Team2021Group19

h1. Wiki

{{>toc}}

h2. [[Redmine Documentation Standards]]

A breakdown of how the team is to use the redmine ticketing system and formatted +*[[ticket templates]]*+ for quick and easy issue logging.

h2. [[2021 Aims]]

[[2021 AimsPlanning]]

h2. Executable

* [[How to install OnkoDICOM application]]

h2. HowTos

* "HowTo Redmine Text Formating Syntax":https://www.redmine.org/help/en/wiki_syntax_detailed.html and "HowTo Redmine Text Formatting Textile":http://www.redmine.org/projects/redmine/wiki/RedmineTextFormattingTextile

* [[HowTo create an Ubuntu Environment and make it run with python]]

* [[HowTo get OnkoDICOM running in Ubuntu 20.04 VM]]

h2. Tutorials

[[dicompyler_installation]]

[[dicompyler_installation_and_code_modification]]

h2. 2021 Training

[[Basics of displaying DICOM images]]

h2. Meetings

* [[Team2021Group19Meetings2021]]

h2. [[Group policy]]

Contains all Git accounts, a copy of the Code of conduct, Project proposal and logo for quick reference.

h2. [[Notes on the project]]

Contains the notes on how the project was developed 

h2. [[Naming Conventions]]

[[BackLogTicketsFeedback]]

h2. Team19

*Product log done*

GUI Image Fusion

*Product log pending*

h3. GUI PET/CT VIEWER

PET stands for Positron Emission Tomography. The radionuclides used for PET scanning all release positrons (positive electrons - a.k.a anti-matter electrons!) which annihilate with electrons a short distance from their generation. The result (according to E=mc2!) is the formation of 2 photons of 512keV energy (i.e., X-rays) travelling in opposite directions. These photons are detected and back-traced to form the PET image.

The PET/CT is a very useful oncology investigation that answers the questions - how much? how big? how far? has a cancer spread. The test relies on the altered metabolism of cancers which are inefficient and so tends to use sugar preferentially for metabolism. Normal cells typically use free fatty acids as a far more efficient energy source, with only small sugar use. The brain (only sugar if not starving) and kidney (uses both) are exceptions to this.

The PET/CT provides to the oncologist pictures that usually include an axial CT view, PET view, and overlay view and a rotatable maximal intensity projection (a.k.a MIP). The MIP can be rotated, and if any part is clicked on, the software drives the other images to the site of maximum SUV in that axis. It should be possible to change the view to sagittal or coronal.

[[https://www.sah.org.au/assets/images/Radiology/PET%201.png]]

This is specific instance of Image Fusion. It is now usual that the results of PET scanning is to present the PET scan with an underlying CT scan to clearly demonstrate the structural position on the CT of the functional uptake discovered by the PET. The two scans are presented already fused and should not be adjusted since the alignment comes from a physical pairing of the PET/CT scanning planes.

The display of a PET/CT should not require the user to select both scans, if there is a PET, then there is highly likely to be a matching, fused CT image set (I have not received a PET scan in the last 15 years that did not have a fused CT scan included). There are no RTSTRUCT, RTDOSE or RTPLAN provided with the PET/CT pair, however Team14 will be producing RTSTRUCT files to sit with both the PET and CT image sets.

However, the two scans from the PET/CT should be available for fusion with other scans

h3. Radiomics Configuration (Select function groups, Select specific functions, Multithread calculation)

h3. Machine Learning

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h2. Prof Andrew Miller repository