The information in SimpleITK is different from that in dicom header

I am using SimpleITK in my project, and I find the patient position read by SimpleITK is differaent from that from dicom header (RadiAnt).

Firstly, I use image = sitk.ReadImage(names) to read image, and I am quite sure the names is sorted by the instance number. Then, I use image.TransformIndexToPhysicalPoint((0, 0, 0)) to obtain the patient position.
On the other hand, I use RadiAnt to open the dicom.
There is some result:

The 0-th image:


The position is similar.

The 100-th image:


The position is quite different.

In addition, the image is aquired by sagital.
I don’t know the reason why the obtained position is different.

Hello @zhang-qiang-github,

Is the origin of the 100’th sagittal image the same as the index [0,0,100]? This index belongs to the 100’th axial slice in the simpleitk volume. I suspect these are not the same points, please try [0,100,0].

I have tried [100, 0, 0] and [0, 100, 0], and the results is also pretty different from that from RadiAnt.


Are you sure that your 100’th slice is the 100’th image? When reading DICOM the image names are ignored and the z coordinate is used by GDCM to sort the slices into the volume. As you are looking at a single slice with RadiAnt, we can’t know if that image really corresponds to the 100’th image slice.

Possibly just check that image file with SimpleITK. Instead of reading the volume read the same image file with RadiAnt and with SimpleITK and look at the origin. If they are the same, then it is likely the issue I raised above.

For the single dicom, the position is the same by sitk.TransformIndexToPhysicalPoint and RadiAnt.

For the volume, I get the size is (320, 320, 240) by fixed_image.GetSize(), and the RadiAnt also shows the volume has 240 images. Thus, I print 240 position using SimpleITK as:

for i in range(240):
pos = fixed_image.TransformIndexToPhysicalPoint((0, 0, i))
print(pos[0], pos[1], pos[2])

And the print information is:

