Predictive acoustical processing in human cortical layers.

1. function [M] = LBR_param_priors(N,K,A,B,C),
2. % LBR_parameters defines structure of parameters for laminar BOLD response
3. % (LBR) model (see LBR_model.m). It applies parameter values
4. % as describe in Table 1 of Havlicek, M. & Uludag, K. (2019) BioRxiv
5. %
6. % INPUT: K - Number of cortical depths
7. %
8. % OUTPUT: P - structure with all default parameters for LBR model
9. %
10. % AUTHOR: Martin Havlicek, 5 August, 2019
11. %
12. % REFERENCE: Havlicek, M. & Uludag, K. (2019) A dynamical model of the
13. % laminar BOLD response, BioRxiv, doi: https://doi.org/10.1101/609099
14. %
15. % EXAMPLE:
16. % K = 6;
17. % P = LBR_parameters(K);
18. % disp(P);
19. %--------------------------------------------------------------------------
20. M.N = N; % Number of depths
21. M.K = K;
23. % Neuronal parameter:
24. %--------------------------------------------------------------------------
25. P0.sigma = 3;
26. P0.mu = 1.5;
27. P0.lam = 0.1;
28. P0.A = A;
29. P0.B = B;
30. P0.C = C;
31. P0.Bmu = 0;
32. P0.Blam = 0;
34. % NVC parameters:
35. % --------------------------------------------------------------------------
36. P0.c1 = 0.6;
37. P0.c2 = 1.5;
38. P0.c3 = 0.6;
40. depths = linspace(0,100,2*K+1); % Normalized distance to the center of individual depths (in %)
41. M.depths = depths(2:2:end)';
42. P0.nsig = 0.005;
44. % LAMINAR HEMODYNAMIC MODEL:
45. %--------------------------------------------------------------------------
46. % Baseline physiological parameters:
47. P0.V0t = 3.5; % Total (regional) amount of CBV0 in the gray matter (in mL) [1-6]
48. P0.w_v = 0.5; % CBV0 fraction of microvasculature (i.e. venules here )with respect to the total amount
49. P0.x_v = []; % CBV0 fraction across depths in venules
50. P0.x_d = []; % CBV0 fraction across depths in ascending veins
51. P0.s_v = 0; % Slope of CBV increase (decrease) in venules [0-0.3]
52. P0.s_d = 0.4; % Slope of CBV increase in ascending vein [0-1.5]
53. P0.s_d0 = 0; % Slope of CBV increase in ascending vein [0-1.5]
54. P0.s_d2 = 0; % Slope of CBV increase in ascending vein [0-1.5]
56. P0.t0v = 1; % Transit time through microvasculature(in second)
57. P0.E0v = 0.35; % Baseline oxygen extraction fraction in venules
58. P0.E0d = 0.35; % Baseline oxygen extraction fraction in venules
59. P0.E0p = 0.35; % Baseline oxygen extraction fraction in venules
61. % Parameters describing relative relationship between physiological variable:
62. % CBF-CBV coupling (steady-state)
64. P0.al_v = 0.3; % For venules
65. P0.al_d = 0.2; % For ascending vein
68. % CBF-CMRO2 coupling (steady-state)
69. P0.nr = 4; % n-ratio (Ref. Buxton et al. (2004) NeuroImage)
71. % CBF-CBV dynamic uncoupling
72. P0.tau_v_in = 2; % For venules - inflation
73. P0.tau_v_de = 2; % - deflation
74. P0.tau_d_in = 2; % For AV - inflation
75. P0.tau_d_de = 2; % - deflation
77. % LAMINAR BOLD SIGNAL MODEL:
78. %--------------------------------------------------------------------------
79. M.TE = 0.028; % echo-time (in sec)
81. % Hematocrit fraction
82. P0.Hct_v = 0.35; % For venules, Ref. Lu et al. (2002) NeuroImage
83. P0.Hct_d = 0.38; % For ascending vein
84. P0.Hct_p = 0.42; % For pial vein
87. M.B0 = 7; % Magnetic field strenght (in Tesla)
88. P0.gyro = 2*pi*42.6*10^6; % Gyromagnetic constant for Hydrogen
89. P0.suscep = 0.264*10^-6; % Susceptibility difference between fully oxygenated and deoxygenated blood
91. % Water proton density:
92. P0.rho_t = 0.89; % For gray matter tissue
93. P0.rho_v = 0.95 - P0.Hct_v*0.22; % For blood (venules) Ref. Lu et al. (2002) NeuroImage
94. P0.rho_d = 0.95 - P0.Hct_d*0.22; % For blood (ascending vein)
95. P0.rho_p = 0.95 - P0.Hct_p*0.22; % For blood (pial vein)
96. P0.rho_tp = 0.95; % For gray matter tissue % CSF
98. % Relaxation rates for 7 T (in sec-1)
99. P0.R2s_t = 34; % For gray matter tissue
100. P0.R2s_v = 80; % For blood (venules)
101. P0.R2s_d = 85; % For blood (ascending vein)
102. P0.R2s_p = 90; % For blood (pial vein)
104. % Slope of change in R2* of blood with change in extraction fration during activation
105. P0.r0v = 228; % For venules
106. P0.r0d = 232; % For ascending vein
107. P0.M0 = 100;
109. M.P0 = P0;
110. M.x = zeros(N*4+K*4,1);
111. M.xn = zeros(N,4);
112. M.xk = zeros(K,4);

LBR_param_priors.m at commit 2b29ddc, no license · at the source