M8

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)

pixel

Each element of the 2d array is a ____

VOXEL (volume element)

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

4-D

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

Time

The fourth dimension is

f

- used when mathematics is presented

p

- picture or image is being emphasized

MATRIX

▪ A rectangular arrangement of numbers into rows & columns
▪ Each number in a matrix is referred to as a matrix element or entry

Dimensions

The ____ of a matrix give the number of rows and
columns of the matrix in this order.

2x3

Matrix A has 2 rows and 3 columns, it is called a ___ matrix.

DIGITIZED

if the image is obtained through a digitizer

DIGITAL IMAGES

if it is generated digitally

8-bit

0-255

9-bit

0-511

10-bit

0-1023

11-bit

0-2045

12-bit

0-4095

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

Represents the relative linear attenuation coefficient of the tissue

1000

Hounsfield unit of Bone:

0

Hounsfield unit of Water:

-1000

Hounsfield unit of Air:

MRI

▪ Corresponds to the MR signal response of the tissue

Ultrasound

▪ Echo signal of the utz beam when it penetrates the tissues

Image Size

▪ 2D projection image is the ordered pair (M,N) signals
▪ Size of the image is the product of M x N bits where 2k
represents the gray level range

SPATIAL RESOLUTION, DENSITY RESOLUTION, SIGNAL-TO-NOISE RATIO

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

SPATIAL RESOLUTION and DENSITY RESOLUTION

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

N

- related to spatial resolution

k

– density resolution

signal-to-noise ratio

A high ___-___-___ ___ 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 (4):

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

bytes

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

color depth

The amount of unformation per pixel is ___ ___

PHOTOMETRIC INTERPRETATION

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

Monochrome images

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

X-ray, CT, MRI

3 kinds of gray scale photometric interpretation

Nuclear Medicine, PET, SPECT

color map or color palette/LUT

color map

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

metadata

▪ Information that describes the image
▪ Stored at the beginning of the file as a header & contains at least the image matrix dimensions, spatial resolutions, pixel depth, & photometric interpretation
▪ Thanks to ____, a software application is able to recognize & correctly open an image in a supported file format

PIXEL DATA

▪ Numerical values of the pixels are stored

DICOM
Analyze, Nifti and Minc

2 CATEGORIES FOR MEDICAL IMAGE FILE FORMATS:

1. One in which a single file contains both the metadata and image data, with the metadata stored at the beginning of the file.
2. The second configuration stores the metadata in one file and the image data in a second one.

Medical image files are typically stored using one of the following two possible configurations.

Analyze

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

.img

contains the voxel raw data

.hdr

header file, contains metadata

Neuroimaging Informatics Technology Initiative

NIFTI meaning

2000s

When was NIFTI created?

National Institute of Health

Who created NIFTI?

NIFTI

▪ With the intent to create a format for neuroimaging maintaining
the advantages of the Analyze format
▪ Can be thought as revised Analyze format

A. Merging of the header & image information into one file “.nii”
B. Possibility of extending the header information

NIFTI is almost identical to the Analyze format, but offers a few
improvements:

1992

When was MINC created?

Montreal Neurological Institute (MNI)

Who created MINC?

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

When was DICOM created?

ACR (American College of Radiology) and
NEMA (National Electric Manufacturers Association)

Who created DICOM

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

meaningless

an image that is separate from its metadata becomes ____ as medical image

header

The DICOM _____ contains the most complete
description of the entire procedure

.img and .hdr

Analyze extension

.nii

Nifti extension

.mnc

MINC extension

.dcm

DICOM extension

Analyze Header

Fixed-length: 348 byte binary format

Nifti Header

Fixed Length: 352 byte binary format

Minc Header

Extensible binary format

DICOM Header

Variable length binary format