public class FileBRUKER
extends FileBase

Reads a BRUKER file by first reading in the d3proc header file or if the d3proc header file is not\ present the visu_pars file, second the reco header file, third the acqp file in the same directory or up one or two two parent directories, then the method file,l and finally the 2dseq binary file. Paravision uses a subject patient coordinate system (L->R, P->A, F->H), with X = L->R, Y = P->A, and Z = F->H. This is different from the DICOM R->L, A->P, F->H. Paravision also has a (r, p, s) read, phase, slice coordinate system. ND is the total number of diffusion experiments. The B Matrix (PVM_DwBMat)(implemented as symmetric 3x3 matrix array of size ND) is calculated for each diffusion experiment in the imaging coordinate system (r,p,s). Diffusion Gradient Vector (PVM_DwGradVec) - Parameter of dimension ND X 3 specifying the diffusion gradient amplitudes in the x,y,z coordinate system. Eff. B Value (PVM_DwEffBval) - The trace of the b-matrix (is implemented as an array of size ND. ACQ_patient_pos - defines the patient position inside the magnet. According to the defined patient position. ACQ_patient_pos may have the values: • Head_Supine - negates Gx and Gz. • Head_Prone - negates Gy and Gz. • Head_Left - negates Gz. Gx and Gy are exchanged. • Head_Right - negates Gx, Gy and Gz. Gx and Gy are exchanged. • Foot_Supine - all gradients remain unchanged. • Foot_Prone - negates Gx and Gy. • Foot_Left - negates Gy. Gx and Gy are exchanged. • Foot_Right - negates Gx. Gx and Gy are exchanged. Look at O05_GeoEditor Figure 5.1. The description of gradient interchanges and negations together with the figure show that the x, y, and z must be remaining constant independent of patient position. Therefore, once you have x, y, z directly from PVM_DwGradVec or use ACQ_grad_matrix to convert PVM_DwBMat from r,p,s to x,y,z, there is no need to consider ACQ_patient_pos. ACQ_slice_sepn_mode - defines the slice separation mode of a multi slice experiment. It can be either Contiguous, Equidistant, Var_Parallel or Var_Angle. In case of Contiguous, Equidistant and Var_Parallel, the parameter ACQ_grad_matrix has only one item in the slice dimension, since these slice orientations produce parallel slices. In case of Var_Angle, ACQ_grad_matrix has to have NSLICES items in the slice dimension to define the orientation for each slice separately. NSLICES - defines the number of slices of a multi slice experiment. ACQ_grad_matrix[ ][3][3] - is a three dimensional array describing the slice orientation of the images to be measured. For ACQ_grad_matrix[i][j][k] i = 0, ..., NSLICES - 1 specifies the slice index during the acquisition, j = 0, 1, 2 specifies the read-, phase- and slice gradients, k = 0, 1, 2 specifies the x, y and z components of the slice direction independent of the patient position. The gradient matrix of each slice is orthonormal, which means that the read-, phase- and slice-gradient vectors are normalized to 1.0 and that they are orthogonal to each other. The following Example shows a two slice experiment with slice orientation Cor_Sag_oblique with ACQ_slice_sepn_mode Var_Angle with 0o for the first slice and 30o for the second slice. Example: Cor_Sag_oblique ACQ_slice_sepn_mode = Var_Angle NSLICES = 2, (0 and 30 degree orientation) ACQ_grad_matrix[0][0][0] = 1; 1st slice, read, Gx ACQ_grad_matrix[0][0][1] = 0; 1st slice, read, Gy ACQ_grad_matrix[0][0][2] = 0; 1st slice, read, Gz ACQ_grad_matrix[0][1][0] = 0; 1st slice, phase, Gx ACQ_grad_matrix[0][1][1] = 0; 1st slice, phase, Gy ACQ_grad_matrix[0][1][2] = 1; 1st slice, phase, Gz ACQ_grad_matrix[0][2][0] = 0; 1st slice, slice, Gx ACQ_grad_matrix[0][2][1] = 1; 1st slice, slice, Gy ACQ_grad_matrix[0][2][2] = 0; 1st slice, slice, Gz ACQ_grad_matrix[1][0][0] = 0.866; 2nd slice, read, Gx ACQ_grad_matrix[1][0][1] = 0.5; 2nd slice, read, Gy ACQ_grad_matrix[1][0][2] = 0; 2nd slice, read, Gz ACQ_grad_matrix[1][1][0] = 0; 2nd slice, phase, Gx ACQ_grad_matrix[1][1][1] = 0; 2nd slice, phase, Gy ACQ_grad_matrix[1][1][2] = 1; 2nd slice, phase, Gz ACQ_grad_matrix[1][2][0] = -0,5; 2nd slice, slice, Gx ACQ_grad_matrix[1][2][1] = 0.866; 2nd slice, slice, Gy ACQ_grad_matrix[1][2][2] = 0; 2nd slice, slice, Gz [x, y, z] = [r, p, s] * [ACQ_grad_matrix] Let A = ACQ_grad_matrix [x] [r] [y] = ATranspose [p] [z] [s] [x] [x][y][z] = ATranspose [r] [r][p][s] A [y] [p] [z] [s] so the to the BMatrix expressed in terms of xyz is ATranspose B A [x] [y] [z] [x] = [r][p][s] A ATranspose [r] [y] [p] [z] [s] For orthonormal matrices ATranspose = AInverse, so the trace of the B matrix is the same for both x,y,z and r,p,s coordinates.