I'm guessing that the fragments might cause problems later either in gtmseg as
a hard failure or in gtmpvc as an ill-conditioned matrix. But you can try it
out:)
On 1/11/2020 6:04 PM, Boris Rauchmann wrote:
External Email - Use Caution
Thanks, that solution seems to work finally. I just ignored the remaining
voxels labeled according to the standard aseg scheme and proceeded with the the
PET analysis and the combined LUT.
I will ignore the remaining fragment labels from the original aseg and only use
the output from the BN labels (starting with 211), these are the only results
im really interested in. Is that ok?
Here an example stats file I got:
1 2 Left-Cerebral-White-Matter wm 41550 13909.534
0.989 0.0935
2 7 Left-Cerebellum-White-Matter wm 2276 1037.525
0.854 0.0811
3 8 Left-Cerebellum-Cortex cortex 10936 6010.637
1.015 0.1339
4 10 Left-Thalamus-Proper subcort_gm 3 0.024
-0.815 0.2251
5 11 Left-Caudate subcort_gm 3 0.035
21.480 0.1746
6 12 Left-Putamen subcort_gm 25 0.459
3.161 0.0615
7 13 Left-Pallidum subcort_gm 49 1.497
1.474 0.0667
8 16 Brain-Stem subcort_gm 4599 2714.856
0.929 0.1000
9 17 Left-Hippocampus subcort_gm 2 0.023
-3.152 0.1702
10 18 Left-Amygdala subcort_gm 1 0.005
-7.082 0.1060
11 24 CSF csf 7468 2623.527
0.251 0.2568
12 26 Left-Accumbens-area subcort_gm 0 0.004
0.879 nan
13 28 Left-VentralDC subcort_gm 714 205.288
1.358 0.1427
14 31 Left-choroid-plexus csf 220 18.333
5.945 0.6080
15 41 Right-Cerebral-White-Matter wm 40645 13911.597
0.987 0.0841
16 46 Right-Cerebellum-White-Matter wm 2146 990.941
0.862 0.0826
17 47 Right-Cerebellum-Cortex cortex 11029 6187.241
0.985 0.1317
18 49 Right-Thalamus-Proper subcort_gm 11 0.140
0.032 0.2024
19 50 Right-Caudate subcort_gm 1 0.009
-2.162 0.0258
20 51 Right-Putamen subcort_gm 44 2.020
3.727 0.1893
21 52 Right-Pallidum subcort_gm 24 0.316
5.739 0.1814
22 53 Right-Hippocampus subcort_gm 3 0.026
16.575 0.2951
23 54 Right-Amygdala subcort_gm 7 0.081
4.637 0.0897
24 58 Right-Accumbens-area subcort_gm 0 0.000
-4.474 nan
25 60 Right-VentralDC subcort_gm 728 198.051
1.430 0.2142
26 63 Right-choroid-plexus csf 136 10.088
6.633 0.5924
27 211 mAmyg_L subcort_gm 264 48.960
1.126 0.1262
28 212 mAmyg_R subcort_gm 268 46.429
1.292 0.1920
29 213 lAmyg_L subcort_gm 131 6.503
1.889 0.1003
30 214 lAmyg_R subcort_gm 181 13.490
1.382 0.1237
31 215 rHipp_L subcort_gm 1020 260.090
1.166 0.1828
32 216 rHipp_R subcort_gm 833 241.777
1.149 0.2291
33 217 cHipp_L subcort_gm 911 288.346
1.578 0.3201
34 218 cHipp_R subcort_gm 1050 330.445
1.273 0.2312
35 219 vCa_L subcort_gm 626 170.254
1.205 0.0829
36 220 vCa_R subcort_gm 477 84.269
1.491 0.0933
37 221 GP_L subcort_gm 597 133.161
1.369 0.0977
38 222 GP_R subcort_gm 514 93.978
1.491 0.0811
39 223 NAC_L subcort_gm 412 67.647
1.348 0.1591
40 224 NAC_R subcort_gm 503 87.917
1.240 0.1258