-61.007415771484375 -84.11436462402344 92.94839477539062
-61.537387898868026 -84.11887861966818 92.94557745809786
-62.06736002625167 -84.12339261531292 92.94276014080509
-62.59733215363532 -84.12790661095767 92.93994282351233
-63.12730428101897 -84.13242060660241 92.93712550621956
-63.657276408402616 -84.13693460224714 92.9343081889268
-64.18724853578627 -84.14144859789188 92.93149087163404
-64.71722066316991 -84.14596259353662 92.92867355434127
-65.24719279055357 -84.15047658918137 92.9258562370485
-65.77716491793721 -84.15499058482611 92.92303891975574
-66.30713704532086 -84.15950458047085 92.92022160246297
-66.83710917270452 -84.1640185761156 92.9174042851702
-67.36708130008816 -84.16853257176034 92.91458696787744
-67.8970534274718 -84.17304656740507 92.91176965058467
-68.42702555485546 -84.17756056304981 92.90895233329192
-68.9569976822391 -84.18207455869455 92.90613501599915
-69.48696980962275 -84.1865885543393 92.90331769870639
-70.01694193700641 -84.19110254998404 92.90050038141362
-70.54691406439005 -84.19561654562878 92.89768306412086
-71.0768861917737 -84.20013054127352 92.89486574682809
-71.60685831915734 -84.20464453691827 92.89204842953532
-72.136830446541 -84.209158532563 92.88923111224256
-72.66680257392464 -84.21367252820774 92.88641379494979
-73.1967747013083 -84.21818652385248 92.88359647765704
-73.72674682869194 -84.22270051949722 92.88077916036427
-74.25671895607559 -84.22721451514197 92.8779618430715
-74.78669108345923 -84.23172851078671 92.87514452577874
-75.31666321084289 -84.23624250643145 92.87232720848597
-75.84663533822653 -84.2407565020762 92.8695098911932
-76.37660746561019 -84.24527049772092 92.86669257390044
-76.90657959299384 -84.24978449336567 92.86387525660767
-77.43655172037748 -84.25429848901041 92.8610579393149
-77.96652384776112 -84.25881248465515 92.85824062202214
-78.49649597514478 -84.2633264802999 92.85542330472938
-79.02646810252843 -84.26784047594464 92.85260598743662
-79.55644022991208 -84.27235447158938 92.84978867014385
-80.08641235729573 -84.27686846723412 92.84697135285109
-80.61638448467937 -84.28138246287885 92.84415403555832
-81.14635661206302 -84.2858964585236 92.84133671826555
-81.67632873944667 -84.29041045416834 92.83851940097279
-82.20630086683032 -84.29492444981308 92.83570208368002
-82.73627299421398 -84.29943844545782 92.83288476638725
-83.26624512159762 -84.30395244110257 92.8300674490945
-83.79621724898126 -84.30846643674731 92.82725013180173
-84.32618937636491 -84.31298043239205 92.82443281450897
-84.85616150374857 -84.31749442803678 92.8216154972162
-85.38613363113221 -84.32200842368152 92.81879817992343
-85.91610575851587 -84.32652241932627 92.81598086263067
-86.44607788589951 -84.33103641497101 92.8131635453379
-86.97605001328316 -84.33555041061575 92.81034622804513
-87.5060221406668 -84.3400644062605 92.80752891075237
-88.03599426805046 -84.34457840190524 92.80471159345961
-88.5659663954341 -84.34909239754998 92.80189427616685
-89.09593852281776 -84.35360639319471 92.79907695887408
-89.6259106502014 -84.35812038883945 92.79625964158132
-90.15588277758505 -84.3626343844842 92.79344232428855
-90.68585490496869 -84.36714838012894 92.79062500699578
-91.21582703235235 -84.37166237577368 92.78780768970302
-91.745799159736 -84.37617637141842 92.78499037241025
-92.27577128711964 -84.38069036706317 92.78217305511748
-92.8057434145033 -84.38520436270791 92.77935573782473
-93.33571554188694 -84.38971835835264 92.77653842053196
-93.86568766927059 -84.39423235399738 92.7737211032392
-94.39565979665423 -84.39874634964212 92.77090378594643
-94.92563192403789 -84.40326034528687 92.76808646865366
-95.45560405142155 -84.40777434093161 92.7652691513609
-95.98557617880519 -84.41228833657635 92.76245183406813
-96.51554830618883 -84.4168023322211 92.75963451677536
-97.04552043357248 -84.42131632786584 92.7568171994826
-97.57549256095612 -84.42583032351057 92.75399988218985
-98.10546468833978 -84.43034431915531 92.75118256489708
-98.63543681572344 -84.43485831480005 92.74836524760431
-99.16540894310708 -84.4393723104448 92.74554793031155
-99.69538107049073 -84.44388630608954 92.74273061301878
-100.22535319787437 -84.44840030173428 92.73991329572601
-100.75532532525801 -84.45291429737902 92.73709597843325
-101.28529745264167 -84.45742829302377 92.73427866114048
-101.81526958002533 -84.4619422886685 92.73146134384771
-102.34524170740897 -84.46645628431324 92.72864402655495
-102.87521383479262 -84.47097027995798 92.7258267092622
-103.40518596217626 -84.47548427560272 92.72300939196943
