params.json 3.4 KB

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  1. {
  2. "paths": {
  3. "topdir": "..",
  4. "agecsv": "config/ages.csv",
  5. "imgcsv": "config/subjects.csv",
  6. "tmpdir": "cache",
  7. "outdir": "output"
  8. },
  9. "images": {
  10. "default": "t2w",
  11. "ref": "config/domain.nii.gz",
  12. "t1w": {
  13. "prefix": "images/t1w/",
  14. "suffix": ".nii.gz",
  15. "interp": "linear",
  16. "datatype": "float",
  17. "normalization": "z-score",
  18. "rescaling": [1, 100],
  19. "sharpen": true,
  20. "bkgrnd": 0,
  21. "bins": 0
  22. },
  23. "t2w": {
  24. "prefix": "images/t2w/",
  25. "suffix": ".nii.gz",
  26. "interp": "linear",
  27. "datatype": "float",
  28. "normalization": "z-score",
  29. "rescaling": [1, 100],
  30. "sharpen": true,
  31. "bkgrnd": 0,
  32. "bins": 0
  33. },
  34. "tissues": {
  35. "prefix": "labels/tissues/",
  36. "suffix": ".nii.gz",
  37. "labels": "1..9",
  38. "interp": "nn"
  39. },
  40. "structures": {
  41. "prefix": "labels/structures/",
  42. "suffix": ".nii.gz",
  43. "labels": "1..87",
  44. "interp": "nn"
  45. }
  46. },
  47. "iterations": 8,
  48. "registration": {
  49. "affine": {
  50. "prefix": "global/",
  51. "suffix": ".dof"
  52. },
  53. "config": [
  54. {
  55. "energy": "Symmetric",
  56. "model": "SVFFD",
  57. "ffdim": "SS",
  58. "intsteps": 64,
  59. "liederiv": false,
  60. "bchterms": 2,
  61. "channels": ["t2w"],
  62. "measures": {"t2w": "NMI"},
  63. "padding": true,
  64. "interpolation": "Linear with padding",
  65. "foreground": "Union",
  66. "levels": 3,
  67. "resolution": 1.0,
  68. "spacing": [8.0, 16.0, 32.0],
  69. "bending": 1e-3,
  70. "jacobian": 0e-0,
  71. "blurring": {"tissues": 2, "structures": 2}
  72. },
  73. {
  74. "levels": 4,
  75. "resolution": 0.5,
  76. "spacing": [8.0, 8.0, 16.0, 32.0]
  77. },
  78. {
  79. "spacing": 4.0
  80. },
  81. {
  82. "spacing": 4.0
  83. },
  84. {
  85. "spacing": 4.0
  86. },
  87. {
  88. "bending": 5e-3,
  89. "jacobian": 1e-5,
  90. "spacing": 2.0
  91. },
  92. {
  93. "spacing": 2.0
  94. },
  95. {
  96. "spacing": 2.0
  97. }
  98. ],
  99. "growth": {
  100. "enabled": true,
  101. "exclavg": false,
  102. "bchterms": 3
  103. }
  104. },
  105. "regression": {
  106. "means": [36, 37, 38, 39, 40, 41, 42, 43, 44],
  107. "sigma": [1.64, 1.31, 1.0, 0.77, 0.64, 0.73, 0.86, 1.18, 1.5],
  108. "epsilon": 0.01,
  109. "precision": 2
  110. },
  111. "evaluation": {
  112. "measures": {
  113. "t2w": ["sdev", "gini", "entropy", "grad"],
  114. "tissues": ["entropy", "label-consistency", "grad(2)"],
  115. "structures": ["entropy", "label-consistency"]
  116. },
  117. "rois": {
  118. "structure={l:02d}": ["structures", "all"],
  119. "tissue={l:d}": ["tissues", "all"]
  120. }
  121. },
  122. "environment": {
  123. "queue": {
  124. "short": "local",
  125. "long": "local"
  126. },
  127. "threads": 8
  128. }
  129. }