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Update notebooks and database for fixed ROI
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@mathieuboudreau
mathieuboudreau committed Dec 4, 2023
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30 changes: 15 additions & 15 deletions 08_wholedataset_scatter_Human.ipynb
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74 changes: 38 additions & 36 deletions 09_human_stats.ipynb
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28 changes: 25 additions & 3 deletions 10_NIST_stats.ipynb
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Expand Up @@ -836,8 +836,8 @@
"name": "stderr",
"output_type": "stream",
"text": [
"[1126/235322.206183:WARNING:angle_platform_impl.cc(49)] RendererVk.cpp:1962 (initialize): ANGLE VMA version: 2003000\n",
"88722 bytes written to file /var/folders/l1/1xswjffd73l8yp7dd7pq9lyw0000gn/T/tmpq_6ks1e4/temp.png\n"
"[1127/120717.955615:WARNING:angle_platform_impl.cc(49)] RendererVk.cpp:1962 (initialize): ANGLE VMA version: 2003000\n",
"88722 bytes written to file /var/folders/l1/1xswjffd73l8yp7dd7pq9lyw0000gn/T/tmpw7tgjw7k/temp.png\n"
]
},
{
Expand Down Expand Up @@ -875,7 +875,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"/var/folders/l1/1xswjffd73l8yp7dd7pq9lyw0000gn/T/ipykernel_54857/1943462326.py:63: FutureWarning: \n",
"/var/folders/l1/1xswjffd73l8yp7dd7pq9lyw0000gn/T/ipykernel_58494/1943462326.py:63: FutureWarning: \n",
"\n",
"The `scale` parameter has been renamed and will be removed in v0.15.0. Pass `density_norm='count'` for the same effect.\n",
" ax = sns.violinplot(x='', y='T1 (ms)', hue='Type', data=df, split=True, inner=\"quartile\", scale=\"count\", palette=\"Set2\")\n"
Expand Down Expand Up @@ -964,6 +964,28 @@
"plt.show()"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"#66c2a5\n",
"#fc8d62\n"
]
}
],
"source": [
"# Set the color palette\n",
"sns.set_palette(\"Set2\")\n",
"pal = sns.color_palette()\n",
"print(pal.as_hex()[0])\n",
"print(pal.as_hex()[1])"
]
},
{
"cell_type": "code",
"execution_count": null,
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22 changes: 11 additions & 11 deletions databases/3T_human_T1maps_database.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -75,14 +75,14 @@ id,OSF dataset,OSF link,NIFTI filename,Data type,contact,site name,MRI vendor,MR
1188.3 1222.9 1181.1 1297.4 1196.1]","[1518.8 1525.6 1441.5 1554.1 1461.2 1277.1 1460. 1347.9 1267.1 1603.2
1528.4 1613.5 1721.8 1488.8 1581.9 1616.9 1718.7 1556.6 1195.9 1559.5
1459.4 1499.8 1515.1 1750.9 1655.8 1586.4 1441.8]",,,,,,,,,,,,,,
5.001,jorgejovicich_cimec_human,https://osf.io/g5z4e/download/,20200207_jorgejovicich_cimec_human/subject_1/20200207_jorgejovicich_cimec_human_sub1_20ch_T1map.nii.gz,Magnitude,Jorge Jovicich,CIMeC - Universita' di Trento,Siemens,Prisma syngo_MR_E11,3.0,,,,,51,male,_tir2d1_4,Spin-echo inversion recovery,['256 256 10'],['1 1 2'],2D,2550.0,13.0,"[50, 400, 1100, 2500]",465.0,"[ 875.3 696.8 756.3 851.6 1030.9 1007.7 878.8 794. 973.1 1133.6
5.001,jorgejovicich_cimec_human,https://osf.io/g5z4e/download/,20200207_jorgejovicich_cimec_human/subject_1/20200207_jorgejovicich_cimec_human_sub1_20ch_T1map.nii.gz,Magnitude,Jorge Jovicich,CIMeC - Universita' di Trento,Siemens,Prisma syngo_MR_E11,3.0,,,,,51,male,_tir2d1_4,Spin-echo inversion recovery,['256 256 10'],['1 1 2'],2D,2550.0,13.0,"[50, 400, 1100, 2500]",465,"[ 875.3 696.8 756.3 851.6 1030.9 1007.7 878.8 794. 973.1 1133.6
977.1 887.2 696.6 704.9 1062.9 564.4 730.3 967.7 712.9 787.6
717.7 1034.6 905.6 595. 724.8]","[ 997. 838.2 800.8 792.2 895.8 789.7 851.9 1029.8 830.7 961.
