MR imaging: Anatomical Model

Let's assume that our anatomical model consists of N different tissue types and M isochromats. The computer model of the anatomical object consists of the following six (6) arrays/matrices:

  • model_tissues [N x 4]: Each row represents a different tissue type. The first column holds the T1 value (in sec) of the tissue type, the second column holds the T2 value (in sec) of the tissue type, the third column holds the PD value (unitless number) of the tissue type and the fourth column holds the CS value (in Hz) of the tissue type.
Matrix: model_tissues
Matrix: model_tissues
  • model_new [M x 1]: Each row represents a single isochromat in the anatomical model. The value of each row corresponds to the row of the tissue type in the model_tissues matrix where the isochromat belongs to. 
  • model_spatial [M x 3]: Each row corresponds to the same isochromat from the model_new matrix and holds its spatial coordinates in a cartesian coordinate system (in meters). The first column holds the x-coordinate, the second column holds the y-coordinate and the third column holds the z-coordinate.
Matrices: model_new and model_spatial
Matrices: model_new and model_spatial
  • inhom [M x 1]: Each row corresponds to the same isochromat from the model_new and model_spatial matrices and holds the main field inhomogeneity that the isochromat experiences [in Tesla]. Caution: it is the difference from the main magnetic field strength, not the actual magnetic field strength that the isochromat experiences (for example, for a main magnetic field of 1.5T, an isochromat that experiences a magnetic field of 1.500010T has an inhom value of 0.000010T).
  • model_dim [1 x 3]: the size of the anatomical model in the cartesian coordinate system (in meters). The first column holds the x-dimension, the second column holds the y-dimension and the third column holds the z-dimension.
  • model_elementsize [1 x 3]: the size of the voxel of the anatomical model in the cartesian coordinate system (in meters). The first column holds the x-dimension, the second column holds the y-dimensionand the third column holds the z-dimension. It is actually the distance between consecutive isochromats in three dimensions.