-103.9351580895599 -84.47999827124747 92.72019207467666
-104.46513021694356 -84.48451226689221 92.7173747573839
-104.99510234432721 -84.48902626253695 92.71455744009113
-105.52507447171087 -84.4935402581817 92.71174012279836
-106.05504659909451 -84.49805425382644 92.7089228055056
-106.58501872647815 -84.50256824947117 92.70610548821283
-107.1149908538618 -84.50708224511591 92.70328817092006
-107.64496298124546 -84.51159624076065 92.70047085362731
-108.1749351086291 -84.5161102364054 92.69765353633454
-108.70490723601276 -84.52062423205014 92.69483621904178
-109.2348793633964 -84.52513822769488 92.69201890174901
-109.76485149078005 -84.52965222333962 92.68920158445624
-110.29482361816369 -84.53416621898437 92.68638426716348
-110.82479574554735 -84.5386802146291 92.68356694987071
-111.35476787293099 -84.54319421027384 92.68074963257794
-111.88474000031465 -84.54770820591858 92.67793231528518
-112.4147121276983 -84.55222220156332 92.67511499799242
-112.94468425508194 -84.55673619720807 92.67229768069966
-113.47465638246558 -84.56125019285281 92.66948036340689
-114.00462850984924 -84.56576418849755 92.66666304611412
-114.53460063723288 -84.5702781841423 92.66384572882136
-115.06457276461654 -84.57479217978702 92.66102841152859
-115.59454489200019 -84.57930617543177 92.65821109423582
-116.12451701938383 -84.58382017107651 92.65539377694306
-116.65448914676747 -84.58833416672125 92.65257645965029
-117.18446127415113 -84.592848162366 92.64975914235754
-117.71443340153478 -84.59736215801074 92.64694182506477
-118.24440552891843 -84.60187615365548 92.644124507772
-118.77437765630208 -84.60639014930022 92.64130719047924
-119.30434978368572 -84.61090414494495 92.63848987318647
-119.83432191106937 -84.6154181405897 92.6356725558937
-120.36429403845302 -84.61993213623444 92.63285523860094
-120.89426616583667 -84.62444613187918 92.63003792130817
-121.42423829322033 -84.62896012752392 92.6272206040154
-121.95421042060397 -84.63347412316867 92.62440328672265
-122.48418254798761 -84.63798811881341 92.62158596942989
-123.01415467537126 -84.64250211445815 92.61876865213712
-123.5441268027549 -84.64701611010288 92.61595133484435
-124.07409893013856 -84.65153010574763 92.61313401755159
-124.60407105752222 -84.65604410139237 92.61031670025882
-125.13404318490586 -84.66055809703711 92.60749938296605
-125.66401531228951 -84.66507209268185 92.60468206567329
-126.19398743967315 -84.6695860883266 92.60186474838052
-126.72395956705681 -84.67410008397134 92.59904743108775
-127.25393169444045 -84.67861407961608 92.596230113795
-127.7839038218241 -84.68312807526081 92.59341279650224
-128.31387594920776 -84.68764207090555 92.59059547920947
-128.8438480765914 -84.6921560665503 92.5877781619167
-129.37382020397504 -84.69667006219504 92.58496084462394
-129.90379233135872 -84.70118405783978 92.58214352733117
-130.43376445874236 -84.70569805348453 92.5793262100384
-130.963736586126 -84.71021204912927 92.57650889274564
-131.49370871350965 -84.71472604477401 92.57369157545287
-132.0236808408933 -84.71924004041874 92.57087425816012
-132.55365296827694 -84.72375403606348 92.56805694086735
-133.08362509566058 -84.72826803170823 92.56523962357458
-133.61359722304422 -84.73278202735297 92.56242230628182
-134.14356935042787 -84.73729602299771 92.55960498898905
-134.67354147781154 -84.74181001864245 92.55678767169628
-135.20351360519518 -84.7463240142872 92.55397035440352
-135.73348573257883 -84.75083800993194 92.55115303711075
-136.2634578599625 -84.75535200557667 92.54833571981798
-136.79342998734614 -84.75986600122141 92.54551840252523
-137.3234021147298 -84.76437999686615 92.54270108523247
-137.85337424211343 -84.7688939925109 92.5398837679397
-138.38334636949708 -84.77340798815564 92.53706645064693
-138.91331849688072 -84.77792198380038 92.53424913335417
-139.44329062426436 -84.78243597944513 92.5314318160614
-139.973262751648 -84.78694997508987 92.52861449876863
-140.50323487903165 -84.7914639707346 92.52579718147587
-141.03320700641532 -84.79597796637934 92.5229798641831
-141.56317913379897 -84.80049196202408 92.52016254689035
-142.0931512611826 -84.80500595766883 92.51734522959758
-142.62312338856628 -84.80951995331357 92.51452791230481
-143.15309551594993 -84.81403394895831 92.51171059501205
-143.68306764333357 -84.81854794460305 92.50889327771928
-144.21303977071722 -84.8230619402478 92.50607596042651
-144.74301189810086 -84.82757593589253 92.50325864313375
-145.2729840254845 -84.83208993153727 92.50044132584098
