Alvar: Adult whole-body anatomic phantom for computational dosimetry
(documentation is work in progress)
The phantom, Alvar, is based on freely available online anatomic atlas, BodyParts3D (http://lifesciencedb.jp/bp3d/), which consists of 3D surface meshes of over 2000 organs or their parts. Alvar weights 72 kg, is 176 cm tall, and has a surface area of 1.83 m^2.
For making the Alvar phantom, each surface mesh was voxelized with a uniform resolution of 0.5 mm x 0.5 mm x 0.5 mm. After voxelization, the size of the voxels was increased to 0.5116 mm x 0.5116 mm x 0.5116 mm to match the height of the model with that of the ICRP reference man (ICRP 2002). The final model consists of 513.4 million non-air voxels [version 14].
The model is divided into 82 tissues [version 14], organs, anatomic regions, and/or bodily fluids, which are (in alphabetical order): accumbens, adrenal gland, air, amygdala, artery, bile, bladder, blood, brainstem, bronchi, cancellous bone, cartilage, caudate, cavernous body, cerebellar grey matter, cerebellar white matter, cortical bone, CSF, diaphragm, duodenum, dura, ear cartilage, epididymis, esophagus, eye anterior chamber, eye choroid, eye cornea, eye humour, eye iris, eye lens, eye retina, eye sclera, eye suspensory ligament, fat, gall bladder, gingiva, gland, grey matter, heart, hippocampus, intervertebral disk, kidney, lacrimal duct, lacrimal gland, large intestine, large intestine contents, larynx, ligament, liver, lung, meninges, mesentery, muscle, nerve, pallidum, pancreas, prostate, putamen, salivary gland, skin, small intestine, small intestine contents, spinal cord, spleen, stomach, stomach contents, teeth, tendon, testis, thalamus, thymus, thyroid gland, tongue, trachea, ureter, urethra, urine, vas deferens, vein, ventral diencephalon, ventricular CSF, and white matter.
The Alvar model [version 14]. Left: Overview of the model. Tissues have been cut to make internal organs visible. Right: Panels show the skin, muscles, skeleton, vasculature and central nervous system. The picture has bee generated by creating smooth polygonal surfaces from the voxel data using the VTK library.
To make the model suitable for electromagnetic dosimetry, several modifications were applied when the original surface-based models were voxelized. The most important are listed below.
The brain of Alvar is based on ICBM 2009a nonlinear asymmetric template MR images, which represent the average brain of 152 healthy individuals (Fonov et al 2009, 2011). The FreeSurfer image analysis software (Dale et al 1999, Fischl et al 1999) was used to segment the brain from the template images. The process produced segmentation of white and grey matter of the cerebrum and cerebellum, brainstem, and subcortical nuclei. The cerebral cortex is further subdivided into 76 gyral regions (Desikan et al 2006). An affine transformation was applied to map the template brain to the coordinates of Alvar. The inferior and ventral parts of temporal lobes were slightly deformed to make the brain fit within the skull of Alvar.
The original skin model of the BodyParts3D database does not fully follow the boundaries of other tissues. At several occasions, other tissues ”pop out” from the skin, and at some anatomic sites, the subcutaneous space is excessively thick. To correct these problems, the original skin was completely replaced.
The new skin is 2 mm thick and smoothly follows the boundaries of muscles, bones, vasculature, and internal organs. The thickness of the subcutaneous fat layer depends on the body region and was determined so that the total body fat content agreed with the reference values (ICRP 2002).
The BodyParts3D atlas does not include subcutaneous fat or fat that surrounds internal organs. In Alvar, all cavities between tissues and the subcutaneous cavity are filled with fat. Consequently, all tissues that are not included, e.g., peripheral nerves, are automatically modelled as fat.
Because the muscle mass of the BodyParts3D model was less than that of the ICRP reference man, the size of all muscles was slightly increased. The size of large muscles was increased more than the size of small muscles. Approximations of facial muscles were also added because they were not included in the BodyParts3D atlas.
In version 16, the original and expanded muscles are separated.
Spinal canal and spinal cord
As the BodyParts3D database did not include a model of the spinal subarachnoid space, a new model of the spinal canal was generated based on the data of the cross sectional areas of the spinal subarachnoid space and the spinal cord (Edsbagge et al 2011). Furthermore, the model of the spinal cord was replaced. A hole was opened in the sacrum to accommodate the caudal end of the spinal subarachnoid space. The initial version of the Alvar phantom does not include spinal dura matter, spinal nerve roots, or the cauda equina.
Bones were segmented to cortical bone and cancellous bone (including bone marrow). The outer layer was segmented as cortical bone, and the rest was treated as cancellous bone. The thickness of the cortical bone depends on the type of the bone, and has been selected so that the ratio of cortical and cancellous bone mass is 80:20 [version 16]. The cortical bone thickness will be further fine-tuned in future versions.
Heart [new in version 15]
Heart is based on BodyParts3D version 5.0i. The original surface based models were voxelized and connected to each other, and any holes were removed using closing (image processing). Fat was added to fill auriculoventricular and interventricular grooves. Finally, a thin layer of pericardium (not in the original model) was added to separate the heart from other tissues. The conduction system of the heart was separated from other hearth muscles.
Dale A M, Fischl B and Sereno M I 1999 Cortical surface-based analysis. i. segmentation and surface reconstruction. Neuroimage 9(2) 179–94
Desikan R S, Ségonne F, Fischl B, Quinn B T, Dickerson B C, Blacker D, Buckner R L, Dale A M, Maguire R P, Hyman B T, Albert M S and Killiany R J 2006 An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. Neuroimage 31(3) 968–980
Edsbagge M, Starck G, Zetterberg H, Ziegelitz D and Wikkelso C 2011 Spinal cerebrospinal fluid volume in healthy elderly individuals. Clin. Anat. 24(6) 733–740
Fischl B, Sereno M I and Dale A M 1999 Cortical surface-based analysis. ii: Inflation, flattening, and a surface-based coordinate system. Neuroimage 9(2) 195–207
Fonov V, Evans A C, Botteron K, Almli C R, McKinstry R C, Collins D L and Brain Development Cooperative Group 2011 Unbiased average age-appropriate atlases for pediatric studies. Neuroimage 54(1) 313–27
Fonov V, Evans A, McKinstry R, Almli C and Collins D 2009 Unbiased nonlinear average age-appropriate brain templates from birth to adulthood. Neuroimage 47, Supplement 1 S102
ICRP 2002 Basic anatomical and physiological data for use in radiological protection: reference values ICRP Publication 89