CERROptions (user defined settings) - cerr/CERR GitHub Wiki

Various parameters for import and display can be set via CERROptions.json, including:

Import options

  • loadCT : Load CT scans into planC? ('yes' or 'no').

  • loadDoseSet : Fraction group ID to load into planC (will match with any Fx Grp ID with the same initial letters, independent of case). Note: To load all, set to 'any'.

  • loadStructures : Cell array of structure names to load. Set to {'any'} to load all structures.

  • CTEndian : Byte ordering of CT scans and digital films ('big' or 'little').

  • loadFilm : Load digital films ('any' or 'none').

  • zipSave : Zip the resulting planC file using bzip2 ('yes' or 'no').

  • scanStructures : Cell array of structure names to convert to raster/scan segment format for DVH calculations ({'any'} {'none'} or list)

  • DSHMaxPointInterval : Maximum interval (in cm) between surface sampling points for dose-surface histograms.

  • surfPtStructures = : Any structure whose name matches this name, up to the number of letters given, will have surface points generated during import, e.g.: 'lun' will match 'lung' or 'lung_all'.

Dose Import options

  • downsampleLargeDoses : If 'yes', downsamples doses that are exceptionally large. For example, Corvis doses are usually defined at all points on the CT, which can lead to dose distributions that are 300MB+ in size.

  • doseSizeThreshold : Maximum size in MB of a dose array before it will be downsampled. Only active if downsampleLargeDoses is set to 'yes'.

  • promptForNewSize : If 'yes', prompts the user to input a voxel size, to be used for the downsampled dose distribution. If 'no', uses the value specifed in downsampledVoxelSize.

  • downsampledVoxelSize : Size of a voxel in the downsampled dose distribution, [dx, dy, dz].

  • importDICOMsubDirs : If 'yes', imports DICOM data from within sub-directories, if 'no', imports DICOM data from the passed directory only.

Scan uniformization options

Given a set of CT values, we choose the largest block which CT slice spacing which falls within the limits of lowerLimitUniformCTSliceSpacing and upperLimitUniformCTSliceSpacing. Otherwise we create a set with a spacing equal to alternateUniformCTSliceSpacing. If the user desires a uniformized scan with a spacing of exactly alternateUniformCTSliceSpacing, then set optS.lowerLimitUniformCTSliceSpacingto be larger than optS.upperLimitUniformCTSliceSpacing.

  • createUniformizedDataset : Create uniformized & registered CT and structures datasetsduring import ('yes' or 'no'). The uniformized scan set has a uniform axial (z) spacing and the same transverse resolution as the normal CT-scan (usually, but not always, 512 x 512).

  • uniformizeExcludeStructs : Cell array of structures to leave out of uniformization process. In particular, leaving out skin increases program speed and decreases memory requirements.

  • uniformizedDataType : Datatype for uniformized dataset ('uint16'; %'uint8' or 'uint16').

  • structureArrayDataType : Datatype used to create uniformized structure array. Effectively sets max structures in a plan to 32 or 52 -- the number of bits in the respective datatypes ('uint32'; %'uint32' or 'double').

  • lowerLimitUniformCTSliceSpacing : Smallest allowed uniformized slice spacing. We take the largest block which is within the smallest and largest slice spacing requirements, inclusive of the endpoints.

  • upperLimitUniformCTSliceSpacing : Largest allowed uniformized slice spacing.

  • alternateLimitUniformCTSliceSpacing : If there are no initial CT slices between the largest and smallest slice width allowed, make a uniformized dataset with this width.

Slice viewer options

  • useOpenGL : 1 to use openGL, 0 to avoid openGL.

  • isodoseLevelMode : Isodose line calculation ('auto' or 'manual').

  • isodoseLevels : Isodose levels to show if optS.isodoseLevelMode = 'manual'.

  • autoIsodoseLevels : Number of levels displayed if optS.isodoseLevelMode = 'auto'.

