interpretation of the pixel data for correct image display as a monochrome image or a color image.

Metadata

Information that describes the image. Stored at the beginning of the file a a header

Pixel data

Numerical values of the pixels are stored

DICOM

Formats intended to standardize the images generated by diagnostic modalities

Analyze, Nifti & Minc

Formats born with the aim to facilitate & strengthen post-

processing analysis

Analyze

1980s Mayo Clinic in Rochester, MN, USA

Consists of two binary files: image file with extension: .img, .hdr

NIFTI

With the intent to create a format for neuroimaging maintaining the advantages of the Analyze format

Neuroimaging Informatics Technology Initiative

NIFTI meaning

NIFTI

Can be thought of as revised Analyze format

Merging of the header & image information into one file ".nii"

Possibility of extending the header information

NIFTI offers a few improvements:

2000s National Institute of Health

NIFTI origin

MINC

Provide a flexible data format for medical imaging. Based on the Network Common Data Format (NetCDF) _____ 1 to Hierarchical Data Format version 5 (HDF5) ____ 2

1992 Montreal Neurological Institute (MNI)

MINC origin

DICOM

Backbone of every medical imaging department. Pixel data cannot be separated from the description of the medical procedure which led to the formation in the image itself (format)

1990s

ACR -American College of Radiology

NEMA - National Electric Manufacturers Association

DICOM