irAEMM/templates/segmentationTCIA.json

{
 "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":"/Test/segmentationTest",
 "targetSchema":"study",
 "targetQuery":"Imaging1",
 "viewName":"segmentationReview",
 "participantField":"ParticipantId",
 "segmentationSchema":"study",
 "segmentationQuery":"Segmentations",
 "imageDir":"preprocessedImages",
 "version":"v5",
 "versionNumber":"5",
 "images":{
	"CT":{
		"queryField":"ctResampled",
		"tempFile":"__ctFile__"},
	"PET":{
		"queryField":"petResampled",
		"tempFile":"__petFile__"},
	"patientmask":{
		"queryField":"ROImask",
		"tempFile":"__roiFile__"},
	"segmentation":{
		"suffix":".nii.gz"
	}
 },
 "replacePattern":{
	 "__workDir__":"__tempBase__",
	 "__roi__":"__tempBase__/__roiFile__",
	 "__pet__":"__tempBase__/__petFile__",
	 "__ct__":"__tempBase__/__ctFile__",
	 "__seg__":"__tempBase__/__segFile__",
	 "__model__":"__modelName__"
 },
 "nnUNet":{
	 "ModelId":"501",
	 "configuration":"3d_fullres",
	 "env":{
		"nnUNet_raw_data_base":"__tempBase__",
		"nnUNet_preprocessed":"__tempBase__",
		"RESULTS_FOLDER":"/home/studen/software/src/iraemmsegmentationmodels"
	 }
 },
 "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"
		}



	 }
 }



}