-145.80295615286815 -84.83660392718201 92.49762400854821
-146.3329282802518 -84.84111792282675 92.49480669125546
-146.86290040763544 -84.8456319184715 92.4919893739627
-147.39287253501908 -84.85014591411624 92.48917205666993
-147.92284466240275 -84.85465990976098 92.48635473937716
-148.4528167897864 -84.85917390540573 92.4835374220844
-148.98278891717004 -84.86368790105047 92.48072010479163
-149.5127610445537 -84.8682018966952 92.47790278749886
-150.04273317193736 -84.87271589233994 92.4750854702061
-150.572705299321 -84.87722988798468 92.47226815291333
-151.10267742670464 -84.88174388362943 92.46945083562056
-151.6326495540883 -84.88625787927417 92.46663351832781
-152.16262168147193 -84.89077187491891 92.46381620103504
-152.69259380885558 -84.89528587056365 92.46099888374228
-153.22256593623922 -84.8997998662084 92.45818156644951
-153.75253806362286 -84.90431386185313 92.45536424915674
-154.28251019100654 -84.90882785749787 92.45254693186398
-154.81248231839018 -84.91334185314261 92.44972961457121
-155.34245444577383 -84.91785584878735 92.44691229727844
-155.8724265731575 -84.9223698444321 92.44409497998568
-156.40239870054114 -84.92688384007684 92.44127766269293
-156.93237082792479 -84.93139783572158 92.43846034540016
-157.46234295530843 -84.93591183136633 92.43564302810739
-157.99231508269207 -84.94042582701105 92.43282571081463
-158.52228721007572 -84.9449398226558 92.43000839352186
-159.05225933745936 -84.94945381830054 92.4271910762291
-159.582231464843 -84.95396781394528 92.42437375893633
-160.11220359222665 -84.95848180959003 92.42155644164356
-160.64217571961032 -84.96299580523477 92.4187391243508
-161.17214784699397 -84.96750980087951 92.41592180705804
-161.7021199743776 -84.97202379652425 92.41310448976527
-162.23209210176128 -84.97653779216898 92.41028717247251
-162.76206422914493 -84.98105178781373 92.40746985517974
-163.29203635652857 -84.98556578345847 92.40465253788697
-163.8220084839122 -84.99007977910321 92.40183522059421
-164.35198061129586 -84.99459377474795 92.39901790330144
-164.8819527386795 -84.9991077703927 92.39620058600867
-165.41192486606315 -85.00362176603744 92.39338326871591
-165.9418969934468 -85.00813576168218 92.39056595142316
-166.47186912083043 -85.01264975732691 92.38774863413039
-167.0018412482141 -85.01716375297165 92.38493131683762
-167.53181337559775 -85.0216777486164 92.38211399954486
-168.0617855029814 -85.02619174426114 92.37929668225209
-168.59175763036507 -85.03070573990588 92.37647936495932
-169.1217297577487 -85.03521973555063 92.37366204766656
-169.65170188513235 -85.03973373119537 92.37084473037379
-170.181674012516 -85.04424772684011 92.36802741308102
-170.71164613989964 -85.04876172248484 92.36521009578827
-171.2416182672833 -85.05327571812958 92.3623927784955
-171.77159039466693 -85.05778971377433 92.35957546120274
-172.30156252205057 -85.06230370941907 92.35675814390997
-172.83153464943422 -85.06681770506381 92.3539408266172
-173.3615067768179 -85.07133170070855 92.35112350932444
-173.89147890420153 -85.0758456963533 92.34830619203167
-174.42145103158518 -85.08035969199804 92.3454888747389
-174.95142315896885 -85.08487368764277 92.34267155744614
-175.4813952863525 -85.08938768328751 92.33985424015339
-176.01136741373614 -85.09390167893226 92.33703692286062
-176.54133954111978 -85.098415674577 92.33421960556785
-177.07131166850343 -85.10292967022174 92.33140228827509
-177.60128379588707 -85.10744366586648 92.32858497098232
-178.13125592327071 -85.11195766151123 92.32576765368955
-178.66122805065436 -85.11647165715597 92.32295033639679
-179.191200178038 -85.1209856528007 92.32013301910402
-179.72117230542167 -85.12549964844544 92.31731570181125
-180.25114443280532 -85.13001364409018 92.31449838451849
-180.78111656018896 -85.13452763973493 92.31168106722573
-181.3110886875726 -85.13904163537967 92.30886374993297
-181.84106081495628 -85.14355563102441 92.3060464326402
-182.37103294233992 -85.14806962666916 92.30322911534743
-182.90100506972357 -85.1525836223139 92.30041179805467
-183.4309771971072 -85.15709761795863 92.2975944807619
-183.96094932449085 -85.16161161360337 92.29477716346913
-184.4909214518745 -85.16612560924811 92.29195984617637
-185.02089357925814 -85.17063960489286 92.2891425288836
-185.5508657066418 -85.1751536005376 92.28632521159085
-186.08083783402543 -85.17966759618234 92.28350789429808
-186.6108099614091 -85.18418159182708 92.28069057700532
-187.14078208879275 -85.18869558747183 92.27787325971255
-187.6707542161764 -85.19320958311656 92.27505594241978