  • autoIsodoseRangeMode : Range used for autoIsodoseLevels (1 or 2, where 1 is max/min, and 2 is user defined).

  • autoIsodoseRange : Default range used for autoIsodoseLevels if optS.autoIsodoseRangeMode = 'User'.

  • isodoseLevelType : 'absolute' or 'percent'

  • isodoseUseColormap : Set to 1 if isodose line colors should be determined based on colorbar values.

  • isodoseThickness : Thickness of isodose lines

  • structureThickness : Thickness of structure lines

  • structureDots : Set to 0 to disable black dots on structure lines.

  • displayDoseSet : The dose distribution to be displayed. Defaults to the first dose distribution if this is not available.

  • doseInterpolationMethod : Interpolation method for dose on to CT grid ('linear' or 'nearest').

  • tickInterval : Ruler tick interval in cm.

  • CTLevel : Beginning CT level and width

  • CTWidth

  • fontsize : GUI font size

  • UIColor : Color of UI buttons

  • colorOrder : Color order for contour display. Each 3 number triple is r, g, b. Note: do not put commas into the colorOrder.

  • contourToSliceTolerance : Snap contour to slice located within this distance (cm).

  • inactiveSegStyle : Line style for inactive contouring segments

  • activeSegStyle : Line style for active contouring segments

  • displayPatientName : 1 ('on') or 0 ('off').

  • initialZoomTrans : Initial transverse zoom factor

  • initialZoomSag = 1.0; %Initial saggital zoom factor

  • initialZoomCor : Initial coronal zoom factor

  • zoomFactor : x-y scale factor when zooming.

  • dosePlotType : Method of dose distribution display ('isodose' or 'colorwash').

  • doseColormap : Colormap for dose colorwash read from CERRColormap.m. Options: 'jetmod' (modified jet), 'full' (full rainbow), 'ppt'(powerpoint based) 'star (14 non-blending colors)', 'starinterp', 'gray' or 'gray256'.

  • CTColormap : CT colormap, usually grayscale. Also read from CERRColormap.m. Same choices as doseColormap.

  • colorbarChoices : List of available colormaps : {'coolwarm','jetmod', 'ppt', 'full', 'full2', 'star', 'starinterp', 'gray', 'gray256', 'grayud64', 'doublecolorinvert', 'thedrewspecial', 'graycenter0width300', 'hotcold', 'copper', 'weather'};

  • staticColorbar : Set to 1 to have the same colors represent the same dose values when switching between does distributions.

  • colorbarMin : Colorbar minimum value. Set to '' to default to minimum dose value.

  • colorbarMax : Colorbar maximum value. Set to '' to default to maximum dose value.

  • transparentZeroDose : If set to '1', dose that is zero is always transparent even if the colorbar suggests it should have color.

  • doubleSidedColorbar : If set to '1', the colorbar is inverted onto itself to create a double-headed colorbar that is useful for viewing negative values.

  • negativeTexture : If 1, negative values (those < doseOffset) are displayed with a raster texture.

  • colorbarMarks : Ticks on colorbar to indicate dose levels (in Gy). Examples: [70], [50,70]. To leave it empty, type [].

  • visualRefColormapRows : Number of rows in visual reference colorwash colormap.

  • visualRefTopColormap : Colormap between visualRefDose and max dose.

  • visualRefBottomColormap : Colormap between zero dose and visualRefDose.

  • visualRefDose : If visualReferenceDoseMode is 'on', the color in the dose colorwash at this dose is set to white. The colormap above this dose will be modified to make it easy to pick out this dose.

  • initialTransparency: Alpha for colorwash (0-1). 1 is opaque, 0 transparent. Makes CT visible through wash.

  • calcDoseInsideSkinOnly : Set to '1' to calculate only dose inside the skin on the transverse viewer for increased speed.

  • CERRStatusStringEnabled : Change to zero to mute all CERRStatusString outputs to GUI and Matlab prompt.

