Date written: 2020-06-26
Last ran: 2020-07-10

Description

As shown in prior analyses (namely here), we lose key tracts at Siemens sites, but not GE sites. Some of the lost tracts include large, reliable tracts that should be evident even in sub-ideal data, such as the IOFF. Here, we focus on the IOFF, to determine at what point in tractography it is lost.

The IOFF is a large association tract. In the ORG atlas, it combines 8 clusters (00681, 00683, 00713, 00716, 00724, 00749, 00752, 00769). Its representation in the ORG atlas is shown on the right below; on the left, the IOFF segmentation from TractSeg is shown for comparative purposes.

Participants

As before, we review data from the same set of SPINS participants. The CMH participant ('CMH0135') was randomly selected from those scanned on the GE. The other participants ('CMP0182', 'MRC0053', 'MRP0096', 'ZHH0030', 'ZHP0158') are among 'good' participant from each of the Siemens sites, selected randomly from those not missing more than 10 tracts.

Data summary

Below, we show a summary of data for each of a total of n=72 tracts isolated by Slicer (n=41 unique), after all whitematteranalysis steps have been run. Tracts comprised of <= 40 fibers are shown in red. Rows of tracts of interest to our hypotheses are emphasized in yellow; the IOFF is highlighted in orange.

CMH0135
CMP0182
MRC0053
MRP0096
ZHH0030
ZHP0158
tract fibers length fibers length fibers length fibers length fibers length fibers length
AF -- L 257 115.18 133 105.41 42 100.51 620 108.85 305 105.08 3 80.53
AF -- R 219 119.33 316 104.97 0 0 25 77.74 97 117.22 79 106.37
CB -- L 637 87.57 357 62.3 467 59.66 423 87.92 459 91.02 139 69.22
CB -- R 492 75.02 358 72.94 374 55.33 696 97.95 353 80.07 90 49.55
CC1 -- C 153 98.01 214 86.26 138 74.75 176 91.49 177 89.96 203 90.81
CC2 -- C 1112 100.04 1159 90.94 1314 92.98 1366 90.8 1219 91.43 783 87.04
CC3 -- C 881 108.55 679 85.64 493 85.56 804 101.21 795 103.96 492 102.03
CC4 -- C 798 106.78 649 95.16 582 99.78 529 107.46 694 111.87 486 109.96
CC5 -- C 721 115.75 430 107.42 410 113.85 427 119.92 465 109.48 449 113.36
CC6 -- C 1656 141.22 824 123.65 599 125.97 587 124.5 819 117.62 144 117.99
CC7 -- C 376 171.16 249 136.25 446 166.66 507 148.29 468 134.05 12 131.83
CR-F -- L 207 123.3 222 118.78 449 124.23 113 122.74 190 133.67 45 125.24
CR-F -- R 305 123.41 257 114.57 151 119.71 107 116.21 206 126.66 60 132.71
CR-P -- L 109 128.02 11 104.1 47 118.73 21 120.41 110 118.67 49 117.92
CR-P -- R 53 120.54 64 114.96 28 121.12 24 119.88 70 129.55 30 112.76
CST -- L 368 123.26 401 103.23 506 117.4 145 105.62 504 124.57 146 116.8
CST -- R 727 124.27 344 105.33 415 112.27 251 114.68 509 118.25 117 116.61
EC -- L 100 153.8 66 108.76 11 95.59 28 154.11 80 150.2 2 113.27
EC -- R 94 155.05 42 125.57 28 127.64 93 144.72 109 138.92 16 130.37
EmC -- L 63 143.14 3 126.53 0 0 36 140.36 91 141.72 11 129.61
EmC -- R 77 146.4 16 130.72 0 0 99 114.68 124 122.34 0 0
ICP -- L 47 53.21 17 52.82 0 0 1 52.86 24 55.5 2 50.45
ICP -- R 44 51.53 29 54.66 0 0 2 41.34 43 55.89 0 0
ILF -- L 616 117.17 242 95.34 498 106.54 338 90.07 245 97.73 214 99.1
ILF -- R 549 110.51 237 94.1 804 99.32 272 100.1 111 98.37 558 102.07
IOFF -- L 217 165.05 3 129.51 0 0 134 161.24 74 161.46 21 159.5
IOFF -- R 233 163.49 32 137.16 0 0 85 165.49 62 157.62 0 0
Intra-CBLM-I&P -- L 250 57.61 66 49.01 57 44.3 57 46.76 95 55.31 90 54.2
Intra-CBLM-I&P -- R 212 53.26 53 54.45 24 44.98 52 46.78 84 57.09 76 57.3