From the above result, I find all the position by SimpleITK is pretty different from the RadiAnt result (-8.54, -83.67, 93.23).

Hello @zhang-qiang-github,
These results show that SimpleITK is likely reading the data correctly:

  1. When reading the same single slice the origin is the same.
  2. Because your original slice is a sagittal, your loop index should be on the y coordinate and not the z coordinate as in your code (this was one of the previous issues we discussed above).

I have printed all the position as following:

First, loop index on the first index:

fixed_image = sitk.ReadImage(names)
shape = fixed_image.GetSize()
for i in range(shape[0]):
    pos = fixed_image.TransformIndexToPhysicalPoint((i, 0, 0))
    print(pos)

And the results are:

(-61.007415771484375, -84.11436462402344, 92.94839477539062)
(-61.01167869122247, -83.58513115366586, 92.90234780080411)
(-61.01594161096056, -83.05589768330826, 92.85630082621759)
(-61.020204530698656, -82.52666421295068, 92.81025385163106)
(-61.02446745043675, -81.99743074259308, 92.76420687704454)
(-61.02873037017484, -81.4681972722355, 92.71815990245803)
(-61.03299328991294, -80.93896380187792, 92.67211292787151)
(-61.037256209651034, -80.40973033152032, 92.62606595328499)
(-61.04151912938912, -79.88049686116274, 92.58001897869848)
(-61.04578204912722, -79.35126339080516, 92.53397200411194)
(-61.050044968865315, -78.82202992044756, 92.48792502952543)
(-61.054307888603404, -78.29279645008998, 92.44187805493891)
(-61.0585708083415, -77.7635629797324, 92.3958310803524)
(-61.062833728079596, -77.2343295093748, 92.34978410576588)
(-61.067096647817685, -76.70509603901722, 92.30373713117936)
(-61.07135956755578, -76.17586256865962, 92.25769015659283)
(-61.07562248729388, -75.64662909830204, 92.21164318200631)
(-61.079885407031966, -75.11739562794446, 92.1655962074198)
(-61.08414832677006, -74.58816215758686, 92.11954923283328)
(-61.08841124650816, -74.05892868722928, 92.07350225824676)
(-61.09267416624625, -73.52969521687169, 92.02745528366025)
(-61.096937085984344, -73.0004617465141, 91.98140830907371)
(-61.10120000572243, -72.47122827615652, 91.9353613344872)
(-61.10546292546053, -71.94199480579893, 91.88931435990068)
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(-62.23513665605536, 68.30487483896167, 79.68686609447307)
(-62.23939957579345, 68.83410830931925, 79.64081911988656)
(-62.243662495531545, 69.36334177967683, 79.59477214530004)
(-62.24792541526964, 69.89257525003444, 79.54872517071351)
(-62.25218833500773, 70.42180872039202, 79.502678196127)
(-62.256451254745826, 70.9510421907496, 79.45663122154048)
(-62.26071417448392, 71.48027566110719, 79.41058424695396)
(-62.26497709422201, 72.00950913146477, 79.36453727236744)
(-62.26924001396011, 72.53874260182238, 79.31849029778093)
(-62.273502933698204, 73.06797607217996, 79.2724433231944)
(-62.27776585343629, 73.59720954253754, 79.22639634860788)
(-62.28202877317439, 74.12644301289512, 79.18034937402136)
(-62.286291692912485, 74.6556764832527, 79.13430239943484)
(-62.290554612650574, 75.18490995361029, 79.08825542484833)
(-62.29481753238867, 75.7141434239679, 79.0422084502618)
(-62.299080452126766, 76.24337689432548, 78.99616147567528)
(-62.303343371864855, 76.77261036468306, 78.95011450108876)
(-62.30760629160295, 77.30184383504064, 78.90406752650225)
(-62.31186921134105, 77.83107730539822, 78.85802055191573)
(-62.31613213107914, 78.36031077575583, 78.81197357732921)
(-62.32039505081723, 78.88954424611342, 78.7659266027427)
(-62.32465797055532, 79.418777716471, 78.71987962815616)
(-62.32892089029342, 79.94801118682858, 78.67383265356965)
(-62.333183810031514, 80.47724465718616, 78.62778567898313)
(-62.3374467297696, 81.00647812754374, 78.58173870439661)
(-62.3417096495077, 81.53571159790135, 78.5356917298101)
(-62.345972569245795, 82.06494506825894, 78.48964475522357)
(-62.350235488983884, 82.59417853861652, 78.44359778063705)
(-62.35449840872198, 83.1234120089741, 78.39755080605053)
(-62.358761328460076, 83.65264547933168, 78.35150383146402)
(-62.363024248198165, 84.18187894968929, 78.3054568568775)
(-62.36728716793626, 84.71111242004687, 78.25940988229098)

