CERROptions.json

{
"loadCT" : "yes",

"loadDoseSet" : "any" ,

"loadStructures" : ["any"],

"CTEndian" : "big",

"loadFilm" : "none",

"zipSave" : "yes",

"scanStructures" : ["any"],

"DSHMaxPointInterval" : 0.2,

"surfPtStructures" : [""],

"downsampleLargeDoses" : "yes",

"doseSizeThreshold" : 100,

"promptForNewSize" : "no",

"downsampledVoxelSize" : [0.2, 0.2, 0.3],

"importDICOMsubDirs" : "yes",

"saveDICOMheaderInPlanC" : "yes",

"structuresToImport" : "",

"structuresImportMatchCriteria" : "regex",

"createUniformizedDataset" : "yes",

"uniformizeExcludeStructs"  : ["normaltissue", "CT_EXTERNAL"],

"uniformizedDataType"  :  "uint16",

"structureArrayDataType" : "uint32",

"lowerLimitUniformCTSliceSpacing" :  0.005,

"upperLimitUniformCTSliceSpacing" :  10,

"alternateLimitUniformCTSliceSpacing" : 0.3,

"useOpenGL" : 1,

"isodoseLevelMode" : "auto",

"isodoseLevels" : [70, 65, 60, 55, 50, 45, 40, 20, 10],

"autoIsodoseLevels" : 6,

"autoIsodoseRangeMode" : 1,

"autoIsodoseRange" : [0, 100],

"isodoseLevelType" : "absolute",

"isodoseUseColormap" : 1,

"isodoseThickness" : 1,

"structureThickness" : 2,

"structureDots" : 1,

"displayDoseSet"  : "",

"doseInterpolationMethod" : "linear",

"tickInterval"   : 1,

"CTLevel" : 0,

"CTWidth" : 300,

"fontsize" : 8,

"UIColor" : [0.9,0.9,0.9],

"colorOrder" : [[0.9, 0.63, 0], [0, 0.9,0], [0.9, 0, 0], [0,  0.81, 0.81], [0.675, 0, 0.6750], [0.675, 0.675, 0], [0.54, 0.675, 0.9], [0.72, 0.225, 0.225], [0.9, 0, 0.9], [0.675, 0.45, 0], [0, 0.9, 0.45], [0.9, 0.45, 0.9], [0.45, 0.9, 0], [0.27, 0, 0.81], [0, 0.63, 0.27], [0.63, 0.27, 0], [0, 0.72, 0.81], [0.63, 0, 0.72], [0.81, 0.54, 0], [0.297, 0.594, 0.9000], [0.9, 0.297, 0.297], [0.9, 0, 0.81], [0.81, 0.45, 0], [0, 0.9, 0.36], [0.81, 0.54, 0.81], [0.54, 0.81, 0], [0.63, 0.36, 0.72], [0.54, 0.81, 0.18]],

"contourToSliceTolerance" : 0.008,

"inactiveSegStyle" : "--",

"activeSegStyle" : "-",

"displayPatientName" : 0,

"initialZoomTrans" : 1.7,

"initialZoomSag" : 1.0,

"initialZoomCor" : 1.0,

"zoomFactor" : 2.0,

"dosePlotType" : "colorwash",

"doseColormap" : "starinterp",

"CTColormap" : "gray256",

"colorbarChoices" : ["coolwarm","jetmod", "ppt", "full", "full2", "star", "starinterp", "gray", "gray256", "grayud64", "doublecolorinvert", "thedrewspecial", "graycenter0width300", "hotcold", "copper", "weather"],

"staticColorbar" : 0,

"colorbarMin" : "",

"colorbarMax" : "",

"transparentZeroDose" : 1,

"doubleSidedColorbar" : 0,

"negativeTexture" : 1,

"colorbarMarks" : [],

"visualRefColormapRows" : 256,

"visualRefTopColormap"  : "grayud64",

"visualRefBottomColormap" : "full2",

"visualRefDose" : 65,

"visualRefDoseMode" : "off",

"initialTransparency" : 0.5,

"calcDoseInsideSkinOnly" : 0,

"CERRStatusStringEnabled" : 1,

"fusionDisplayMode" : "colorblend",

"fusionCheckSize" : 2,

"fusionAlgorithms" : ["Manual", "ControlPts - Affine", "ControlPts - Perspective", "Exhaustive Search - MI", "Stocastic - MI", "Contour Based"],