Intra-CBLM-PaT -- L 100 53.41 48 49.32 4 46.97 39 49.12 63 51.22 48 55.58
Intra-CBLM-PaT -- R 74 57.03 8 53.79 8 45.65 34 52.9 22 52.45 17 57.23
MCP -- C 324 121.22 46 116.28 2 125.82 118 100.65 620 138.74 56 119.87
MdLF -- L 358 104.27 170 90 146 86.54 297 89.87 326 90.34 332 82.06
MdLF -- R 432 94.8 188 91.44 158 87.39 177 84.52 183 93.66 558 91.31
PLIC -- L 52 107.71 62 96.11 98 116.87 33 90.9 55 96.69 21 105.74
PLIC -- R 116 103.77 61 89.21 134 111.09 114 100.07 142 103.88 75 91.46
SF -- L 412 66.59 270 61.93 497 72.42 452 64.61 459 67.14 375 64.58
SF -- R 627 69.02 214 56.31 481 73.86 495 68.88 463 68.75 561 66.17
SLF-I -- R 0 0 2 120.42 0 0 1 116.84 0 0 0 0
SLF-II -- R 0 0 0 0 1 136.86 206 93.83 0 0 0 0
SLF-II -- L 0 0 0 0 0 0 39 95.62 0 0 0 0
SLF-III -- L 33 79.03 108 68.75 101 65.93 88 64.22 8 65.19 7 84.56
SLF-III -- R 203 82.07 38 65.52 232 73.58 320 76.6 79 56.37 13 87.69
SO -- L 13 100.78 8 91.17 17 89.57 8 106.58 15 98.9 30 99.9
SO -- R 43 83.47 9 78.53 3 108.18 18 102.72 8 96.63 0 0
SP -- L 285 77.92 72 66.39 123 85.02 156 73.94 132 74.94 337 79.32
SP -- R 248 78.99 84 72.72 232 88.28 227 76.13 43 72.86 433 78.64
Sup-F -- L 1203 56.39 859 55.11 2111 61.11 925 54.82 1069 60.77 1147 58.86
Sup-F -- R 1506 58.03 638 54.16 1964 59.28 1287 60.56 1127 58.66 1323 59.58
Sup-FP -- L 236 57.22 115 49.95 215 54.02 75 51.96 118 53.02 308 60.1
Sup-FP -- R 153 57.13 31 45.85 204 51.45 81 50.41 148 57.61 157 52.27
Sup-O -- L 110 50.57 104 48.03 283 49.43 57 51.49 35 47.81 11 42.98
Sup-O -- R 70 44.21 67 44.88 125 48.59 60 44.12 20 49.71 1 50.88
Sup-OT -- L 350 78.75 159 54.17 151 77.96 65 60.68 134 53.19 81 57.26
Sup-OT -- R 136 59.35 47 61.26 128 52.86 24 49.74 210 79.44 35 62.57
Sup-P -- L 705 57.12 274 52.17 539 53.37 673 65.81 644 59.82 621 57.1
Sup-P -- R 521 55.5 339 57.33 940 61.8 272 60.06 431 56.59 412 53.13
Sup-PO -- L 84 52.99 88 45.74 172 53.22 82 49.51 99 51.04 8 46.27
Sup-PO -- R 21 44.36 55 46.26 258 51.49 90 50.11 82 46.94 26 45.35
Sup-PT -- L 966 74.4 694 68.76 671 70.57 499 61.63 436 60.36 284 61.06
Sup-PT -- R 709 71.7 571 62.56 653 68.52 297 58.42 423 66.82 310 61.66
Sup-T -- L 246 58.33 189 50.7 583 60.17 321 59.14 234 50.65 602 58.48
Sup-T -- R 177 54.97 179 50.75 390 55.04 276 60.72 477 64.27 600 53.97
TF -- L 653 81.31 522 91.06 669 82.8 722 83.44 453 80.37 152 76.1
TF -- R 493 81.55 684 78.62 802 90.16 578 88.49 480 78.29 392 81.66
TO -- L 115 98.41 100 58.72 106 101.98 68 94.76 99 92.71 180 76.71
TO -- R 76 86.63 74 75.44 62 93.41 8 88.49 29 86.83 45 75.38
TP -- L 149 88.45 238 77.72 300 88.39 159 82.77 167 82.27 178 77.44
TP -- R 265 87.5 279 73.84 173 92.45 413 77.74 123 88.12 161 67.77
UF -- L 201 72.77 154 50.79 119 50.28 199 72.67 121 76.29 212 79.3
UF -- R 406 91.57 234 59.25 139 53.34 442 85.52 151 70.43 380 77.25

Tracts

Below, we visualize whitematteranalysis outputs for the IOFF at each stage of the fiber clustering process, from the initial registered tracts, to the final tracts summarized above. We see that, though tracts lose some fibers in the outlier removal process, poor segmentation of the IOFF is evident at the initial stage, indicating that the issue exists in the input data.

      CMH0135          CMP0182          MRC0053         MRP0096          ZHH0030          ZHP0158

[1] Initial clusters -- whole brain

[1b] Initial clusters -- IFOF

[2] Outliers removed

[3] Transformed clusters (convert into original space)

[4] Separated by hemisphere

Left

Right

[5] Final tracts (top view)

Link: tract descriptions