1002.5 878.8 888.9 740.2 943.4 972. 831.2 732.4 1026.5 835.3
770.9 769.8 695.8 1462.5 847.1]",[1322.3 1470.4 921.6 1067.6 1049. 1015.3 891.9 1352.1 930.1],"[1582.9 1482.3 1521.1 1527. 1503.8 1138.6 1341. 1671.7 1159.1 1192.6
1851.4 1327. 1437.6 1481.3 1595.6 1475. 1015.6 1579.3 1842.8 1570.1
1218.5 1606.6 1481.8 1418. 1512.9 1505.2 1583. ]",,,,,,,,,,,,,,
5.002,jorgejovicich_cimec_human,https://osf.io/g5z4e/download/,20200207_jorgejovicich_cimec_human/subject_1/20200207_jorgejovicich_cimec_human_sub1_64ch_T1map.nii.gz,Magnitude,Jorge Jovicich,CIMeC - Universita' di Trento,Siemens,Prisma syngo_MR_E11,3.0,,,,,51,male,_tir2d1_4,Spin-echo inversion recovery,['256 256 10'],['1 1 2'],2D,2550.0,13.0,"[50, 400, 1100, 2500]",465.0,"[ 935.6 836.3 753.7 901.7 844.6 845.2 845.2 795.5 753.5 804.1
5.002,jorgejovicich_cimec_human,https://osf.io/g5z4e/download/,20200207_jorgejovicich_cimec_human/subject_1/20200207_jorgejovicich_cimec_human_sub1_64ch_T1map.nii.gz,Magnitude,Jorge Jovicich,CIMeC - Universita' di Trento,Siemens,Prisma syngo_MR_E11,3.0,,,,,51,male,_tir2d1_4,Spin-echo inversion recovery,['256 256 10'],['1 1 2'],2D,2550.0,13.0,"[50, 400, 1100, 2500]",465,"[ 935.6 836.3 753.7 901.7 844.6 845.2 845.2 795.5 753.5 804.1
845. 836.5 800.2 837.4 914.8 856.7 828.4 817.5 1020.7 961.8
758.1 764.5 827.8 1127.1 880.1]","[777.6 829.3 811.7 871.5 813.8 875.5 949.2 852.7 787.7 704.1 849.2 891.2
845.1 856.9 805. 804.7 828.4 919.4 915.9 802.5 921.6 796.4 790.1 738.8
Expand All @@ -91,7 +91,7 @@ id,OSF dataset,OSF link,NIFTI filename,Data type,contact,site name,MRI vendor,MR
1113.2 1109.8 1227. 1082.3 939.1]","[1520.5 1302.7 1250.1 1351.9 1387.7 1483.7 1241.3 1278.1 1254. 1573.5
1919.8 1512.1 1516.2 1357.7 1234.4 1307.6 1215.7 1207.8 1376.5 1294.3
1501.2 1411.4 1390.9 1449.6 1212.1 1110.9 1365.4]",,,,,,,,,,,,,,
5.003,jorgejovicich_cimec_human,https://osf.io/g5z4e/download/,20200207_jorgejovicich_cimec_human/subject_2/20200207_jorgejovicich_cimec_human_sub2_20ch_T1map.nii.gz,Magnitude,Jorge Jovicich,CIMeC - Universita' di Trento,Siemens,Prisma syngo_MR_E11,3.0,,,,,37,male,_tir2d1_4,Spin-echo inversion recovery,['256 256 10'],['1 1 2'],2D,2550.0,13.0,"[50, 400, 1100, 2500]",465.0,"[ 925. 813.1 776.5 975.4 653.3 653.3 1241.5 861.9 1399.9 896.2
5.003,jorgejovicich_cimec_human,https://osf.io/g5z4e/download/,20200207_jorgejovicich_cimec_human/subject_2/20200207_jorgejovicich_cimec_human_sub2_20ch_T1map.nii.gz,Magnitude,Jorge Jovicich,CIMeC - Universita' di Trento,Siemens,Prisma syngo_MR_E11,3.0,,,,,37,male,_tir2d1_4,Spin-echo inversion recovery,['256 256 10'],['1 1 2'],2D,2550.0,13.0,"[50, 400, 1100, 2500]",465,"[ 925. 813.1 776.5 975.4 653.3 653.3 1241.5 861.9 1399.9 896.2
885.3 1278.1 754.3 683.1 823.3 1067.5 854.1 856. 929.3 752.8
1022.4 777.4 983.9 1170.1 850.2]","[1097.8 922.4 829. 855.9 931.3 1050.4 1009.8 813.9 978.9 992.2
1004.1 925.7 1036.1 1129.4 830.8 797.3 711.9 866.4 975.4 936.7
Expand All @@ -102,7 +102,7 @@ id,OSF dataset,OSF link,NIFTI filename,Data type,contact,site name,MRI vendor,MR
2046. 1413.4 1019.7 1532.9 1465.5 1572.1 1289.3 1481.8 1478.8 2381.6
