**Reconstruction planes:**

More instructions can be found on GitHub.

**Definitions and Clarifications on software:**

- PTV is the "Planning Target Volume" that should be irradiated.

- GTV is the gross tumor volume (what in general can be seen on the image)

- CTV is the clinical target volume (where the physician thinks there is still cancerous tissue despite being directly visible in the image).

- OAR means "Organ at risk", basically organs that are more sensitive than the general healthy tissue.

The PTV adds safety margins for the irradiation and thus usually encloses CTV which itself contains GTV.

Optimisation - The optimizer optimizes a non-linear constrained optimization problem with an interior-point algorithm. The objective function and constraint functions are built from the specific objectives one can set in the table.

For example, "TARGET"s usually have a "squared deviation" objective, which mathematically is the sum of the squared difference of dose to the set prescription dose in all voxels within the target. For OARs, there is usually a "squared overdosing", which corresponds to the sum of squared positive differences (so only if the dose is above the assigned dose). That's why one can assign a dose also to OARs with these objectives, to let them tolerate dose up to certain extents.

The full objective function is just the sum of all objectives, each multiplied with their respective "penalty". They are respectively "squared deviation" and "squared overdosing" for the Masterclass. For the exact formulation of the objectives one can see the open-access paper from 2018 https://aapm.onlinelibrary.wiley.com/doi/10.1002/mp.12251 - Regarding failing optimization: "Priority" is NOT giving information about the importance to the optimization.

One needs in general to know the "penalty" instead. About Priority: For the Masterclass version, one is not able to change priorities and all priorities are set correctly in the patient data to avoid confusion.

For Info: Before the optimization, there is an internal step of organizing organs into layers to manage overlap. Priority assigns the layer of the organ, where lowest number means highest layer. If one gives, for example, the PTV a higher number than the remaining tissue, it will be masked by the healthy tissue and not used in optimization. When one changes irradiation volumes, one has to take care that the priorities are set correctly (which is not the case for the Masterclass version).

- Changing the irradiation volume is not recommended: PTVs are the volumes that are delineated and required for irradiation. Irradiating the GTV only might reduce the dose somewhere else, but that's only because one does not irradiate what one should irradiate. Better to focus on changing gantry angles and modalities, or even changing the optimization penalty.