MPHY-501

Bushberg Chapter 5

Medical Imaging Informatics

During the next two years you will learn the basics of Diagnostic Imaging. Ultimately after this period you will enroll in a Medical Physics Residency Program and finally take the Board examination that, once you pass, will certify you as a medical physicist.

1

Digits, Base 10, Binary

Base 10

The number: 3406 = (3 X 103) + (4 X 102) + (0 X 101) + (6 X 100)

Base 2 (Binary)

The number: 1011 = (1 X 23) + (0 X 22) + (1 X 21) + (1 X 20)

Conversion Binary to Base 10

1011 (Binary) = (1 X 23) + (0 X 22) + (1 X 21) + (1 X 20) = 8+0+2+1 = 11 (Base 10)

We write the binary number “1011” as 10112 and the Base 10 number “11” as 1110

Analog Versus Digital form in Imaging

Image Capture is in analog form

Today analogue information is converted to digital immediately for storage, manipulation and display.

You may find some rare fully analogue devices including Fluoroscopy, Nuclear Medicine and Ultrasound.

Transistor Transistor Logic (TTL) Pulse:

Digital electronics: A TTL pulse is 5 volts considered “High”

Otherwise 0 volts Considered “Low”

The 0 volts or 5 volts constitute the Binary logic of digital electronics

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

16 – bit chip

Pins and pin numbers

Pins and pin numbers

16-Bit Addressing:

From: 0000,0000 0000,0000

To: 1111,1111 1111,1111

Two 8-bit words

Understanding word order:

From: 0000,0000 0000,0000

To: 1111,1111 1111,1111

Two byte words

From: 0000,0000 0000,0000

To: 1111,1111 1111,1111

Two byte words (16 bits)

From: 1111,1111 1111,1111

To: 0000,0000 0000,0000

Two byte words

Higher order

digits

Lower order

digits

8-bits = 1 byte

Higher order

digits

Lower order

digits

Little Endian

Big Endian

Middle Endian

This needs to be verified, could be wrong

Nonetheless order matters

Other uses of Words (Use your words wisely)

0000,0000

The first 4 bits are numbers and the second four are decimal numbers

The first 4 bits are numbers and the second four powers of 2 (20000)

The first bit is a sign bit where 0 = “+” and 1 = “-”

Hence 0000,0001 = 2

And 1000,0001 = -2

Examples of Digital Voltage Representations:

0000

0

10

20

30

10

5

0

0101

1010

Sampled Voltages

Time (in milliseconds)

10 volts

5 volts

0 volts

Unipolar representations

Pulses of 0 or +5 volts only

Disambiguation: Digital Memory Versus Digital Storage

Units for describing Computer Memory Capaciy and Information Storage Capicity
Computer Memory Capicity
1 Kilobyte kB 2^10 bytes 1,024 bytes onethousand bytes
1 megabyte MB 2^20 bytes 1,024 kilobytes 1,048,576 bytes onemillion bytes
1 gigabyte GB 2^30 bytes 1,024 Megabytes 1,073,741,824 bytes onebillion bytes
Digital Storrage Device of Media Capicity
1 Kilobyte kB 10^3 bytes 1,000 bytes onethousand bytes
1 megabyte MB 10^6 bytes 1,000 kilobytes 1,000,000 bytes onemillion bytes
1 gigabyte GB 10^9 bytes 1,000 megabytes 1,000,000,000 bytes onebillion bytes
1 terabyte TB 10^12 bytes 1,000 gigabytes 1,000,000,000,000 bytes onetrillion bytes
1 petabyte PB 10^15 bytes 1,000 terabytes 1,000,000,000,000,000 bytes onequadrillion bytes
How to interpret .11111111 in Binary

Right of Point 1 1 1 1 1 1 1 1
Power of 2 -1 -2 -3 -4 -5 -6 -7 -8
Then the fractional part (right of the point):

= 1 x 2^-1 + 1 x 2^-2 + 1 x 2^-3 + 1 x 2^-4 + 1 x 2^-5 + 1 x 2^-6 + 1 x 2^-7 + 1 x 2^-8

= 1 x 1/2 + 1 x 1/4 + 1 x 1/8 + 1 x 1/16 + 1 x 1/32 + 1 x 1/64 + 1 x 1/128 + 1 x 1/256

= 0.99609375,

Quiz

What is:

.11111111 (binary) X 2 01001111 (binary)

Mapping ASCII and Unicode

American Standard Code for Information Interchange (ASCII)

Maps the American alphabet, upper and lower case, numbers 0 – 9, punctuation marks and several carriage control characters to 8-bit.