"fusionTemplates" : ["Manual", "CTP_Affine", "CTP_Perspective", "Exhaustive", "Stocastic", "ContourBased"],

"visual3DxyDownsampleIndex" : 128,

"numDoseProfileSamples" : 200,

"ROISampleRate" : 1,

"DVHBinWidth" : 0.1,

"DVHBlockSize" : 5000,

"DVHLineWidth"  : 1.5,

"IVHBinWidth" : 0.02,

"IVHBlockSize" : 5000,

"IVHLineWidth"  : 1.5,

"defaultVOINames" : ["GTV", "CTV", "PTV", "spinal cord", "heart", "total lung", "rt kidney", "lt kidney"],

"nudgeDistance" : 0.5,

"navigationMontageColormap" : "grayCenter0Width300",
"navigationMontageOnImport" : "no",
"navigationMontage" : "no",

"wavletcompresthreshpersent" : 1,
"wavletcompressiondecomplevel" : 5,

"IMRTCheckResolution" : "on",

"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" : ["meanDose", "maxDose", "minDose", "Vx", "Dx", "EUD", "ERP", "LKB", "stdDevDose","MOCx","MOHx"],

"windowPresets" : [{"name": "--Manual--", "center": 0, "width": 0}, {"name": "Abd/Med", "center": -10, "width": 330}, {"name": "Head", "center": 45, "width": 125}, {"name": "Liver", "center": 80, "width": 305}, {"name": "Lung", "center": -500, "width": 1500}, {"name": "Spine", "center": 30, "width": 300},  {"name": "Vrt/Bone", "center": 400, "width": 1500}, {"name": "PET", "center": 4500, "width": 11000}, {"name": "MR", "center": -500, "width": 1350}, {"name": "SPECT", "center": 400, "width": 1000}, {"name": "Top 90", "center": 400, "width": 1000}],

"scanColorMap" : [{"name": "gray256"}, {"name": "copper"}, {"name": "Red"}, {"name": "Green"}, {"name": "Blue"}, {"name": "StarInterp"}, {"name": "hotCold"}, {"name": "weather"}],

"cachingEnabled" : 0,
"colorWashCacheSize" : 64,

"saveFormat" : "-mat",

"plotObjFormat" : "v6",

"chkMicroRT" : 0,

"CompressType" : "bz2",

"format" : "DICOM",

"layout" : 5,

"logOnStartup" : 0,

"tmpDecompressDir" : "",

"ROIInterpretedType" : "initROIInterpretedType",

"convert_PET_to_SUV" : 1,

"suvType": "BW",

"overwrite_CERR_File" : 0,

"sinc_filter_on_display" : 0,

"store_scan_as_mr_philips_precise_value" : "yes",

"retainOriginalUIDonExport" : "yes",

"plastimatch_command_file" : "bspline_register_cmd_dir.txt",
"plastimatch_build_dir" : "C:\\software\\plastimatch-build\\Release",

"elastix_build_dir" : "C:\\software\\Elastix_5.0",

"linePoolSize" : 30,

"ROEProtocolPath" : "fullfile(getCERRPath,'PlanAnalysis/sampleFilesForROE/Protocols')",
"ROEModelPath" : "fullfile(getCERRPath,'PlanAnalysis/sampleFilesForROE/Models')",
"ROECriteriaPath" : "fullfile(getCERRPath,'PlanAnalysis/sampleFilesForROE/Criteria')",
"ROEDoseScaleRange": [0.5,1.5],

"sitkLibPath" : "C:\\Program Files\\Python38\\Lib\\site-packages",

"antspath_dir" : "/lab/deasylab1/Eve/LDDMM/antsbin",

"condaPath" : "/usr/local/"
}