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+{
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+ "setVariables":["__tempBase__","__segBase__","__roiFile__","__petFile__","__ctFile__","__segFile__","__modelName__","__suffix__"],
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+ "setVariablesComment":"this variables will get updated with local values like home and can be used to set variables further on",
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+ "__tempBase__":"__home__/temp/segmentation",
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+ "__segBase__":"/home/andrej/software/src/irAEMM/segmentation",
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+ "__roiFile__":"testMask",
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+ "__ctFile__":"testCT",
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+ "__petFile__":"testPET",
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+ "__segFile__":"segmentation",
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+ "__modelName__":"DM_defaults.DM_train_VISCERAL16_Fold1.final.2019-10-01.07.46.19.932616.model.ckpt",
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+ "__suffix__":"nii.gz",
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+ "tempBase":"__tempBase__",
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+ "model":"__model__",
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+ "project":"iPNUMMretro/Study",
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+ "targetSchema":"study",
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+ "targetQuery":"Imaging1",
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+ "participantField":"PatientId",
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+ "imageDir":"preprocessedImages",
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+ "segmentationSchema":"study",
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+ "segmentationQuery":"Segmentations",
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+ "version":"v3",
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+ "images":{
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+ "comment":"weight is coded as a sequence of intervals and [k,n] of linear function inbetween",
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+ "crop":{
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+ "00":{
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+ "range":["0","0.5"],
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+ "axis":"2",
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+ "n":"NONE",
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+ "w":[
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+ {"range":["0.0","0.3333"],"n":"1"},
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+ {"range":["0.3333","0.4166"],"k":"-12","n":"5"},
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+ {"range":["0.4166","1"],"n":"0"}
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+ ]
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+ },
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+ "01":{
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+ "range":["0.25","0.75"],
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+ "axis":"2",
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+ "n":"NONE",
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+ "w":[
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+ {"range":["0.0","0.3333"],"n":"0"},
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+ {"range":["0.3333","0.4166"],"k":"12","n":"-4"},
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+ {"range":["0.4166","0.5833"],"n":"1"},
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+ {"range":["0.5833","0.6666"],"k":"-12","n":"8"},
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+ {"range":["0.6666","1"],"n":"0"}
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+ ]
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+ },
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+ "02":{
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+ "range":["0.5","1"],
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+ "axis":"2",
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+ "n":"NONE",
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+ "w":[
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+ {"range":["0.0","0.5833"],"n":"0"},
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+ {"range":["0.5833","0.6666"],"k":"12","n":"-7"},
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+ {"range":["0.6666","1"],"n":"1"}
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+ ]
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+ }
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+ },
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+ "images":{
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+ "CT":{
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+ "queryField":"ctResampled",
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+ "tempFile":"__tempBase__/__ctFile__.__suffix__",
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+ "fileList":"__tempBase__/testChannels_CT.cfg"
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+ },
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+ "patientmask":{
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+ "queryField":"ROImask",
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+ "tempFile":"__tempBase__/__roiFile__.__suffix__",
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+ "fileList":"__tempBase__/testRoiMasks.cfg"
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+ },
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+ "segmentations":{
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+ "tempFile":"__segFile__.__suffix__",
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+ "fileList":"__tempBase__/testNamesOfPredictions.cfg"
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+ }
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+ }
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+ },
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+ "replacePattern":{
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+ "__workDir__":"__tempBase__",
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+ "__roi__":"__tempBase__/__roiFile__.__suffix__",
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+ "__pet__":"__tempBase__/__petFile__.__suffix__",
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+ "__ct__":"__tempBase__/__ctFile__.__suffix__",
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+ "__seg__":"__segFile__.__suffix__",
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+ "__model__":"__modelName__",
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+ "__segmentBase__":"__segBase__",
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+ "__sfx__":"__suffix__"
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+ },
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+ "deepmedic": {
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+ "config":{
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+ "model":{
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+ "template":"__segBase__/model/modelConfig.cfg.template",
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+ "out":"__tempBase__/modelConfig.cfg"
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+ },
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+ "test":{
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+ "template":"__segBase__/test/testConfig.cfg.template",
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+ "out":"__tempBase__/testConfig.cfg"
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+ }
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+ }
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+ }
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+
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+
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+}
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Andrej Studen/Merlin