1529.9 1183.2 1273.1 1523.6 2026.8 1478.5 1607.3 1393.5 2483.1 1870.3
1526.8 1436.6 1383.4 1567.3 1873.4 1817.3 1163.2 1269.1]",,,,,,,,,,,,,,
5.004,jorgejovicich_cimec_human,https://osf.io/g5z4e/download/,20200207_jorgejovicich_cimec_human/subject_2/20200207_jorgejovicich_cimec_human_sub2_64ch_T1map.nii.gz,Magnitude,Jorge Jovicich,CIMeC - Universita' di Trento,Siemens,Prisma syngo_MR_E11,3.0,,,,,37,male,_tir2d1_4,Spin-echo inversion recovery,['256 256 10'],['1 1 2'],2D,2550.0,13.0,"[50, 400, 1100, 2500]",465.0,"[ 896.8 779.5 994.3 1242.1 838.7 946.4 895.1 838.2 879.5 744.8
5.004,jorgejovicich_cimec_human,https://osf.io/g5z4e/download/,20200207_jorgejovicich_cimec_human/subject_2/20200207_jorgejovicich_cimec_human_sub2_64ch_T1map.nii.gz,Magnitude,Jorge Jovicich,CIMeC - Universita' di Trento,Siemens,Prisma syngo_MR_E11,3.0,,,,,37,male,_tir2d1_4,Spin-echo inversion recovery,['256 256 10'],['1 1 2'],2D,2550.0,13.0,"[50, 400, 1100, 2500]",465,"[ 896.8 779.5 994.3 1242.1 838.7 946.4 895.1 838.2 879.5 744.8
840.9 841.5 835.1 638.8 842.8 776.7 794.5 896.1 805.5 935.8]","[898.9 907.1 890.5 895.4 907.1 905.4 892.5 854.9 828.4 929.3 802.9 880.4
922.7 824. 835.3 882.7 929.7 901.4 761.4 942.5]","[1219.8 1050.7 1077. 1183.3 1087.5 1203.6 980. 1061.5 1117.3 1147.7
1022.2 1011.5 1191.9 1199.6 1258.1 1070.4 1230.5 1098.1 1247.1 1191. ]","[1161.9 1279.8 1357. 1610.6 1400.8 1334.2 1241.6 1252.7 1257.3 1178.2
Expand All @@ -116,7 +116,7 @@ id,OSF dataset,OSF link,NIFTI filename,Data type,contact,site name,MRI vendor,MR
1417.9 1340. 1278.5 1307.9 1325.7]","[1559.1 1591.4 1567.1 1530.5 1574.6 1591.8 1624.8 1554.5 1515.6 1571.1
1439.1 1410.2 1628. 1519. 1406.3 1667.7 1512.4 1482.1 2009.2 1822.5
1677. 2217. 1771.8 1729.4 2199.9 1710.9 1623.9]",,,,,,,,,,,,,,
7.001,madelinecarr_lha_human,https://osf.io/h7fqs/download/,20200221_madelinecarr_lha_human/20200221_madelinecarr_lha_human_T1map.nii.gz,Magnitude,Madeline Carr,Liverpool Hospital Australia,Siemens,Magnetom Skyra,3.0,,,,,24,female,SE_IR,Spin-echo inversion recovery,['128 128 1'],['1.95 1.95 2'],2D,2550.0,14.0,"[50, 400, 1100, 2500]",130.0,"[827.2 828. 807.8 810.4 826.1 820. 840. 861.2 877.3 950.1 939.1 802.1
7.001,madelinecarr_lha_human,https://osf.io/h7fqs/download/,20200221_madelinecarr_lha_human/20200221_madelinecarr_lha_human_T1map.nii.gz,Magnitude,Madeline Carr,Liverpool Hospital Australia,Siemens,Magnetom Skyra,3.0,,,,,24,female,SE_IR,Spin-echo inversion recovery,['128 128 1'],['1.95 1.95 2'],2D,2550.0,14.0,"[50, 400, 1100, 2500]",130,"[827.2 828. 807.8 810.4 826.1 820. 840. 861.2 877.3 950.1 939.1 802.1
777.7 829.2 810.4 792.7 814. 865.4]","[826.1 843.5 868. 796.1 815.9 797.6 773.5 770. 759.3 765.2 801.8 793.1
809.5 815.8 780.5 853.3 821.9 840.8]","[1246.3 1177.4 1207.4 1196.5 1089. 1135.9 1011.9 1180.1 1277.7 1262.3
1232.8 1272.6 1197. 1259.2 1273. 1299.1 1263.6 1145.8]","[1176.7 1152.5 1333.1 1486.1 1557.2 1655.5 1515.2 1541.8 1644.6 1538.5
Expand Down Expand Up @@ -257,18 +257,18 @@ id,OSF dataset,OSF link,NIFTI filename,Data type,contact,site name,MRI vendor,MR