Then, loop index on the second index:

fixed_image = sitk.ReadImage(names)
shape = fixed_image.GetSize()
for i in range(shape[1]):
    pos = fixed_image.TransformIndexToPhysicalPoint((0, i, 0))
    print(pos)

and the information is:

(-61.007415771484375, -84.11436462402344, 92.94839477539062)
(-61.00421034097021, -84.16038661745696, 92.41915167072546)
(-61.001004910456054, -84.20640861089049, 91.8899085660603)
(-60.99779947994189, -84.25243060432402, 91.36066546139513)
(-60.994594049427725, -84.29845259775755, 90.83142235672996)
(-60.99138861891356, -84.34447459119107, 90.3021792520648)
(-60.988183188399404, -84.3904965846246, 89.77293614739963)
(-60.98497775788524, -84.43651857805813, 89.24369304273446)
(-60.981772327371075, -84.48254057149165, 88.7144499380693)
(-60.97856689685691, -84.52856256492518, 88.18520683340414)
(-60.975361466342754, -84.57458455835871, 87.65596372873897)
(-60.97215603582859, -84.62060655179224, 87.1267206240738)
(-60.968950605314426, -84.66662854522576, 86.59747751940864)
(-60.96574517480026, -84.71265053865929, 86.06823441474347)
(-60.962539744286104, -84.75867253209282, 85.5389913100783)
(-60.95933431377194, -84.80469452552634, 85.00974820541315)
(-60.956128883257776, -84.85071651895987, 84.48050510074798)
(-60.95292345274362, -84.8967385123934, 83.9512619960828)
(-60.949718022229455, -84.94276050582693, 83.42201889141765)
(-60.94651259171529, -84.98878249926045, 82.89277578675248)
(-60.943307161201126, -85.03480449269398, 82.36353268208731)
(-60.94010173068697, -85.0808264861275, 81.83428957742214)
(-60.936896300172805, -85.12684847956103, 81.30504647275698)
(-60.93369086965864, -85.17287047299456, 80.77580336809181)
(-60.930485439144476, -85.21889246642809, 80.24656026342666)
(-60.92728000863032, -85.26491445986161, 79.71731715876149)
(-60.924074578116155, -85.31093645329514, 79.18807405409632)
(-60.92086914760199, -85.35695844672867, 78.65883094943115)
(-60.91766371708783, -85.4029804401622, 78.129587844766)
(-60.91445828657367, -85.44900243359572, 77.60034474010082)
(-60.911252856059505, -85.49502442702925, 77.07110163543565)
(-60.90804742554534, -85.54104642046278, 76.5418585307705)
(-60.904841995031184, -85.5870684138963, 76.01261542610533)
(-60.90163656451702, -85.63309040732983, 75.48337232144016)
(-60.898431134002855, -85.67911240076336, 74.95412921677499)
(-60.89522570348869, -85.72513439419689, 74.42488611210983)
(-60.892020272974534, -85.77115638763041, 73.89564300744466)
(-60.88881484246037, -85.81717838106394, 73.3663999027795)
(-60.885609411946206, -85.86320037449747, 72.83715679811434)
(-60.88240398143204, -85.909222367931, 72.30791369344917)
(-60.879198550917884, -85.95524436136452, 71.778670588784)
(-60.87599312040372, -86.00126635479803, 71.24942748411884)
(-60.872787689889556, -86.04728834823156, 70.72018437945367)
(-60.86958225937539, -86.09331034166509, 70.19094127478851)
(-60.866376828861235, -86.13933233509862, 69.66169817012334)
(-60.86317139834707, -86.18535432853214, 69.13245506545817)
(-60.859965967832906, -86.23137632196567, 68.603211960793)
(-60.85676053731875, -86.2773983153992, 68.07396885612785)
(-60.853555106804585, -86.32342030883272, 67.54472575146268)
(-60.85034967629042, -86.36944230226625, 67.01548264679751)
(-60.847144245776256, -86.41546429569978, 66.48623954213235)
(-60.8439388152621, -86.4614862891333, 65.95699643746718)
(-60.840733384747935, -86.50750828256683, 65.42775333280201)
(-60.83752795423377, -86.55353027600036, 64.89851022813684)
(-60.83432252371961, -86.59955226943389, 64.36926712347169)
(-60.83111709320545, -86.64557426286741, 63.84002401880652)
(-60.827911662691285, -86.69159625630094, 63.310780914141354)
(-60.82470623217712, -86.73761824973447, 62.78153780947619)
(-60.821500801662964, -86.783640243168, 62.25229470481102)
(-60.8182953711488, -86.82966223660152, 61.72305160014586)
(-60.815089940634635, -86.87568423003505, 61.193808495480695)
(-60.81188451012047, -86.92170622346858, 60.664565390815525)
(-60.808679079606314, -86.9677282169021, 60.13532228615036)
(-60.80547364909215, -87.01375021033563, 59.60607918148519)
(-60.802268218577986, -87.05977220376916, 59.07683607682003)
(-60.79906278806382, -87.10579419720268, 58.54759297215487)
(-60.795857357549664, -87.15181619063621, 58.0183498674897)
(-60.7926519270355, -87.19783818406974, 57.489106762824534)
(-60.789446496521336, -87.24386017750327, 56.959863658159364)
(-60.78624106600717, -87.28988217093679, 56.4306205534942)
(-60.783035635493015, -87.33590416437032, 55.90137744882904)
(-60.77983020497885, -87.38192615780385, 55.37213434416387)
(-60.776624774464686, -87.42794815123737, 54.842891239498705)
(-60.77341934395053, -87.4739701446709, 54.31364813483354)
(-60.770213913436365, -87.51999213810443, 53.78440503016837)
(-60.7670084829222, -87.56601413153795, 53.25516192550321)
(-60.763803052408036, -87.61203612497148, 52.72591882083805)
(-60.76059762189388, -87.65805811840501, 52.19667571617288)
(-60.757392191379715, -87.70408011183854, 51.667432611507714)
(-60.75418676086555, -87.75010210527206, 51.138189506842544)
(-60.75098133035139, -87.79612409870559, 50.60894640217738)
(-60.74777589983723, -87.84214609213912, 50.07970329751222)
(-60.744570469323065, -87.88816808557264, 49.55046019284705)
(-60.7413650388089, -87.93419007900617, 49.021217088181885)
(-60.73815960829474, -87.9802120724397, 48.491973983516715)
(-60.73495417778058, -88.02623406587323, 47.96273087885155)
