Computational Human Brain Phantom

brain_phantom

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Summary:

  1. Based on a segmented MRI dataset of a normal subject, including ~100 structures (listed below).
  2. The program also allows simulation of motion (rigid; 3 translations, 3 rotations).

Reference:

Please consult (and reference) the following work wherein the construction of the phantom has been described:
A. Rahmim et al., Accurate event-driven motion compensation in high-resolution PET incorporating scattered and random events , IEEE Trans. Med. Imag., vol. 27, pp. 1018-1033, 2008.

Technical description:

Voxelized phantoms are problematic in that they are fixed to a particular spatial resolution, and also result in interpolation errors when modeling motion (e.g. the volume of a voxelized object may not be conserved after rotation). Alternatively, a mathematical brain phantom was developed, containing continuous structures and thus avoiding the need for interpolations when introducing motion. The brain phantom was constructed using subdivision surfaces. Subdivision surfaces can be used to efficiently model structures with an arbitrary topological type, such as the brain, skull, muscle tissue, and vasculature. Surfaces were modeled based on a segmented MRI dataset of a normal subject. The dataset consisted of 181 slices of the brain (pixel-sizes/slice-widths of 1.0 mm’s). Nearly 100 structures in the brain were identified. A software application was written using the Visualization Toolkit (VTK) to create 3D polygon surfaces. The VTK marching cubes algorithm was first used to create an initial polygon model for each structure. The polygon model was then optimized using the mesh optimization and smoothing routines of the VTK software.

Brain Structures:

The following ~100 structures are included in the phantom, which can be easily merged by assigning similar values.


  1. Grey “superior frontal gyrus” right
  2. “superior frontal gyrus” left
  3. “middle frontal gyrus” right
  4. “middle frontal gyrus” left
  5. “inferior frontal gyrus” right
  6. “inferior frontal gyrus” left
  7. “precentral gyrus” right
  8. “precentral gyrus” left
  9. “lateral front-orbital gyrus” right
  10. “lateral front-orbital gyrus” left
  11. “medial front-orbital gyrus” right
  12. “medial front-orbital gyrus” left
  13. “cingulate region” right
  14. “cingulate region” left
  15. “medial frontal gyrus” right
  16. “medial frontal gyrus” left
  17. “superior parietal lobule” right
  18. “superior parietal lobule” left
  19. “supramarginal gyrus” right
  20. “supramarginal gyrus” left
  21. “angular gyrus” right
  22. “angular gyrus” left
  23. “precuneus” right
  24. “precuneus” left
  25. “postcentral gyrus” right
  26. “postcentral gyrus” left
  27. “superior temporal gyrus” right
  28. “superior temporal gyrus” left
  29. “middle temporal gyrus” right
  30. “middle temporal gyrus” left
  31. “inferior temporal gyrus” right
  32. “inferior temporal gyrus” left
  33. “uncus” right
  34. “uncus” left
  35. “medial occipitotemporal gyrus” right
  36. “medial occipitotemporal gyrus” left
  37. “lateral occipitotemporal gyrus” right
  38. “lateral occipitotemporal gyrus” left
  39. “amygdala” right
  40. “amygdala” left
  41. “parahippocampal gyrus” right
  42. “parahippocampal gyrus” left
  43. “occipital pole” right
  44. “occipital pole” left
  45. “superior occipital gyrus” right
  46. “superior occipital gyrus” left
  47. “middle occipital gyrus” right
  48. “middle occipital gyrus” left
  49. “inferior occipital gyrus” right
  50. “inferior occipital gyrus” left
  51. “cuneus” right
  52. “cuneus” left
  53. “lingual gyrus” right
  54. “lingual gyrus” left
  55. “insula” right
  56. “insula” left
  57. Caudate “caudate nucleus” right
  58. “caudate nucleus” left
  59. Putamen “putamen” right
  60. “putamen” left
  61. “globus palladus” right
  62. “globus palladus” left
  63. “thalamus” right
  64. “thalamus” left
  65. White “corpus callosum”
  66. “subarachnoid cerebro-spinal fluid”
  67. “third ventricle”
  68. “fourth ventricle”
  69. “lateral ventricle” right
  70. “lateral ventricle” left
  71. BrainStem “brain stem”
  72. “white matter”
  73. “frontal lobe WM” right
  74. “frontal lobe WM” left
  75. “occipital lobe WM” right
  76. “occipital lobe WM” left
  77. “parietal lobe WM” right
  78. “parietal lobe WM” left
  79. “temporal lobe WM” right
  80. “temporal lobe WM” left
  81. “background”
  82. “scalp”
  83. “skull”
  84. “dura and sinuses”
  85. “hippocampal formation” right
  86. “hippocampal formation” left
  87. “nucleus accumbens” right
  88. “nucleus accumbens” left
  89. “fornix” right
  90. “fornix” left
  91. “posterior limb of internal capsule inc. cerebral peduncle” right
  92. “posterior limb of internal capsule inc. cerebral peduncle” left
  93. “subthalamic nucleus” right
  94. “subthalamic nucleus” left
  95. “anterior limb of internal capsule” right
  96. “anterior limb of internal capsule” left
  97. Cerebellum “cerebellum” right
  98. “cerebellum” left