00000000 through 01111111

Unicode incorporates the world’s languages and ACSCII

May require 4 bytes (32 bits) to represent one character.

Data transfer

Data is moved from one point to another in the form of digital pulses.

If only 0 volts and +5 volts are used this is called “Unipolar digital encoding”

The pulses can represent numbers, or other maps

A group of wires used to transfer data between several devices is called a “Data Bus”

Only one device at a time can transmit on a bus

Typically one one device at a time received the data

The sending device sends both the data and the address for the device that is intended to receive the data

Data: Digital Versus Analogue

Pros Digital Format

Data is not distorted by amplification

Immune to noise

Inexpensive

Error detection with redundant data

Pros Analogue Format

Can be faster than Digital

Can be continuous data

Cons Analogue Format

Loss of signal

Signal distortions

External Noise can influence data

More expensive

No error detection

Cons Digital Format

Slower that analogue

Not continuous

If signal is interrupted data is lost

Rounding errors (data loss)

Analogue to Digital Conversion (ADCs, or A/Ds)

Most Transducers, Sensors and Detectors are analogue

Conversion from analogue to digital is called “Digitization”

Two Steps to Digitization

Sampling (data in-between sample points is lost)

Quantization (rounding errors and data lost in terms of dynamic range step)

Analogue samples are continuous in time

It is impossible to sample the signal in every point in time

Points are sampled for at discrete points in time and for a specific duration “dwell time” this is called “SAMPLING”

Each sample is converted into a digital sample “Quantization”

Continuous Vs Sampled & Quantized Data

Volts

Volts

Nyquist Violation

Frequency lost

Continuous Vs Sampled & Quantized Data

Volts

Volts

Amplitude Lost

Dwell Time, Sampling Rate, Bandwidth

Dwell Time:

Sampling time/ number of samples

Because the Nyquist sampling theorem states that we must sample at twice the frequency…

Bandwidth = =

Pixel Depth and Contrast Resolution (dynamic range)

The number of bits used to store the grey scale of an image is determined by the contrast resolution required.

Ultrasound ~ 8-bits

X-ray CT ~ 12bits

Pixel Size, Septh and Storage Requirements

Filed of View divided by number of pixels = pixel size

Example:

Fluoroscopy field of view 23cm and matrix size of 512X512

Pixel size = 230mm/512 = .45mm/pixel

Image Size = 5122 x 16-bits = 5122 x 2-bytes = 524 kilobytes or 0.5MB

2-images/Megabyte

2,000 images/GB

For a disc that can store 60GB of data one can store just less tha 120 images (should be about 114,000 images)

Some Computer Terms

Hardware

Software

Console Computer

Image Reconstruction Plane

Image Reconstruction Engine

Software

Application Software

PACS

Radiological Information System

Monitor

Terminal

Key Board

Input Device

Pointer Device

Printer

Display

Work Station

Platform

Storage Devices

Tape

Disc

Magnetic Floppy

Optical

WORM

ROM

DVD

Solid State Drive

Hard Drive

RAID

Jukebox ? Analogue Jukebox!

Flash Memory

Cloud Solution

Mirror

Network Terminology

TCPIP

UIS

IT

VPN

Telnet

FTP

Router

HUB

DICOM

HL7

SMPT

Domain

Subnet

NIS

NOC

https

AE title

Image Display

Film

Monitors TG18, TG 270

CRT

Flat Screen

LCD

LED 2k, 3k, 4k, 8k

QLED

Monitors

Three types of monitors are used for medical imaging.

