MIA Intro

Voxel & Pixel

- Smallest information unit in a 3D image 

Three elements that uniquely describe a voxel position in real units (E.g., mm, cm)

- Image Origin; must not always be (0,0,0); (0,0) 

Why is the description of a voxel/pixel in real units so important?

Because image data is used to locate structures, pathologies, plan treatment (e.g. brain tumor surgery or radiotherapy), measure volumes, growth (of a disease), etc.

Which color model is mostly used?

Medical Images mostly use gray scale --> one channel

Where is hypo intensity and hyper intensity on the grayscale?

- Hypo intensity --> black 

How many levels can we have for 1 byte/ 2 bytes?

- 256 for 1 byte (i.e., 28-1) 

What does the pixel depth mean?

The pixel depth, or bit depth, determines the range of values that a particular raster file can store, which is based on the formula 2^n where n is the pixel depth.

Why is pixel depth important for medical images?

Pixel depth is then important for correct reading and storing of pixel data, but also for computational and memory consumption efficiency

What is DICOM?

Digital Imaging and Communications in Medicine (DICOM). Standard for storing, handling, printing, transmitting information in medical data

Why is DICOM used?

Enables integration of scanners, servers, workstations, printers, and other hardware from multiple vendors into a picture archiving and communication system (PACS)

What DICOM combines?

- Combines image data with meta-data (patient data, acquisition parameters)

What is the PACS system?

At the core of DICOM resides the PACS system, which is the computational unit at hospitals and clinics where imaging information is stored, and used to handle patient information related to imaging scans.

What are the parameters saved in the DICOM File format?

- Hardware, imaging à Model, Software 

What can DICOM handle?

- Hardware includes vendor type, specific parameter values (e.g. energy values for a CT scan), etc. Treatment and patient data are crucial as well to follow-up patients and to inform treating doctors. 

DICOM Network Protocol

- Search studies 

Structure of DICOM file format

A DICOM file, with extension .dcm, describes a single slice. It includes a header and data sets. The header has a so-called anarchic zone, left to the user, and it’s followed by the four chars D, I, C and M. The data sets follow the displayed structure. TAGs are predefined and part of the standard. In the next slides we will focus on some specific tags.

What is the difference between study and series?

Study: patient A has a CT scan 

What is the orientation TAG describing? DICOM?

The orientation TAG is described via two cosines directions. Setting/reading the image orientation is crucial to have a good readout of pixel data in world coordinates. -

What would be the TAG value in this image? (Here a image would be needed)

-       There is a 45 degrees rotation (and cos(45)=0.707) - The cosines are then 6 values, and the TAG values would llike this: (0.707,-0.707,0, 0.707,0.707,0) the negative -0.707 corresponds to the component of the (new) LR axis moving in the negative direction of the (old) RA axis.

Voxel based representation

- These representations are derived directly from images