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aghaeifar · Mar 20, 2024 · 99ad786 · 99ad786
1 parent 3212c9c
commit 99ad786
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Showing 7 changed files with 18 additions and 29 deletions.
diff --git a/config/config_default.ini b/config/config_default.ini
@@ -24,15 +24,14 @@ M0[1]        =
 
 [TISSUE_PARAMETERS]
 ; Probability to diffuse from tissue X to tissue Y. X and Y are taken from the levels in the mask
-P_XY[0] = 1.00 0.75
-P_XY[1] = 0.25 1.00
+P_XY[0] = 1.00 0.0
+P_XY[1] = 0.0 1.00
 ; T1 and T2 in seconds
 T1[0] = 2.2
-T1[1] = 1.8
-T1[2] = 2.08
+T1[1] = 2.2
 T2[0] = 41e-3
-T2[1] = 14e-3
-T2[2] = 20e-3
+T2[1] = 41e-3
+
 
 [SCAN_PARAMETERS]
 TR = 0.010
@@ -83,10 +82,13 @@ B0   = 9.4
 ; use 0 for random seed generation, otherwise use a positive integer to make a reproducible simulation
 SEED = 0
 NUMBER_OF_SPINS = 1e5
+; if 0, spins will not cross boundary. If 1, spins will cross boundary and appear on the other side of the boundary
 CROSS_BOUNDARY = 0
+; if 1, spins random-walk will be stored in XYZ1 file
 RECORD_TRAJECTORY = 0
 ; m^2/Sec.
 DIFFUSION_CONSTANT = 1e-9
+; scale fieldmap length to simulate different sample sizes
 SAMPLE_LENGTH_SCALES[0] = 0.0093691
 SAMPLE_LENGTH_SCALES[1] = 0.012177
 SAMPLE_LENGTH_SCALES[2] = 0.015825

diff --git a/config/gradient.ini b/config/gradient.ini
@@ -1,13 +1,15 @@
+SEQ_NAME    = gradient
+
 [PARENT]
 PARENT_CONFIG = config_default.ini
 
 [FILES]
 FIELDMAP[0]  = ../../field_maps/fieldmap_allzero.dat
-M1[0]        = ../../outputs/gradient_m1.dat
 XYZ0[0]      = ../../field_maps/xyz0_allzero.dat
-XYZ1[0]      = ../../outputs/gradient_xyz1.dat
+
 
 [TISSUE_PARAMETERS]
+P_XY[0] = 1.00
 T1[0] = 1000.0
 T2[0] = 1000.0
 

diff --git a/config/grase.ini b/config/grase.ini
@@ -1,3 +1,6 @@
+
+SEQ_NAME    = grase
+
 [PARENT]
 PARENT_CONFIG = config_default.ini
 

diff --git a/config/gre.ini b/config/gre.ini
@@ -2,12 +2,6 @@ SEQ_NAME     = gre
 [PARENT]
 PARENT_CONFIG = config_default.ini
 
-[FILES]
-
-
-[TISSUE_PARAMETERS]
-MultiTissue = 0
-
 
 [SCAN_PARAMETERS]
 TR = 0.04

diff --git a/config/se.ini b/config/se.ini
@@ -2,12 +2,6 @@ SEQ_NAME    = se
 [PARENT]
 PARENT_CONFIG = config_default.ini
 
-[FILES]
-
-
-[TISSUE_PARAMETERS]
-MultiTissue = 0
-
 [SCAN_PARAMETERS]
 TR = 0.04
 TE[0] = 0.02

diff --git a/config/ssfp.ini b/config/ssfp.ini
@@ -2,11 +2,6 @@ SEQ_NAME     = ssfp
 [PARENT]
 PARENT_CONFIG = config_default.ini
 
-[FILES]
-
-
-[TISSUE_PARAMETERS]
-MultiTissue = 0
 
 [SCAN_PARAMETERS]
 TR = 0.010

diff --git a/config/stimulated_echo.ini b/config/stimulated_echo.ini
@@ -1,9 +1,8 @@
+SEQ_NAME    = ste
+
 [PARENT]
 PARENT_CONFIG = config_default.ini
 
-[FILES]
-M1[0]        = ../../outputs/ste_m1_0.dat
-M1[1]        = ../../outputs/ste_m1_1.dat
 
 [TISSUE_PARAMETERS]
 T1[0] = 2.2
@@ -40,6 +39,6 @@ DEPHASING_T[3] = 0.07
 [SIMULATION_PARAMETERS]
 ; use 0 for random seed generation, otherwise use a positive integer to make a reproducible simulation
 SEED = 10
-DIFFUSION_CONSTANT = 1e-9
+