@@ -23,7 +23,7 @@ def phantom(bvalue, noise, TR=3000, TE=40, motion=False, rician=False, interleav
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# Access the variables in the loaded .mat file
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XCAT = mat_data ['IMG' ]
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- XCAT = XCAT [0 : - 1 :2 , 0 :- 1 : 2 ,10 :160 :4 ]
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+ XCAT = XCAT [- 1 :0 :- 2 , - 1 : 0 : - 2 ,10 :160 :4 ]
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D , f , Ds = contrast_curve_calc ()
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S , Dim , fim , Dpim , legend = XCAT_to_MR_DCE (XCAT , TR , TE , bvalue , D , f , Ds )
@@ -95,15 +95,19 @@ def contrast_curve_calc():
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D [8 ] = 3e-3 # 8 Blood ra
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D [10 ] = 1.37e-3 # 8 Muscle: 10.3389/fresc.2022.910068
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D [13 ] = 1.5e-3 # 13 liver: Delattre et al. doi: 10.1097/RLI.0b013e31826ef901
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+ D [14 ] = 3.0e-3 # 13 Galbladder
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D [17 ] = 1.67e-3 # 17 esophagus : Huang et al. doi: 10.1259/bjr.20170421
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D [18 ] = 1.67e-3 # 18 esophagus cont : Huang et al. doi: 10.1259/bjr.20170421
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D [20 ] = 1.5e-3 # 20 stomach wall: Li et al. doi: 10.3389/fonc.2022.821586
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+ D [21 ] = 2.0e-3 # 21 stomach content
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D [22 ] = 1.3e-3 # 22 Pancreas (from literature)
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D [23 ] = 2.12e-3 # 23 right kydney cortex : van Baalen et al. Doi: jmri.25519
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D [24 ] = 2.09e-3 # 23 right kydney medulla : van Baalen et al. Doi: jmri.25519
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D [25 ] = 2.12e-3 # 23 left kydney cortex : van Baalen et al. Doi: jmri.25519
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D [26 ] = 2.09e-3 # 23 left kydney medulla : van Baalen et al. Doi: jmri.25519
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D [30 ] = 1.3e-3 # 30 spleen : Taimouri et al. Doi: 10.1118/1.4915495
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+ D [34 ] = 4.1e-4 # 34 spinal cord :doi: 10.3389/fonc.2022.961473
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+ D [35 ] = 0.43e-3 # 35 Bone marrow : https://pubmed.ncbi.nlm.nih.gov/30194746/
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D [36 ] = 3e-3 # 36 artery
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D [37 ] = 3e-3 # 37 vein
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D [40 ] = 1.31e-3 # 40 asc lower intestine : Hai-Jing et al. doi: 10.1097/RCT.0000000000000926
@@ -124,15 +128,19 @@ def contrast_curve_calc():
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f [8 ] = 1.00 # 8 Blood ra
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f [10 ] = 0.10 # 8 Muscle: 10.3389/fresc.2022.910068
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f [13 ] = 0.11 # 13 liver : Delattre et al. doi: 10.1097/RLI.0b013e31826ef901
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+ f [14 ] = 0 # 13 Gal
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f [17 ] = 0.32 # 17 esophagus : Huang et al. doi: 10.1259/bjr.20170421
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f [18 ] = 0.32 # 18 esophagus cont : Huang et al. doi: 10.1259/bjr.20170421
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f [20 ] = 0.3 # 20 stomach wall: Li et al. doi: 10.3389/fonc.2022.821586
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+ f [21 ] = 0.0 # 20 stomach content
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f [22 ] = 0.15 # 22 Pancreas (from literature)
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f [23 ] = 0.097 # 23 right kydney cortex : van Baalen et al. Doi: jmri.25519
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f [24 ] = 0.158 # 23 right kydney medulla : van Baalen et al. Doi: jmri.25519
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f [25 ] = 0.097 # 23 left kydney cortex : van Baalen et al. Doi: jmri.25519
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f [26 ] = 0.158 # 23 left kydney medulla : van Baalen et al. Doi: jmri.25519
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f [30 ] = 0.2 # 30 spleen : Taimouri et al. Doi: 10.1118/1.4915495
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+ f [34 ] = 0.178 # 34 spinal cord :doi: 10.3389/fonc.2022.961473
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+ f [35 ] = 0.145 # 35 Bone marrow : https://pubmed.ncbi.nlm.nih.gov/30194746/
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f [36 ] = 1.0 # 36 artery
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f [37 ] = 1.0 # 37 vein
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f [40 ] = 0.69 # 40 asc lower intestine : Hai-Jing et al. doi: 10.1097/RCT.0000000000000926
@@ -153,15 +161,19 @@ def contrast_curve_calc():
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Ds [8 ] = 0.1 # 8 Blood ra
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Ds [10 ] = 0.0263 # 8 Muscle: 10.3389/fresc.2022.910068
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Ds [13 ] = 0.1 # 13 liver: Delattre et al. doi: 10.1097/RLI.0b013e31826ef901
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+ Ds [14 ] = 0.1 # 14 Gal
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Ds [17 ] = 0.03 # 17 esophagus : Huang et al. doi: 10.1259/bjr.20170421
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Ds [18 ] = 0.03 # 18 esophagus cont : Huang et al. doi: 10.1259/bjr.20170421
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Ds [20 ] = 0.012 # 20 stomach wall: Li et al. doi: 10.3389/fonc.2022.821586
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+ Ds [21 ] = 0.1 # 20 stomach content
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Ds [22 ] = 0.01 # 22 Pancreas (from literature)
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Ds [23 ] = 0.02 # 23 right kydney cortex : van Baalen et al. Doi: jmri.25519
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Ds [24 ] = 0.019 # 23 right kydney medulla : van Baalen et al. Doi: jmri.25519
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Ds [25 ] = 0.02 # 23 left kydney cortex : van Baalen et al. Doi: jmri.25519
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Ds [26 ] = 0.019 # 23 left kydney medulla : van Baalen et al. Doi: jmri.25519
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Ds [30 ] = 0.03 # 30 spleen : Taimouri et al. Doi: 10.1118/1.4915495
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+ Ds [34 ] = 0.0289 # 34 spinal cord :doi: 10.3389/fonc.2022.961473
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+ Ds [35 ] = 0.05 # 35 Bone marrow :
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Ds [36 ] = 0.1 # 36 artery
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Ds [37 ] = 0.1 # 37 vein
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Ds [40 ] = 0.029 # 40 asc lower intestine : Hai-Jing et al. doi: 10.1097/RCT.0000000000000926
@@ -261,7 +273,7 @@ def XCAT_to_MR_DCE(XCAT, TR, TE, bvalue, D, f, Ds, b0=3, ivim_cont = True):
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73 : 'Pancreas tumor' ,
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}
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###############################################################################
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- np .random .seed (42 )
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+ np .random .seed (41 )
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Tissue = np .zeros ((74 , 4 ))
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Tissue [1 ] = [1030 , 40 , 1471 , 47 ]
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Tissue [2 ] = [1030 , 40 , 1471 , 47 ]
@@ -427,7 +439,7 @@ def parse_bvalues_file(file_path):
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# sig = np.flip(sig,axis=0)
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# sig = np.flip(sig,axis=1)
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res = np .eye (4 )
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- res [2 ]= 2
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+ res [2 , 2 ]= 2
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voxel_selector_fraction = 0.5
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D , f , Ds = contrast_curve_calc ()
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