Hi,

We have two subjects, one with a lhcab that looks ~OK (somewhat noisy) and one with a lhcab that is almost completely missing (please see attached figures). And yet, looking at their respective pathstats.byvoxel.txt (under dpath/lh.cab_PP_avg33_mni_bbr) we find that both have data for this tract and that the subject with a seemingly missing tract (70) has more observations. Is this a thresholding issue? 

The default threshold in Freeview when viewing these files is 20% of the 99th percentile of the posterior probability distribution for the path, so how does that affect the data in pathstats.byvoxel and pathstats.overall; are they also thresholded?



# subjectname 17
# pathwayname lh.cab
#
# pathway start
x y z AD RD MD FA AD_Avg RD_Avg MD_Avg FA_Avg
56 35 27 0.000890712 0.000603441 0.000699198 0.315126 0.00105762 0.000596839 0.000750432 0.362276
56 36 26 0.00107635 0.000545558 0.000722489 0.41169 0.00104539 0.000615595 0.000758858 0.335287
56 37 26 0.00106187 0.000590571 0.000747672 0.372333 0.00105743 0.000602726 0.000754296 0.354483
56 38 25 0.00102202 0.000600078 0.000740726 0.368605 0.00100576 0.000632157 0.000756689 0.313797
56 39 25 0.00119029 0.000522558 0.000745135 0.485075 0.00107733 0.000611676 0.00076689 0.358958
56 39 24 0.000901928 0.000700433 0.000767598 0.204508 0.0010547 0.000622021 0.000766243 0.338646
56 40 24 0.000983715 0.000610012 0.00073458 0.333454 0.00105292 0.000634273 0.00077382 0.330426
56 41 23 0.00109975 0.000657692 0.000805043 0.318553 0.00115473 0.000602686 0.000786698 0.395328
57 42 23 0.00119796 0.000512441 0.000740946 0.50737 0.00119982 0.00058122 0.000787428 0.43539
57 43 22 0.00108816 0.000588772 0.000755234 0.368538 0.00120245 0.000589771 0.000793995 0.417918
57 44 22 0.00145913 0.000457154 0.000791146 0.628211 0.00131065 0.000556036 0.00080757 0.48867
57 45 21 0.00142093 0.000463346 0.000782542 0.617307 0.0013404 0.000544065 0.000809509 0.514237
57 46 21 0.00142182 0.000445771 0.000771122 0.632204 0.00139366 0.000547482 0.000829538 0.525517
57 47 20 0.000968663 0.000475497 0.000639886 0.434747 0.001285 0.000583274 0.000817181 0.448241
58 48 19 0.00121939 0.000531887 0.000761053 0.482488 0.00133092 0.000590401 0.000837236 0.462653
58 49 19 0.00159589 0.000576742 0.000916457 0.569308 0.00136598 0.000635182 0.000878787 0.437028
58 50 19 0.00164139 0.000624262 0.000963304 0.549971 0.00138664 0.000658869 0.000901467 0.426815
58 50 18 0.00157653 0.000942457 0.00115382 0.332295 0.00137177 0.000715268 0.000934107 0.385317
58 51 18 0.00118225 0.000642473 0.0008224 0.36823 0.00118518 0.000684428 0.000851342 0.330996
58 52 18 0.00109238 0.000519084 0.000710181 0.435882 0.00107605 0.000632073 0.000780059 0.324378
58 53 18 0.00129725 0.000623659 0.000848189 0.430382 0.00108778 0.000647922 0.000794535 0.315793
# pathway end



# subjectname 70
# pathwayname lh.cab
#
# pathway start
x y z AD RD MD FA AD_Avg RD_Avg MD_Avg FA_Avg
53 32 26 0.00117731 0.000928949 0.00101174 0.143923 0.00116391 0.00090839 0.000993563 0.153213
53 33 26 0.0010364 0.000859843 0.000918695 0.128905 0.00103869 0.000848443 0.000911856 0.138848
53 33 25 0.00105938 0.000877392 0.000938055 0.127225 0.00105752 0.000865256 0.000929355 0.135088
54 34 25 0.000944648 0.000719044 0.000794246 0.162868 0.000957389 0.000725472 0.000802768 0.16744
54 35 25 0.000972687 0.000738523 0.000816578 0.208351 0.000986717 0.000739063 0.000821629 0.213113
54 36 24 0.00101603 0.000621378 0.000752929 0.305637 0.0010253 0.000631396 0.000762693 0.302995
54 37 24 0.00113992 0.000642822 0.000808521 0.369124 0.0011217 0.000646204 0.000804698 0.353409
55 38 23 0.000890718 0.000584601 0.00068664 0.265622 0.000916719 0.000590972 0.000699556 0.273432
55 39 23 0.0013084 0.000657441 0.000874427 0.41632 0.00129438 0.000656492 0.000869102 0.409684
55 40 22 0.000897226 0.000549981 0.000665729 0.294657 0.000926128 0.000565056 0.000685412 0.294239
56 41 22 0.00129446 0.000643583 0.000860544 0.416518 0.00128053 0.000641873 0.000854761 0.410811
56 42 21 0.00095897 0.000527739 0.000671483 0.356436 0.000986408 0.00054246 0.000690451 0.355442
56 43 21 0.00126047 0.000576778 0.000804674 0.460586 0.00120436 0.000578402 0.000787051 0.4315
57 44 21 0.00141709 0.000815438 0.00101599 0.333322 0.00136115 0.000786714 0.000978188 0.330026
57 45 20 0.00107155 0.000547688 0.000722309 0.398732 0.0010439 0.000565023 0.000724638 0.366345
57 46 19 0.00106184 0.000688623 0.000813027 0.276355 0.00106565 0.000721324 0.000836098 0.250311
58 46 18 0.00138626 0.00111282 0.00120397 0.13344 0.00133896 0.00105932 0.00115254 0.147013
58 46 17 0.00190569 0.00154603 0.00166592 0.127639 0.0017048 0.00136742 0.0014799 0.141036
58 47 17 0.00182424 0.00136918 0.00152086 0.176476 0.00170912 0.00128364 0.00142549 0.178103
58 48 17 0.00179186 0.00155183 0.00163184 0.121897 0.0016827 0.00141198 0.00150224 0.137642
58 49 17 0.00173965 0.00152012 0.00159329 0.0828833 0.00156972 0.00134741 0.00142152 0.101404
58 50 17 0.00146827 0.00123617 0.00131354 0.105179 0.0013648 0.00113875 0.00121408 0.115824
59 51 17 0.000939683 0.000730799 0.000800427 0.151144 0.000913724 0.000729779 0.000791094 0.140851
59 52 17 0.000973182 0.000776841 0.000842288 0.136551 0.000937145 0.000762049 0.00082041 0.130533
59 53 17 0.000974158 0.000799803 0.000857921 0.120722 0.000938325 0.000778099 0.000831516 0.119775
59 54 17 0.00100004 0.000821513 0.000881023 0.135361 0.000956475 0.000793336 0.000847705 0.130042
# pathway end


Thank you!


sincerely yours,

Knut Jørgen Bjuland, PhD
Sørlandet sykehus