GLT.getDoseROIVoxels: Returns the dose voxels internal to a specified ROI

In kbolab/moddicom: Package for handling DICOM RT files

Description

Returns the dose voxels internal to a specified ROI. Please consider that this function return the voxel of the main dose serie. It does not work properly if you have more RD associated to the same SeriesInstanceUID. Because of this function uses mesh calculus, a quite high number of parameters can be passed in order to tune the computation. However, in the most case, the simplest form is preferreable.

N.B: if you are reading this help probably your car is burning

Usage

GLT.getDoseROIVoxels(obj.geoLet, Structure, ROIName,
  newPixelSpacing = NA, plotIT = FALSE, verbose = FALSE,
  forceReCalculus = FALSE, fastEngine = TRUE, decimation = FALSE,
  decimation.percentage = 0.8, smoothing = FALSE,
  smoothing.iterations = 10, interpolate.dose = TRUE)

Arguments

obj.geoLet	the object geoLet to load the DICOM serie in
ROIName	the ROIName that 'contains' the interested voxels. In order to know which are the structure available, please refers to the GTL.getROIList() and GTL.getROIPointList functions.
newPixelSpacing	Optional. By default it uses same pixelValues of the main CT scan: using this parameter you can pass an array (i.e.: c(.9, .9, 1.5 ) ) to interpolate the voxel space by a trilinear interpolation
plotIT	Optional. By default it does not plot anything but if you want, during the comuputation, it can plot the CT scan and the related overlapped dose.
verbose	Optional. FALSE by default. Set to TRUE it allow to see some logs during the computation
forceReCalculus	Optional. FALSE by default. Due to a caching system, implemented to improve performances, If a previous calculus has been interrupted the afterwards computations (on the same ROI) could have problems. If a computation has been interrupted it is a good practice to set this parameter to TRUE in the next computation in order to let the algorithm to re-build anything.
fastEngine	TRUE by default. By default it uses the vcgClostKD() function which should be quicker but probably a bit less accurate (?). If you want to try something different you can set this parameter on FALSE and it will use the most classical vcgClost
decimation	Optional. FALSE by default. Set it to TRUE if you want to enable decimation to the mesh structure
smoothing	Optional, FALSE by default. This parameter, if se to TRUE allow to smooth the mesh by a numerical factor indicated in the parameter smoothing.iterations.
interpolate.dose	Optional, TRUE by default. By default (TRUE) the returned 3D grid of voxel doses is interpolated according to the pixel spacing of the main CT scan. If you want back a 3D grid voxel doses specified with the same pixelValue but whitout interpolation of the dose value, set this parameter to FALSE. Personally, I cannot see a good reason to set it to FALSE but perhaps you need to fit your data with some old algorithm of dose computation and set it to FALSE can help you in getting more similar results.
decimationpercentage.	Optional. 0.8 by default. If the parameter decimation is set to TRUE this parameter indicates the percentage of triangles that should be sacrified in the first (and biggest) mesh-model. Killing triangles allows to have an easier to handle mesh and less memory-consumer but reduce the quality of the approximation. In most cases the optimal value has to be defined empirically. If decimation is set to FALSE dont's waste your time in tuning this parameter: decimation will not be performed!
smoothing.terations	Optional, 10by default. Setting this parameter makes sense only if smoothing was previously set to TRUE. Increasing the number of iterations we can improve the "smoothing" applied to the original mesh.

Value

It returns a list of tree main elements:

• voxelCube.CT this is a 3D array which contains the voxel cube of the original CT scan

• voxelCube.Dose this is a 3D array which contains the voxel cube of the DOSES. The dimension is the same of the voxelCube because the dose value in the space has been interpolated (via triliear interpolation) in order to overlap the centroids of the voxels between voxelCube.CT and voxelCube.Dose. This should allow to quickly plot the expected dose value on a specific pixel/voxel in the CT scan.

• mesh is the mesh as returned fro the mesh package.

Examples

## Not run: 

obj<-geoLet()
obj$openDICOMFolder(pathToOpen='./DICOMSeries/pat001' );
obj$GLT.getDoseROIVoxels( Structure = "GTV" )


## End(Not run)

kbolab/moddicom documentation built on Nov. 29, 2020, 9:11 p.m.