41 225 vmPu_L subcort_gm 465 128.509
1.740 0.0783
42 226 vmPu_R subcort_gm 367 83.411
1.588 0.0699
43 227 dCa_L subcort_gm 997 255.259
0.821 0.1448
44 228 dCa_R subcort_gm 1271 405.156
1.017 0.1380
45 229 dlPu_L subcort_gm 678 122.256
1.356 0.0960
46 230 dlPu_R subcort_gm 585 150.878
1.319 0.0942
47 231 mPFtha_L subcort_gm 278 34.255
0.562 0.0971
48 232 mPFtha_R subcort_gm 293 33.479
0.513 0.1725
49 233 mPMtha_L subcort_gm 166 8.628
0.960 0.0501
50 234 mPMtha_R subcort_gm 316 41.442
0.915 0.0645
51 235 Stha_L subcort_gm 222 25.913
1.007 0.0551
52 236 Stha_R subcort_gm 241 53.103
1.229 0.0608
53 237 rTtha_L subcort_gm 344 12.690
2.379 0.2204
54 238 rTtha_R subcort_gm 240 35.057
0.800 0.1077
55 239 PPtha_L subcort_gm 331 23.986
1.627 0.0688
56 240 PPtha_R subcort_gm 319 21.868
0.954 0.1150
57 241 Otha_L subcort_gm 244 28.491
0.014 0.1617
58 242 Otha_R subcort_gm 158 7.610
0.548 0.1713
59 243 cTtha_L subcort_gm 212 10.919
1.547 0.1571
60 244 cTtha_R subcort_gm 250 25.427
3.840 0.2807
61 245 lPFtha_L subcort_gm 532 94.580
1.016 0.0732
62 246 lPFtha_R subcort_gm 466 54.950
1.086 0.0751
63 1001 ctx-lh-bankssts cortex 595 124.965
1.709 0.0686
64 1002 ctx-lh-caudalanteriorcingulate cortex 370 66.174
1.304 0.0951
65 1003 ctx-lh-caudalmiddlefrontal cortex 1039 223.909
1.706 0.0871
66 1005 ctx-lh-cuneus cortex 598 78.428
1.719 0.1002
67 1006 ctx-lh-entorhinal cortex 332 50.969
1.633 0.1099
68 1007 ctx-lh-fusiform cortex 1787 368.987
1.610 0.1025
69 1008 ctx-lh-inferiorparietal cortex 2521 591.841
1.773 0.1011
70 1009 ctx-lh-inferiortemporal cortex 2209 565.372
1.514 0.1144
71 1010 ctx-lh-isthmuscingulate cortex 558 100.622
1.419 0.1414
72 1011 ctx-lh-lateraloccipital cortex 2243 461.999
1.620 0.1021
73 1012 ctx-lh-lateralorbitofrontal cortex 1540 367.233
1.539 0.1629
74 1013 ctx-lh-lingual cortex 1158 218.085
1.641 0.1091
75 1014 ctx-lh-medialorbitofrontal cortex 1065 254.158
1.480 0.1427
76 1015 ctx-lh-middletemporal cortex 2187 515.131
1.615 0.1146
77 1016 ctx-lh-parahippocampal cortex 382 47.547
1.106 0.1159
78 1017 ctx-lh-paracentral cortex 644 106.788
1.464 0.1035
79 1018 ctx-lh-parsopercularis cortex 832 168.841
1.478 0.0728
80 1019 ctx-lh-parsorbitalis cortex 554 117.573
1.381 0.1071
81 1020 ctx-lh-parstriangularis cortex 678 130.710
1.667 0.0828
82 1021 ctx-lh-pericalcarine cortex 390 47.638
1.575 0.0770
83 1022 ctx-lh-postcentral cortex 2099 367.425
1.527 0.0933
84 1023 ctx-lh-posteriorcingulate cortex 529 95.601
1.554 0.1022
85 1024 ctx-lh-precentral cortex 2722 535.813
1.465 0.0852
86 1025 ctx-lh-precuneus cortex 1849 381.092
1.666 0.1002
87 1026 ctx-lh-rostralanteriorcingulate cortex 336 64.563
1.368 0.0903
88 1027 ctx-lh-rostralmiddlefrontal cortex 2737 619.430
1.574 0.0873
89 1028 ctx-lh-superiorfrontal cortex 4575 1101.963
1.552 0.0923
90 1029 ctx-lh-superiorparietal cortex 2505 430.339
