segmentationIRAEMM_ONKO.json 2.4 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/iraemm",
  5. "__segBase__":"/home/studen/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. "viewName":"segmentationReview",
  17. "participantField":"ParticipantId",
  18. "segmentationSchema":"study",
  19. "segmentationQuery":"Segmentations",
  20. "reportQuery":"reportImages",
  21. "reportSchema":"lists",
  22. "percentileQuery":"SUVQuantiles",
  23. "imageDir":"preprocessedImages",
  24. "version":"v5",
  25. "versionNumber":"5",
  26. "images":{
  27. "CT":{
  28. "queryField":"ctResampled",
  29. "tempFile":"__ctFile__"},
  30. "PET":{
  31. "queryField":"petResampled",
  32. "tempFile":"__petFile__"},
  33. "patientmask":{
  34. "queryField":"ROImask",
  35. "tempFile":"__roiFile__"},
  36. "segmentation":{
  37. "suffix":".nii.gz"
  38. }
  39. },
  40. "replacePattern":{
  41. "__workDir__":"__tempBase__",
  42. "__roi__":"__tempBase__/__roiFile__",
  43. "__pet__":"__tempBase__/__petFile__",
  44. "__ct__":"__tempBase__/__ctFile__",
  45. "__seg__":"__tempBase__/__segFile__",
  46. "__model__":"__modelName__"
  47. },
  48. "nnUNet":{
  49. "ModelId":"501",
  50. "configuration":"3d_fullres",
  51. "env":{
  52. "nnUNet_raw_data_base":"__tempBase__",
  53. "nnUNet_preprocessed":"__tempBase__",
  54. "RESULTS_FOLDER":"/home/studen/software/src/iraemmsegmentationmodels"
  55. }
  56. },
  57. "deepmedic": {
  58. "config":{
  59. "model":{
  60. "template":"__segBase__/model/modelConfig.cfg.template",
  61. "out":"__tempBase__/modelConfig.cfg"
  62. },
  63. "test":{
  64. "template":"__segBase__/test/testConfig.cfg.template",
  65. "out":"__tempBase__/testConfig.cfg"
  66. },
  67. "predictions":{
  68. "template":"__segBase__/test/testNamesOfPredictions.cfg.template",
  69. "out":"__tempBase__/testNamesOfPredictions.cfg"
  70. },
  71. "CT":{
  72. "template":"__segBase__/test/testChannels_CT.cfg.template",
  73. "out":"__tempBase__/testChannels_CT.cfg"
  74. },
  75. "ROI":{
  76. "template":"__segBase__/test/testRoiMasks.cfg.template",
  77. "out":"__tempBase__/testRoiMasks.cfg"
  78. }
  79. }
  80. }
  81. }