Adding script use in nnUNet on IRAEMM images

templates/segmentationIRAEMM_ONKO.json

@@ -0,0 +1,84 @@
+{
+ "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",
+ "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"
+		}
+
+
+
+	 }
+ }
+
+
+
+}