Primary Display Monitor

Secondary Display Monitor

Modality Monitor

Each type has its own use and required performance

Performance Criteria for each type are discussed in AAPM reports

AAPM report TG18 Primary and Secondary Display Monitors

TG18 is a bit aged and focuses on CRT technology

AAPM report TG270 Modality Monitor

TG270 as more information on digital display monitors

Monitor Performance

In depth analysis of Photometrics of Displays and Human perception

Grey scale levels

Contrast resolution

Dynamic Range

Spatial Resolution

Linearity

Background Illumination

Display luminance (Amount of light energy emitted from or reflected from a surface)

Intensity

Maximum

Minimum (Black Level)

Uniformity of Luminance over the viewing area

Viewing distance

Glare

Spatial Distortion

Lag & Refresh rate

Luminance

Rate of light energy emitted or reflected from a surface

Per unit area

Per solid angle

Corrected for the photoptic (normal daylight color vision) spectral sensitivity of the human eye

Unit of luminance is candela per square meter (cd/m2)

Doubling luminance a human eye only perceives a small brightness increase

Dynamic Range of a Monitor

Defined in two different ways

Difference between Luminance Max and Luminance Min ( Lmax – Lmin )

Ratio of Luminance Max and Luminance Min ( Lmax / Lmin )

American College of Radiology’s (ACR) Technical Standard for Electronic Practice of Medical Imaging

Monochrome Interpretation Workstation Monitors

Lmax > 171 cd/m2

For Mammography Lmax > 250 cd/m2

For optimal contrast Lmax > 450 cd/m2

Radiological monitors have

built in light sensing hardware

feed back loop keeps luminance constant

Black Level, Contrast Ratio & Veiling Glare

Black Level

Measurement of Lmin with lights off & room in total darkness

Difference between Black Level and Lmin is Veiling Glare:

Veiling Glare

Reduces Contrast

When scattered light reflects off the face of a monitor

Diffuse reflection of ambient light

Veiling Glare = Lmin – Black Level

Contrast Ratio

like dynamic range except using black level instead of Lmin)

Contrast Ratio = Lmax / Black Level

Spatial Linearity

The preservation of geometric shape

Digital monitors maintain straight lines because they are based on a matrix pattern

Mostly a problem with CRT monitors (almost extinct issue)

Perceived Contrast, Threshold Contrast & Just Noticeable Difference (JND)

Perceived Contrast = (Lmax – Lmin)/Lave

Just Noticeable Difference: smallest luminance difference = (L2 – L1) where difference is noticeable by only ½ a group of human observers.

Threshold Contrast = JND/Lave

Visual Degree

1o

60cm

Best perceived image contrast at ~ 5 cycles per visual degree

http://dawnsbrain.com/how-to-draw-a-human-eye-worksheet/

https://monitors.com/collections/monitors/products/dome-s2c-2mp-color-medical-led-monitor

5-cycles

20-cycles

Your monitor may alias this frequency and produce 1D Moire’ pattern

Contrast Sensitivity Function

Webvision: The Organization of the Retina and Visual System, Kolb H, Fernandez E, Nelson R, editors., Salt Lake City (UT): University of Utah Health Sciences Center; 1995.

https://www.ncbi.nlm.nih.gov/books/NBK11509/figure/ch25kallspatial.F23/?report=objectonly

5

Max contrast sensitivity is about 5 cycles per visual degree

50

1/100 contrast sensitivity at 50 cycles/degree

Look Up Table (LUT)

One technique to map bit ranges is window and level

P1

P2

Window = W

W/2

Level

Window and Level control (mapping the LUT)

Level sets the middle range of values

Window sets the extent of the range

Lower level = Level –

Upper level = Level +

All values below lower level are set to 0

All values above Upper level are set to maximum pixel value possible

In between pixel values are set:

P1

P2

W = Window = Upper Level – Lower Level

W/2

Level

Pij’ = (Pij – Lower Level) * (Max allowed Pixel value/Window)

Pij = Pixel Value before Windowing

Pij’ = Pixel Value after Windowing

Luminance Calibration of Display Systems

Display Function: Luminance produced as a function of driving signal

If it is a digital signal this is called “Digital Driving Level”

Effects perceived contrast

Inherent/generic display function of a monitor is not-linear.

Input to display does not increase linearly with linear increase of input driving level

Can be different for every monitor

Changes over time (Re-calibration needed during the life time of the monitor)

Radiological display systems modify display function to enhance contrast

Various options may be available for specific tasks like mammography

Automated Contrast Equalization

Conspicuity can be increased

Grayscale Standard Display Function (GSDF)

Because different monitors have different Display Functions contrast of a displayed object would differ from monitor to monitor. DICOM has addressed this problem by creating GSDF to standardize contrast across monitors.