(-60.731748747266415, -88.07225605930675, 47.43348777418639)
(-60.72854331675225, -88.11827805274028, 46.90424466952122)
(-60.725337886238094, -88.1643000461738, 46.375001564856056)
(-60.72213245572393, -88.21032203960733, 45.84575846019089)
(-60.718927025209766, -88.25634403304086, 45.31651535552572)
(-60.7157215946956, -88.30236602647439, 44.78727225086056)
(-60.712516164181444, -88.34838801990792, 44.2580291461954)
(-60.70931073366728, -88.39441001334144, 43.72878604153023)
(-60.706105303153116, -88.44043200677497, 43.199542936865065)
(-60.70289987263895, -88.4864540002085, 42.670299832199895)
(-60.699694442124795, -88.53247599364202, 42.14105672753473)
(-60.69648901161063, -88.57849798707555, 41.61181362286957)
(-60.693283581096466, -88.62451998050908, 41.0825705182044)
(-60.6900781505823, -88.6705419739426, 40.553327413539236)
(-60.686872720068145, -88.71656396737613, 40.024084308874066)
(-60.68366728955398, -88.76258596080966, 39.4948412042089)
(-60.680461859039816, -88.80860795424319, 38.96559809954374)
(-60.67725642852566, -88.85462994767671, 38.43635499487857)
(-60.674050998011495, -88.90065194111024, 37.90711189021341)
(-60.67084556749733, -88.94667393454377, 37.377868785548245)
(-60.66764013698317, -88.9926959279773, 36.848625680883075)
(-60.66443470646901, -89.03871792141082, 36.31938257621791)
(-60.661229275954845, -89.08473991484435, 35.79013947155275)
(-60.65802384544068, -89.13076190827788, 35.26089636688758)
(-60.65481841492652, -89.1767839017114, 34.731653262222416)
(-60.65161298441236, -89.22280589514493, 34.202410157557246)
(-60.648407553898195, -89.26882788857846, 33.67316705289208)
(-60.64520212338403, -89.31484988201198, 33.14392394822692)
(-60.64199669286987, -89.36087187544551, 32.61468084356175)
(-60.63879126235571, -89.40689386887904, 32.08543773889659)
(-60.635585831841546, -89.45291586231255, 31.556194634231417)
(-60.63238040132738, -89.49893785574608, 31.026951529566254)
(-60.629174970813224, -89.5449598491796, 30.49770842490109)
(-60.62596954029906, -89.59098184261313, 29.96846532023592)
(-60.622764109784896, -89.63700383604666, 29.43922221557076)
(-60.61955867927073, -89.68302582948019, 28.909979110905596)
(-60.616353248756575, -89.72904782291371, 28.380736006240426)
(-60.61314781824241, -89.77506981634724, 27.851492901575256)
(-60.609942387728246, -89.82109180978077, 27.3222497969101)
(-60.60673695721408, -89.8671138032143, 26.79300669224493)
(-60.603531526699925, -89.91313579664782, 26.26376358757976)
(-60.60032609618576, -89.95915779008135, 25.734520482914604)
(-60.597120665671596, -90.00517978351488, 25.205277378249434)
(-60.59391523515744, -90.0512017769484, 24.676034273584264)
(-60.590709804643275, -90.09722377038193, 24.14679116891911)
(-60.58750437412911, -90.14324576381546, 23.61754806425394)
(-60.58429894361495, -90.18926775724898, 23.08830495958877)
(-60.58109351310079, -90.23528975068251, 22.559061854923613)
(-60.577888082586625, -90.28131174411604, 22.029818750258443)
(-60.57468265207246, -90.32733373754957, 21.500575645593273)
(-60.5714772215583, -90.37335573098309, 20.971332540928103)
(-60.56827179104414, -90.41937772441662, 20.442089436262947)
(-60.565066360529975, -90.46539971785015, 19.912846331597777)
(-60.56186093001581, -90.51142171128367, 19.383603226932607)
(-60.55865549950165, -90.5574437047172, 18.85436012226745)
(-60.55545006898749, -90.60346569815073, 18.32511701760228)
(-60.552244638473326, -90.64948769158426, 17.79587391293711)
(-60.54903920795916, -90.69550968501778, 17.266630808271955)
(-60.545833777445004, -90.74153167845131, 16.737387703606785)
(-60.54262834693084, -90.78755367188484, 16.208144598941615)
(-60.539422916416676, -90.83357566531836, 15.67890149427646)
(-60.53621748590251, -90.87959765875189, 15.14965838961129)
(-60.533012055388355, -90.92561965218542, 14.62041528494612)
(-60.52980662487419, -90.97164164561894, 14.091172180280964)
(-60.526601194360026, -91.01766363905247, 13.561929075615794)
(-60.52339576384586, -91.063685632486, 13.032685970950624)
(-60.520190333331705, -91.10970762591953, 12.503442866285468)
(-60.51698490281754, -91.15572961935305, 11.974199761620298)
(-60.513779472303376, -91.20175161278658, 11.444956656955128)
(-60.51057404178921, -91.24777360622011, 10.915713552289958)
(-60.507368611275055, -91.29379559965363, 10.386470447624802)
(-60.50416318076089, -91.33981759308716, 9.857227342959632)
(-60.50095775024673, -91.38583958652069, 9.327984238294462)
(-60.49775231973257, -91.43186157995422, 8.798741133629306)
(-60.494546889218405, -91.47788357338774, 8.269498028964136)
(-60.49134145870424, -91.52390556682127, 7.740254924298966)
(-60.48813602819008, -91.5699275602548, 7.211011819633811)
(-60.48493059767592, -91.61594955368832, 6.681768714968641)
(-60.481725167161756, -91.66197154712185, 6.152525610303471)
(-60.47851973664759, -91.70799354055538, 5.623282505638315)
(-60.47531430613343, -91.7540155339889, 5.094039400973145)
(-60.47210887561927, -91.80003752742243, 4.564796296307975)
(-60.468903445105106, -91.84605952085596, 4.035553191642805)
(-60.46569801459094, -91.89208151428949, 3.506310086977649)
(-60.46249258407678, -91.93810350772301, 2.977066982312479)
(-60.45928715356262, -91.98412550115654, 2.447823877647309)
(-60.456081723048456, -92.03014749459007, 1.9185807729821533)
(-60.45287629253429, -92.0761694880236, 1.3893376683169834)
(-60.449670862020135, -92.12219148145712, 0.8600945636518134)
(-60.44646543150597, -92.16821347489065, 0.3308514589866576)
