The cst cell

The constraints of all defined volumes of interest (VOIs) are stored inside the cst-cell. It is structured as follows:

<a name="cell" /a> Screenshot of the cst-cell:

Column	Content	Description
1	VOI index	number to identify the VOI
2	VOI name	string describing the VOI
3	VOI type	Specification whether the VOI is an organ at risk (OAR), a target volume or should be ignored
4	Voxel indices	Vector containing the indices of all voxels of the CT that are covered by the VOI
5	Tissue parameters	Structure containing information about the tissue of the VOI and it's overlap priority
6	Dose objectives	Structure containing information about the constraints used to calculate the objective function value

<a name="VolInd" /a>

VOI index

All defined VOIs are enumerated starting with 0.

<a name="VolName" /a>

VOI name

The VOI name is a string containing an organ name or a short description of the volume (e.g. 'BODY', 'Liver', 'GTV',...).

<a name="VolType" /a>

VOI type

The VOI type specifies how the volume is considered during treatment planning:

VOI type	handling during treatment planning
TARGET	The VOI will be covered with spot positions (protons / carbon ions) and bixels (photons) as defined in the stf struct. During the fluence optimization it will be considered according to the defined dose objectives.
OAR	The VOI will not be coveres with spot positions or bixels. During the fluence optimization it will be considered according to the defined dose objectives.
IGNORED	The VOI will not be considered during the treatment planning.

<a name="VoxInd" /a>

Voxel indices

The indices of all voxels (of the CT-cube) that are covered by the VOI are stored in a vector (see cst-cell). I.e. we store the segmetation for the VOI as a binary mask, the polygon contour data is not part of matRad's standard data sets. As the same voxel can be covered by more than one VOI, an overlap priority (see tissue parameters) is defined to handle potential discrepancies when calculating the objective function value and generating the stf struct.

<a name="TissParam" /a>

Tissue parameters

Field	Description
Tissue class	The baseData-struct contains depth-dependent α- and β- values, which are different depending on the tissue class. This parameter defines the tissue class of the VOI.
αX	α is the linear parameter of the linear-quadratic model, here the constant value for a photon irradiation is given. It is used to check the consistency of the baseData-struct and the cst settings, and to calculate the reference effect in the biological objective function.
βX	β is the quadratic parameter of the linear-quadratic model, here the constant value for a photon irradiation is given. It is used to check the consistency of the baseData-struct and the cst settings, and to calculate the reference effect in the biological objective function.
Priority	The overlap priority defines to which VOI a voxel belongs, if there are several VOIs covering the same voxel. If the overlap priority is the same for two VOIs, "overlapping" voxels are considered twice (once for each VOI) during the calculation of the objective function value.

Note that the tissue class, α, and β are only considered during biological optimization for carbon ion therapy.

<a name="DoseParam" /a>

Dose objectives

Within this struct, matRad stores the objectives definied for inverse planning. matRad supports inverse planning based on the minimization of a weighted sum of objectives. The following kind of individual objectives, are currently supported:

Type	Effect on the objective function
square underdosing	Only dose values lower than the threshold dose for this VOI are considered for the objective function. The deviations are squared, multiplied with the weighting factor and added to the objective function value. The penalty is normalized to the number of voxels per VOI.
square overdosing	Only dose values larger than the threshold dose for this VOI are considered for the objective function. The deviations are squared, multiplied with the weighting factor and added to the objective function value. The penalty is normalized to the number of voxels per VOI.
square deviation	All deviation from a reference dose for this VOI are considered for the objective function. All deviations are squared, multiplied with the weighting factor and added to the objective function value. The penalty is normalized to the number of voxels per VOI.
mean	All dose values inside this VOI are weighted with the specified, and normalized (see above), weighting factor (for this method no threshold dose is defined) and added to the objective function value.
EUD	EUD is the abbreviation for equivalent uniform dose. For this method a weighting factor and an exponent a have to be defined. For the calculation of the objective function value the dose in each voxel is taken to the power of a. Then the sum of all these values is taken (∑ Dia ) and divided by the number of voxels. The a-th root of this value is then multiplied with the weighting factor and added to the objective function value.

matRad distinguishes between different objectives according to the field type. The relative weighting of the objective within the overall objective function corresponds to the first parameter; potential additional parameters (e.g. a reference dose for the squared deviation dose or and exponent for EUD) are concatenated to the parameter vector. Below you see an example objective struct defining a squared devation objective with weighting factor 100 and a reference dose of 5 Gy.

<a name="doseScreenshot" /a>

<a name="defaultValues" /a>

Default cst-values

The patient data contained within matRad (BOXPHANTOM, HEAD_AND_NECK, LIVER, PROSTATE and TG119) have default values defined within the cst-cell.

These values are chosen to produce a reasonable treatment plan, when using coplanar and equidistant photon beams. They can be used as a reference point for more sophisticated treatment plans.