RT202 Digital Medical Imaging Fundamentals & Medical Image File Formats

DIGITAL IMAGE

• A two-dimensional (2D) function

• f(x,y)

• Where x & y = plane coordinates

• f= amplitude (brightness level)

Plane Coordinates

• f(x,y)

• Where x & y = __________?

Amplitude (Brightness level)

• f(x,y) where f=__________?

VOXEL

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

Volume Element

VOXEL is also known as??

4-D Image Set
(fourth dimension is t)

As f(x,y,z) is collected through time t, the collection becomes a ??

p & f

Symbols _______ are used interchangeably

Used when mathematics is presented

Symbol f is ??

Picture or image is being emphasized

Symbol p is ??

MATRIX

A rectangular arrangement of numbers into rows & columns

matrix element or entry.

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

Digitized

if the image is obtained through a digitizer

Digital Images

 if it is generated digitally

• 0-255 (8-bit)

• 0-511 (9-bit)

• 0-1023 (10-bit)

• 0-2045 (11-bit)

• 0-4095 (12-bit)

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

Depending on the digitization procedure or the medical image generation procedure used 

0-255

(8-bit)

0-511

(9-bit)

0-1023

(10-bit)

0-2045

(11-bit)

0-4095

(12-bit)

Grey 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

CT / COMPUTED TOMOGRAPHY

Represents the relative linear attenuation coefficient of the tissue

Bone = 1000

Muscle = 50

Brain White = 45

Brain Gray = 40

Blood = 20

Water = 0

Fat = -100

Lung = -200

Air = -1000

Hounsfield Units

MRI / Magnetic Resonance Imaging

Corresponds to the MR signal response of the tissue

T1 Weighted Sequence

• (Black)

• Low SI

• Intermediate SI

• High SI

UTZ / Ultrasound

Echo signal of the utz beam when it penetrates the tissues

IMAGE SIZE

2D projection image is the ordered pair (M,N) signals

IMAGE SIZE

Size of the image is the product of M x N bits where 2^k represents the gray level range

IMAGE SIZE

Sectional images of a 3D volume, most of the time M=N

Image Display

Digital image can be printed on film or paper as hard copy or displayed on a CRT & LCD as a soft copy

Image Display

To display a soft copy digital medical image, the pixel values are first converted to analog-signals, to digital-to-analog conversion

Image Display

Current software display devices can display up to a 2K image on one screen

Image Display

Up to date, no commercially available system can handle a 4K image

• Spatial Resolution

• Density Resolution

• Signal-to-Noise Ratio

Quality of a digital image, is measured by three parameters:

SPATIAL RESOLUTION & DENSITY RESOLUTION

related to the number of pixels and the range of pixel values used to represent the object of interest in the image

related to spatial resolution

In a square image,

N x N x k, where:

N is?
k is?

density resolution

In a square image,

N x N x k, where:

k is?

SIGNAL-TO-NOISE RATIO

A high signal-to-noise ratio means that the image has strong signal with little noise, as a result, the image would please the eyes as seeing a good quality image

IMAGE FILE FORMAT

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

1. One or more images representing the projection of an anatomical volume onto an image plane (projection or planar imaging)

2. A series of images representing thin slices through a volume (tomographic or multi-slice 2D imaging)

3. A set of data from a volume (volume or 3D)

4. Multiple acquisition of the same tomographic or volume image over time to produce a dynamic series of acquisitions (4D)

MEDICAL IMAGE DATA SET CONSISTS:

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

• Every image is stored in a file & kept in the memory of a computer as group of bytes(group of 8 bits)

Color Depth

The amount of information per pixel is ??

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

• Specific how the pixel data should be interpreted for the correct image display as a monochrome or color image

• Each pixel of the image is associated with a color in a predefined color map

Monochrome images

have one sample per pixel & no color information is stored in the image.

X-ray, CT, MRI

gray scale photometric interpretation

Nuclear Medicine, PET, SPECT

color map or color palette/LUT

METADATA

• Information that describes the image

• Thanks to it, a software application is able to recognize & correctly open an image in a supported file format

• Matrix Dimensions

• Spatial Resolutions

• Pixel Depth

• Photometric Interpretation

Metadata stored at the beginning of the file as a header & contains at least the image:

PIXEL DATA

Numerical values of the pixels are stored

1. Analog Image

2. Digital Sampling

3. Pixel Quantization

Creation of a Digital Image:

• DICOM

• Analyze, Nifti & Minc

2 CATEGORIES FOR MEDICAL IMAGE FILE FORMATS:

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

1980’s | Mayo Clinic in Rochester, MN, USA

Analyze was founded? Year and Location?

Analyze

• Consists of two binary files: image file with extension:

.img | contains the voxel raw data 

.hdr | header file, contains metadata

Ex: brainct.img 

      brainct.hdr

.img

contains the voxel raw data 

.hdr

header file, contains metadata

Neuroimaging Informatics Technology Initiative

meaning of NIFTI

2000s | National Institute of Health

NIFTI was founded? year & location?

NIFTI (Neuroimaging Informatics Technology Initiative)

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

•  Can be thought as revised Analyze format

• Almost identical to the Analyze format, but offers a few improvements:

  1. Merging of the header & image information into one file “.nii”

  2. Possibility of extending the header information

 Ex. brain.nii 

1992 | Montreal Neurological Institute (MNI)

MINC was founded? year and location?

MINC

• To provide a flexible data format for medical imaging

•  Based on the Network Common Data Format (NetCDF) Minc 1 to Hierarchical Data Format version 5  (HDF5) Minc 2

1990s  

ACR - American College of Radiology

NEMA – National Electric Manufacturers Association

DICOM was founded? year and location?

American College of Radiology

ACR

National Electric Manufacturers Association

NEMA

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 

.img & .hdr

Extension:

Analyze

.nii

Extension:

Nifti

.mnc

Extension:

Minc

.dcm

Extension:

Dicom