segmentationPreproces.json 1.9 KB

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  1. {
  2. "setVariables":["__tempBase__","__segBase__","__roiFile__","__petFile__","__ctFile__","__segFile__","__modelName__"],
  3. "setVariablesComment":"this variables will get updated with local values like home and can be used to set variables further on",
  4. "__tempBase__":"__home__/temp/segmentation",
  5. "__segBase__":"/home/nixUser/software/src/irAEMM/segmentation",
  6. "__roiFile__":"testMask.nii.gz",
  7. "__ctFile__":"testCT.nii.gz",
  8. "__petFile__":"testPET.nii.gz",
  9. "__segFile__":"segmentation.nii.gz",
  10. "__modelName__":"DM_defaults.DM_train_VISCERAL16_Fold1.final.2019-10-01.07.46.19.932616.model.ckpt",
  11. "tempBase":"__tempBase__",
  12. "model":"__model__",
  13. "project":"IPNUMMprospektiva/Study",
  14. "targetSchema":"study",
  15. "targetQuery":"Imaging1",
  16. "participantField":"ParticipantId",
  17. "imageDir":"preprocessedImages",
  18. "images":{
  19. "CT":{
  20. "queryField":"ctResampled",
  21. "tempFile":"__ctFile__"},
  22. "PET":{
  23. "queryField":"petResampled",
  24. "tempFile":"__petFile__"},
  25. "patientmask":{
  26. "queryField":"ROImask",
  27. "tempFile":"__roiFile__"}
  28. },
  29. "replacePattern":{
  30. "__workDir__":"__tempBase__",
  31. "__roi__":"__tempBase__/__roiFile__",
  32. "__pet__":"__tempBase__/__petFile__",
  33. "__ct__":"__tempBase__/__ctFile__",
  34. "__seg__":"__tempBase__/__segFile__",
  35. "__model__":"__modelName__"
  36. },
  37. "deepmedic": {
  38. "config":{
  39. "model":{
  40. "template":"__segBase__/model/modelConfig.cfg.template",
  41. "out":"__tempBase__/modelConfig.cfg"
  42. },
  43. "test":{
  44. "template":"__segBase__/test/testConfig.cfg.template",
  45. "out":"__tempBase__/testConfig.cfg"
  46. },
  47. "predictions":{
  48. "template":"__segBase__/test/testNamesOfPredictions.cfg.template",
  49. "out":"__tempBase__/testNamesOfPredictions.cfg"
  50. },
  51. "CT":{
  52. "template":"__segBase__/test/testChannels_CT.cfg.template",
  53. "out":"__tempBase__/testChannels_CT.cfg"
  54. },
  55. "ROI":{
  56. "template":"__segBase__/test/testRoiMasks.cfg.template",
  57. "out":"__tempBase__/testRoiMasks.cfg"
  58. }
  59. }
  60. }
  61. }