Digital Imaging & Communications in Medicine (DICOM)

Presentation Values (digital pixel values) P-Values with GSDF

Provides same contrast between monitors

Provides same contrast between a monitor and printed material

Provides same contrast from monitor/printed material to the human eye

Electro optical measurements can be different than human eye perception

!!! GDSF pertains to grey scale monitors only !!!

Presentation Values (P-values) Digital Driving Levels (DDLs)

Input display system’s LUT levels are: Presentation Values

Output systems LUT values are: Digital Driving Levels

Use different LUT for each monitor to achieve GSDF

+ LUT = GSDF

SMPTE Pattern 1) Contrasts Quick View: 0% – 5%, 95% – 100%

2) Line Pairs (resolution

3) Iso-Intensity squares

4) Lines (Geometry measurements)

5) Just noticeable difference calibration Squares

Just Noticeable Difference (JND)

JND: Input value to the GSDF, such that one step in JND results in a luminance difference that is a “just noticeable difference”

0

100

200

300

400

500

600

700

800

900

1000

1100

Luminance (cd/m2)

10,000

1,000

100

10

1

0.1

0.01

DICOM Grayscale Standard Display Function

250 cd/m2

2 cd/m2

Min = 2 cd/m2 & Max = 250 cd/m2 for this monitor hence only this portion of the GSDF is used

JND Index

J = jmin + p (jmax – jmin)/pmax

Image Printers

Typically Digital

Silver based (red or infrared-sensitive) film

Dry thermal development

Exposed with a red scanning laser

Still minimum requirement for Mammography

Computer Terminology

Wide Area Network (WAN)

Local Area Network (LAN) i.e. within a department

Server: Provides service to other computers

File Server: Stores files from other computers on the network

E-mail Server: ….

Thick Client: Client computer provides information processing

Thin Client: Client computer serves to display information processed elsewhere

Network Connectivity

Wi-Fi

Coaxial Cable

Other hardwires

Fiberoptic cables (not effected by electrical noise)

Data Passage

Data is passed between computers using Packets

Packets’ headers contain Network Addresses of transmit and destination nodes

Packets can be lost or “dropped”

Network-Interfaces between node and network have unique Network Address

Devices connect to network via network-adapter/network-interface

Internet Protocols: are used to check packets integrity and passage

Network Switches: pass packets between network segments

Each device on a network is a Node (computer, switch, printer, etc.)

Links: Communications between nodes

Network Bandwidth: Maximum data transfer rate

transmission control protocol/Internet protocol (TCP/IP)

Uses 5-layer stack:

Applications Applications

Transport Transport

Network LAN Network LAN

Data Link Data Link

Physical Physical

Router

Router

Layer 5

Layer 4

Layer 3

Layer 2

Layer 1

Layer 5

Layer 4

Layer 3

Layer 2

Layer 1

Network

WAN

Transmission Line

Network

WAN

Applications

Transport

Network LAN

Data Link

Physical

Passes information to transport with Destination Computer Address and Requested Application on destination computer

FOLLOWING TCP: Divides info into packets, adds header to each packet with info on packet sequence and error detection

FOLLOWING IP: Further subdivide packets, adds source address and destination address

FOLLOWING specific LAN or point-to-point protocol, encapsulates packets into packets for transmission over LAN, gives each packet another header such as LAN address of destination computer. Example: if protocol is Ethernet, data link encapsulates packets into ethernet packets and sends data to physical layer where they are converted to electrical, infrared or Wi-Fi and transmitted

Layer 4

Under TCP:

Layer 4 of sending computer

initiates dialogue with Layer 4 of destination computer

negotiates packet size and other aspects

Layer 4 of destination computer

Requests re-transmission of missing or corrupted packets

Places packets in correct order

Recovers information from packets (such as requested application)

Sends information to correct application

IPv4 & IPv6

IPv4 uses for 1-byte binary this permits > 4billion addresses

Looks like 1111.1111.1111.1111 (binary) or 255.255.255.255 (base 10)