1686.4 1607.5 1561.4 1633.2 1703.9 1696.5 1751.7 1621.8]",,,,,,,,,,,,,,
9.016,luisconcha_UNAM_human,https://osf.io/asj3r/download/,20200225_luisconcha_UNAM_human/session_1/58139/20200223_133141_GE/58139_GE_raw_IRData_T1map.nii.gz,Magnitude,Luis Concha,Universidad Nacional Autonoma de Mexico,GE,Discovery MR750,3.0,,,,,22,female,Ax_T1_FSE,Spin-echo inversion recovery,['256 256 1'],['1 1 2'],2D,2550.0,16.72,"[50, 400, 1100, 2500]",83.33,"[826.4 811.9 799.3 797.5 792.8 793.1 852.4 840.4 816. 851.7 800.8 879.2
838. 818.8 864.4 834.7 824.9 794.7 780.5 775.4 856.3 826.1 837.1 806.9
817.1]","[ 813.1 813.2 825.6 820. 864.1 847. 778.3 838.6 827.1 849.3
1093.5 810.8 825.2 855.4 864.8 1423.5 930.8 796.9 830.6 814.3
1454.5 1033. 809. 825.5 829.1]","[1108.2 1100.7 1053.4 1029.7 1049.5 1051.6 1092.5 1042.4 1056.6 1055.
817.1]","[848.5 868.7 858.5 852.7 846.2 824.5 849. 878.1 894.3 873.8 835.9 794.7
821.4 840.7 823.6 852.4 796.2 807.1 794.1 818.5 824.9 815.6 823.5 811.2
872.5]","[1108.2 1100.7 1053.4 1029.7 1049.5 1051.6 1092.5 1042.4 1056.6 1055.
1159.4 1177.6 1101.3 1134.6 1090.8 1140.1 1127.7 1058.9 1097.9 1038.9
1005.8 957.6 968.5 1023.6 947. ]","[1726.4 1833.3 2072.6 1619.1 1678.1 1753.2 1532.3 1580.3 1736.3 1385.3
1251.7 1190.5 1448. 1411.6 1378.8 1552.1 1532.1 1458.1 1586.5 1655.6
1736.7 1422.4 1488.7 1722.2 1488.9 1563.1 1694.2]",,,,,,,,,,,,,,
9.017,luisconcha_UNAM_human,https://osf.io/asj3r/download/,20200225_luisconcha_UNAM_human/session_1/58139/20200223_133141_GE/58139_GE_filtered_IRData_T1map.nii.gz,Magnitude,Luis Concha,Universidad Nacional Autonoma de Mexico,GE,Discovery MR750,3.0,,,,,22,female,Ax_T1_FSE,Spin-echo inversion recovery,['256 256 1'],['1 1 2'],2D,2550.0,16.72,"[50, 400, 1100, 2500]",83.33,"[832.4 814.2 805.7 803.5 792. 812.3 839.7 830.8 813.4 847. 817.1 856.5
829.1 823.4 863.1 833.1 825.4 803.7 783.4 773.5 847.7 825.1 828.9 810.2
814.3]","[ 814.5 820.5 838.1 830.4 852.2 849.4 782.4 844.4 835.5 845.7
1095.2 811. 832.9 851.1 854.8 1418.1 928.5 799.4 823.7 823.6
1454.1 1031.6 809.6 823.3 831.8]","[1088.9 1081. 1047.3 1028.1 1035. 1054.4 1076.6 1043.5 1048.3 1043.9
814.3]","[855.7 850.3 847.7 844. 808.9 855.6 862.7 872.3 860.3 829.9 823.7 829.9
841. 831.4 818.5 816.3 821.8 813.2 829.5 826.8 831.1 833.4 824.7 861.8
840.1]","[1088.9 1081. 1047.3 1028.1 1035. 1054.4 1076.6 1043.5 1048.3 1043.9
1121.8 1129.7 1079.1 1094.8 1071. 1093.5 1083.4 1040. 1068.9 1029.8
980.8 954.8 962.4 998.9 951.3]","[1724.2 1820. 1911.7 1646.3 1764.8 1774.4 1531.3 1650.6 1784.2 1310.4
1241.4 1202.5 1383. 1363.4 1371.1 1477.3 1463.5 1442.6 1581.8 1612.1
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Binary file modified databases/3T_human_T1maps_database.pkl
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Binary file modified databases/3T_human_T1maps_database.xlsx
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Binary file added databases/~$3T_human_T1maps_database.xlsx
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Binary file modified plots/04_alldatasets_scatter_NIST-temperature-corrected/00_alldatasets.png
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