Image Fusion options

  • fusionDisplayMode : 'colorblend'; %'colorblend', 'checked', 'max', or 'canny'.

  • fusionCheckSize : Size in cm of each side of checkerboard elements.

  • fusionAlgorithms = {'Manual', 'ControlPts - Affine', 'ControlPts - Perspective', 'Exhaustive Search - MI', 'Stocastic - MI', 'Contour Based'};

  • fusionTemplates = {@Manual, @CTP_Affine, @CTP_Perspective, @Exhaustive, @Stocastic, @ContourBased};

3D display option

  • visual3DxyDownsampleIndex : Downsample to this resolution in the transverse plane for 3D display

Dose Profile option

  • numDoseProfileSamples : The number of samples to take along dose profile lines.

DVH/DSH options

  • ROISampleRate : Rate of ROI sampling compared to CT spacing, for DVH computations (integer >= 1).

  • DVHBinWidth : Store and display DVHs with this width, in units of Gy.

  • DVHBlockSize : Block processing parameter. 5000 is the default. This results in much less temporary storage for large structure DVH computations. If there is disk-thrashing during the DVH calculation, try reducing this number first.

  • DVHLineWidth : Line thickness of DVH and DSH lines.

IVH (Intensity Volume Histogram) options

  • ROISampleRate : Uses the same as DVH

  • IVHBinWidth : Store and display IVHs with this width, in units of Gy.

  • IVHBlockSize : Block processing parameter. 5000 is the default. This results in much less temporary storage for large structure IVH computations. If there is disk-thrashing during the IVH calculation, try reducing this number first.

  • IVHLineWidth : Line thickness of IVH lines.

%List of standard VOI names for renaming DVH's for export.

  • defaultVOINames = {'GTV', 'CTV', 'PTV', 'spinal cord', 'heart', 'total lung', 'rt kidney', 'lt kidney','a','b','c','d','e','f','g','h','i','j','k','l','m'};

Contouring options

  • nudgeDistance : Number of voxel widths to nudge the active contour.

Navigation montage options

  • navigationMontageColormap = 'grayCenter0Width300';
  • navigationMontageOnImport : Create thumbnails on import ('yes' or 'no').
  • navigationMontage : Display navigation montage when the CERR viewer is started ('yes' or 'no').

Wavelet dose compression options

  • wavletcompresthreshpersent : CZ add wavelet compression parameters 04-24-03
  • wavletcompressiondecomplevel = 5;

IMRT options

  • IMRTCheckResolution : If original plan is 512x512, downsample by factor of 2 if 'on'.

List of installed dose calculation algorithms. First is the string to describe the algorithm, second is a function handle pointing to code that returns a template of options required for the algorithm, and last is the function handle to execute the algorithm. The function will get an IM structure and the structure of its options on execution.

  • IMRTDoseCalculationAlgorithms = {'QIB', 'VMC++'};

  • IMRTDoseCalculationTemplates = {@getQIBTemplate, @getVMCTemplate};

  • IMRTDoseCalculationFunction = {@generateQIBInfluence, @generateVMCInfluence};

  • IMRTScatterReductionAlgorithms = {'Exponential', 'Probabilistic', 'Threshold', 'None'};

  • IMRTScatterReductionTemplates = {@ExponentialTemplate, @ProbabilisticTemplate, @ThresholdTemplate, @NoneTemplate};

  • IMRTAutoIsocenterAlgorithms = {'GeometricCOM','Manual'};

  • IMRTAutoIsocenterFunctions = {@isocenterGeometricCOM, @isocenterManual};

planMetrics options

  • planMetrics : Installed metrics. Metrics must be added to metricSelection.m in the "%function" command for the compiled version Currently available : {'meanDose', 'maxDose', 'minDose', 'Vx', 'Dx', 'EUD', 'ERP', 'LKB', 'stdDevDose','MOCx','MOHx'};

Window presets - name, center, width !do not remove Manual dummy preset! (#1)