1.645 0.0859
91 1030 ctx-lh-superiortemporal cortex 2517 575.940
1.559 0.1020
92 1031 ctx-lh-supramarginal cortex 1925 466.262
1.609 0.0921
93 1032 ctx-lh-frontalpole cortex 293 51.884
1.653 0.1294
94 1033 ctx-lh-temporalpole cortex 547 131.885
1.500 0.1562
95 1034 ctx-lh-transversetemporal cortex 319 49.071
1.572 0.0740
96 1035 ctx-lh-insula cortex 1621 362.309
1.323 0.0805
97 2001 ctx-rh-bankssts cortex 452 80.636
1.581 0.0649
98 2002 ctx-rh-caudalanteriorcingulate cortex 430 84.382
1.328 0.1183
99 2003 ctx-rh-caudalmiddlefrontal cortex 975 201.479
1.678 0.0699
100 2005 ctx-rh-cuneus cortex 582 80.806
1.758 0.0961
101 2006 ctx-rh-entorhinal cortex 289 43.979
1.594 0.1093
102 2007 ctx-rh-fusiform cortex 1607 361.265
1.495 0.0887
103 2008 ctx-rh-inferiorparietal cortex 3102 744.405
1.622 0.0779
104 2009 ctx-rh-inferiortemporal cortex 2324 612.805
1.469 0.1153
105 2010 ctx-rh-isthmuscingulate cortex 449 72.682
1.539 0.1213
106 2011 ctx-rh-lateraloccipital cortex 2145 493.213
1.535 0.1295
107 2012 ctx-rh-lateralorbitofrontal cortex 1519 366.246
1.576 0.1602
108 2013 ctx-rh-lingual cortex 1215 246.293
1.424 0.0999
109 2014 ctx-rh-medialorbitofrontal cortex 1305 339.745
1.431 0.1371
110 2015 ctx-rh-middletemporal cortex 2409 582.090
1.586 0.1214
111 2016 ctx-rh-parahippocampal cortex 379 47.722
1.137 0.1003
112 2017 ctx-rh-paracentral cortex 872 150.762
1.495 0.0849
113 2018 ctx-rh-parsopercularis cortex 692 140.443
1.484 0.0957
114 2019 ctx-rh-parsorbitalis cortex 624 133.260
1.487 0.1093
115 2020 ctx-rh-parstriangularis cortex 848 172.425
1.586 0.1047
116 2021 ctx-rh-pericalcarine cortex 399 47.618
1.599 0.0767
117 2022 ctx-rh-postcentral cortex 1965 341.079
1.497 0.0902
118 2023 ctx-rh-posteriorcingulate cortex 608 110.509
1.490 0.1064
119 2024 ctx-rh-precentral cortex 2851 600.118
1.408 0.0789
120 2025 ctx-rh-precuneus cortex 1991 429.967
1.655 0.0960
121 2026 ctx-rh-rostralanteriorcingulate cortex 407 82.757
1.508 0.1203
122 2027 ctx-rh-rostralmiddlefrontal cortex 3064 725.576
1.621 0.0891
123 2028 ctx-rh-superiorfrontal cortex 4110 1001.983
1.549 0.0944
124 2029 ctx-rh-superiorparietal cortex 2413 427.643
1.638 0.0866
125 2030 ctx-rh-superiortemporal cortex 2326 561.451
1.538 0.1110
126 2031 ctx-rh-supramarginal cortex 2051 456.793
1.586 0.0923
127 2032 ctx-rh-frontalpole cortex 321 60.867
1.478 0.1243
128 2033 ctx-rh-temporalpole cortex 582 141.009
1.623 0.1824
129 2034 ctx-rh-transversetemporal cortex 210 25.529
1.678 0.0695
130 2035 ctx-rh-insula cortex 1499 383.186
1.295 0.0828
Am 10.01.2020 um 18:45 schrieb Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>:
gtmseg --head BN_apas+head.mgz --s 1122_test --o NEU_BN.gtmseg.mgz --ctx-annot
BN_Atlas.annot --ctab
'/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt'
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