IPv6 uses six 1-byte binary > 340 undecillion addresses

Should look like 1111.1111.1111.1111.1111.1111 or 255.255.255.255.255.255

Other Internet Protocols

Simple Mail Transfer Protocol (SMPT)

Hypertext Transfer Protocol (HTTP)

Universal Resource Locater (URL)

Teletype Network (TELNET) provides remote command line control

File Transfer Protocol (FTP)

World Wide Web (WWW)

Picture Archiving and Communications Systems (PACS)

Digital archive to store medical images

Display workstations to display images

Computer network to transfer images between

Archive

Imaging modality

Workstations

Database to track location of images and related information

Exchange information with other systems

Hospital Information System (HIS)

Radiology Information System (RIS)

Electronic Medical Record (EMR)

Other connected Systems

CD/DVD

Film Digitizer

Web Server

Health Level-7 (HL7) Integrating the Healthcare Enterprise (IHE)

Health Level-7 (HL7)

a set of international standards used to transfer and share data between various healthcare providers

Integrating the Healthcare Enterprise (IHE)

Initiative by healthcare professionals and industry

Seeks to improve the way computer systems share information

Seeks to improve the interoperability of healthcare information systems

Typical Image Sizes

Study Typical Storage (in Megabytes)
Chest Radiographs (PS and Lateral 2K by 2.5K) 20
Standard Head CT series (50 5122 images) 26
TI-201 Myocardial perfusion SPECT study 1
Ultrasound (5122, 60 images to PACS archive) 16
Cardio-Catheterization Study (Coronal and LV images (maybe s-ray Bi-plane study) 450 – 3,000
Digital screening mammograms (2cc and 2 MLO) 60 – 132
Image Compression may be needed to store images

!!!Mammograms may not be compressed with lossy!!!

Display Monitors/Viewing Workstations

Work Station is a monitor plus computer with dedicated software

Software includes

Specialty oriented measurement tools

Dentistry

Orthopedics

Neurology

Oncology

Monitor size and placement are critical for reading

High Maximal luminance (400-500 cd/m2)

When the diagonal size of the monitor > 50 inches viewing angle becomes a problem

Curved monitor

Shifting positions to read entire screen

Monitor Performance

Room lighting < 50 lux Reflections from other monitors/light sources (multiple workstations) Viewing distance SMPTE Pattern Software for Workstations Hanging Protocols How the radiologists wishes to see images displayed Magnify (Zoom) Roam (Pan) Window and Level Specialized software Orthopedics (specific angular measurements) Angiographic (Subtractions) Ultrasound (circumference measurements) Image reconstructions and filtering PACS Quality Control Patient Name Right exam right patient Right electronic medical record Proper connection to RIS & HIS Security and Availability Privacy: only those authorized to see data can see it Integrity: error detection to ensure that data is not corrupt Redundancy, back-ups, off-site of data Authentication: Sender-receiver verification Non-repudiation: finalization of reports, transmission of payments are not rejected Availability: Information and services when needed Encryption: Protection against intentional modification Health Insurance Portability Accountability Act (HIPAA, 45 CFR 164) Confidentiality, integrity, availability of data Protect against anticipated threats or hazards to security and integrity of data Protect against reasonably anticipated impermissible uses or disclosures Ensure compliance by the workforce PACS and Teleradiology Security Plan Perform risk analysis Establish Written policies and procedures Train Staff in policies and procedures On and off-site back-ups (fault tolerance) Anti-virus software with up-to-date signature libraries Forbid external data sources (flash drive, e-mails, etc) User authentication Terminate access to former employees “Log off” workstations when not in use Limit access and control on a user / group basis Secure transfer (encrypted) Physically secure room where data is stored/encrypt the data Destroy information on items before they are disposed of Install security patches on syste Install “firewalls” Audit trails: recording of access to protected information Establish an emergency disaster recovery plan (fault tolerance) Plan for risks: against human error against natural disaster For emergency services Redundant system Applied Sciences Architecture and Design Biology Business & Finance Chemistry Computer Science Geography Geology Education Engineering English Environmental science Spanish Government History Human Resource Management Information Systems Law Literature Mathematics Nursing Physics Political Science Psychology Reading Science Social Science Home Homework Answers Blog Archive Tags Reviews Contact google+twitterfacebook Copyright © 2021 HomeworkMarket.com