  • windowPresets = [struct('name', '--Manual--', 'center', 0, 'width', 0) struct('name', 'Abd/Med', 'center', -10, 'width', 330) struct('name', 'Head', 'center', 45, 'width', 125) struct('name', 'Liver', 'center', 80, 'width', 305) struct('name', 'Lung', 'center', -500, 'width', 1500) struct('name', 'Spine', 'center', 30, 'width', 300) struct('name', 'Vrt/Bone', 'center', 400, 'width', 1500) struct('name', 'PET', 'center', 4500, 'width', 11000) struct('name', 'MR', 'center', -500, 'width', 1350) struct('name', 'SPECT', 'center', 400, 'width', 1000) struct('name', 'Top 90', 'center', 400, 'width', 1000)];

Color Map base scan

  • scanColorMap = [struct('name', 'gray256') struct('name', 'copper') struct('name', 'Red') struct('name', 'Green') struct('name', 'Blue') struct('name', 'StarInterp') struct('name', 'hotCold') struct('name', 'weather')];

Caching options

  • cachingEnabled : Caching (1 to enable, 0 to disable).
  • colorWashCacheSize : Amount of memory to use per dose for caching colorwash in megabytes.

Matlab 7 compatibility options

  • saveFormat : Set to [] to use default, '-V6' to save all files in Matlab6 readable format (V6 is used to maintain Matlab 7 backwards compatibility with version 6+) or '-V7.3'.

  • plotObjFormat : Flags for plotObjects that changed, and introduced incompability between Matlab 7 and old versions.

microRT options

  • chkMicroRT = 0;

Compression-type options

  • CompressType : Compression method ('zip' or 'bz2').

Batch process

  • format = 'DICOM';

Initial panel layout

  • layout : Viewer layout ( 1:1-Large, 2:1-Large+Bar, 3:2-Medium, 4:4-Medium, 5:1-Large+3-Small, 9: Perfusion/Diffusion

Generate log on start-up

  • logOnStartup : Generate log (1-Yes, 0-No)

Temporary directory to extract bz2

  • tmpDecompressDir : Path to temporary folder. (tempdir, 'C:\tempCERRExtract')

ROI Interpreted Type

  • ROIInterpretedType = initROIInterpretedType;

Option to convert PET to SUV

  • convert_PET_to_SUV : 0- Do not convert to SUV, 1- Convert to SUV

Option to overwrite CERR file if a bug is found during QA

  • overwrite_CERR_File : 0- Do not overwrite, 1- overwrite

Option to overwrite CERR file if a bug is found during QA

  • sinc_filter_on_display : 0- Do not apply sinc, 1- apply sinc

Filename for plastimatch commands

Note: this file must be stored under ...\CERR\CERR_core\ImageRegistration\plastimatch_command

  • plastimatch_command_file : 'bspline_register_cmd_dir.txt'; %'malcolm_pike_mr_breast_data.txt'; %'mr_ct_edge_based.txt';

Size of pool of line handles.

  • linePoolSize : Anticipated no. of structure segments per view

Paths to JSON protocol, model, and criteria files for ROE

  • optS.ROEProtocolPath = 'Path/To/Protocols';
  • optS.ROEModelPath = 'Path/To/Models';
  • optS.ROECriteriaPath = 'Path/To/Criteria';

Radiomics features calculation parameters

  • shape_rcsV : [r,c,s] Number of rows/cols/slcs to upsample the roi

  • higherOrder_minIntensity

  • higherOrder_maxIntensity

  • higherOrder_numGrLevels

  • higherOrder_patchRadius2dV

  • higherOrder_patchRadius3dV

  • higherOrder_imgDiffThresh

  • peakValley_peakRadius

  • ivh_xForIxV : Percentage volume

  • ivh_xAbsForIxV : Absolute volume [cc]

  • ivh_xForVxV : Percent intensity cutoff

  • ivh_xAbsForVxV : Absolute intensity cutoff (image units)