{ "setVariables":["__tempBase__","__segBase__","__roiFile__","__petFile__","__ctFile__","__segFile__","__modelName__"], "setVariablesComment":"this variables will get updated with local values like home and can be used to set variables further on", "__tempBase__":"__home__/temp/segmentationdm", "__segBase__":"/home/studen/software/src/irAEMM/segmentation", "__roiFile__":"testMask.nii.gz", "__ctFile__":"testCT.nii.gz", "__petFile__":"testPET.nii.gz", "__segFile__":"segmentation.nii.gz", "__modelName__":"DM_defaults.DM_train_VISCERAL16_Fold1.final.2019-10-01.07.46.19.932616.model.ckpt", "tempBase":"__tempBase__", "model":"__model__", "project":"IPNUMMprospektiva/Study", "targetSchema":"study", "targetQuery":"Imaging1", "participantField":"ParticipantId", "imageDir":"preprocessedImages", "images":{ "CT":{ "queryField":"ctResampled", "tempFile":"__ctFile__"}, "PET":{ "queryField":"petResampled", "tempFile":"__petFile__"}, "patientmask":{ "queryField":"ROImask", "tempFile":"__roiFile__"} }, "replacePattern":{ "__workDir__":"__tempBase__", "__roi__":"__tempBase__/__roiFile__", "__pet__":"__tempBase__/__petFile__", "__ct__":"__tempBase__/__ctFile__", "__seg__":"__tempBase__/__segFile__", "__model__":"__modelName__" }, "deepmedic": { "config":{ "model":{ "template":"__segBase__/model/modelConfig.cfg.template", "out":"__tempBase__/modelConfig.cfg" }, "test":{ "template":"__segBase__/test/testConfig.cfg.template", "out":"__tempBase__/testConfig.cfg" }, "predictions":{ "template":"__segBase__/test/testNamesOfPredictions.cfg.template", "out":"__tempBase__/testNamesOfPredictions.cfg" }, "CT":{ "template":"__segBase__/test/testChannels_CT.cfg.template", "out":"__tempBase__/testChannels_CT.cfg" }, "ROI":{ "template":"__segBase__/test/testRoiMasks.cfg.template", "out":"__tempBase__/testRoiMasks.cfg" } } } }