(-60.443260000991806, -92.21423546832418, -0.19839164567851242)
(-60.44005457047764, -92.2602574617577, -0.7276347503436824)
(-60.436849139963485, -92.30627945519123, -1.2568778550088382)
(-60.43364370944932, -92.35230144862476, -1.7861209596740082)
(-60.430438278935156, -92.39832344205828, -2.315364064339178)
(-60.42723284842099, -92.44434543549181, -2.844607169004334)
(-60.424027417906835, -92.49036742892534, -3.373850273669504)
(-60.42082198739267, -92.53638942235887, -3.903093378334674)
(-60.41761655687851, -92.5824114157924, -4.43233648299983)
(-60.41441112636434, -92.62843340922592, -4.961579587665)
(-60.411205695850185, -92.67445540265945, -5.49082269233017)
(-60.40800026533602, -92.72047739609297, -6.02006579699534)
(-60.40479483482186, -92.7664993895265, -6.5493089016604955)
(-60.4015894043077, -92.81252138296003, -7.0785520063256655)
(-60.398383973793536, -92.85854337639356, -7.6077951109908355)
(-60.39517854327937, -92.90456536982708, -8.137038215655991)
(-60.39197311276521, -92.95058736326061, -8.666281320321161)
(-60.38876768225105, -92.99660935669414, -9.195524424986331)
(-60.385562251736886, -93.04263135012766, -9.724767529651487)
(-60.38235682122272, -93.08865334356119, -10.254010634316657)
(-60.37915139070856, -93.13467533699472, -10.783253738981827)
(-60.3759459601944, -93.18069733042825, -11.312496843646983)
(-60.372740529680236, -93.22671932386177, -11.841739948312153)
(-60.36953509916607, -93.2727413172953, -12.370983052977323)
(-60.36632966865191, -93.31876331072883, -12.900226157642493)
(-60.36312423813775, -93.36478530416235, -13.429469262307649)
(-60.359918807623586, -93.41080729759587, -13.958712366972819)
(-60.35671337710942, -93.4568292910294, -14.487955471637989)
(-60.353507946595265, -93.50285128446292, -15.017198576303144)
(-60.3503025160811, -93.54887327789645, -15.546441680968314)
(-60.347097085566936, -93.59489527132997, -16.075684785633484)
(-60.34389165505277, -93.6409172647635, -16.60492789029864)
(-60.340686224538615, -93.68693925819703, -17.13417099496381)
(-60.33748079402445, -93.73296125163056, -17.66341409962898)
(-60.33427536351029, -93.77898324506408, -18.192657204294136)
(-60.33106993299612, -93.82500523849761, -18.721900308959306)
(-60.327864502481965, -93.87102723193114, -19.251143413624476)
(-60.3246590719678, -93.91704922536466, -19.78038651828963)
(-60.32145364145364, -93.96307121879819, -20.3096296229548)
(-60.31824821093947, -94.00909321223172, -20.83887272761997)
(-60.315042780425316, -94.05511520566525, -21.368115832285127)
(-60.31183734991115, -94.10113719909877, -21.897358936950297)
(-60.30863191939699, -94.1471591925323, -22.426602041615467)
(-60.30542648888283, -94.19318118596583, -22.955845146280637)
(-60.302221058368666, -94.23920317939935, -23.485088250945793)
(-60.2990156278545, -94.28522517283288, -24.014331355610963)
(-60.29581019734034, -94.33124716626641, -24.543574460276133)
(-60.29260476682618, -94.37726915969994, -25.07281756494129)
(-60.289399336312016, -94.42329115313346, -25.60206066960646)
(-60.28619390579785, -94.46931314656699, -26.13130377427163)
(-60.28298847528369, -94.51533514000052, -26.660546878936785)
(-60.27978304476953, -94.56135713343404, -27.189789983601955)
(-60.276577614255366, -94.60737912686757, -27.719033088267125)
(-60.2733721837412, -94.6534011203011, -28.24827619293228)
(-60.270166753227045, -94.69942311373462, -28.77751929759745)
(-60.26696132271288, -94.74544510716815, -29.30676240226262)
(-60.263755892198716, -94.79146710060168, -29.83600550692779)
(-60.26055046168455, -94.8374890940352, -30.365248611592946)
(-60.257345031170395, -94.88351108746873, -30.894491716258116)
(-60.25413960065623, -94.92953308090226, -31.423734820923286)
(-60.25093417014207, -94.97555507433579, -31.952977925588442)
(-60.2477287396279, -95.02157706776931, -32.48222103025361)
(-60.244523309113745, -95.06759906120284, -33.01146413491878)
(-60.24131787859958, -95.11362105463637, -33.54070723958394)
(-60.23811244808542, -95.1596430480699, -34.06995034424911)
(-60.23490701757125, -95.20566504150342, -34.59919344891428)
(-60.231701587057096, -95.25168703493695, -35.128436553579434)
(-60.22849615654293, -95.29770902837048, -35.657679658244604)
(-60.22529072602877, -95.343731021804, -36.186922762909774)
(-60.22208529551461, -95.38975301523753, -36.716165867574944)
(-60.218879865000446, -95.43577500867106, -37.245408972240114)
(-60.21567443448628, -95.48179700210459, -37.774652076905255)
(-60.21246900397212, -95.52781899553811, -38.303895181570425)
(-60.20926357345796, -95.57384098897164, -38.833138286235595)
(-60.206058142943796, -95.61986298240517, -39.362381390900765)
(-60.20285271242963, -95.6658849758387, -39.891624495565935)
(-60.19964728191547, -95.71190696927222, -40.420867600231105)
(-60.19644185140131, -95.75792896270575, -40.95011070489625)
(-60.193236420887146, -95.80395095613927, -41.47935380956142)
(-60.19003099037298, -95.8499729495728, -42.00859691422659)
(-60.18682555985882, -95.89599494300633, -42.53784001889176)
(-60.18362012934466, -95.94201693643986, -43.06708312355693)
(-60.180414698830496, -95.98803892987338, -43.5963262282221)
(-60.17720926831633, -96.03406092330691, -44.12556933288727)
(-60.174003837802175, -96.08008291674044, -44.65481243755241)
(-60.17079840728801, -96.12610491017396, -45.18405554221758)
(-60.16759297677385, -96.17212690360749, -45.71329864688275)
(-60.16438754625968, -96.21814889704102, -46.24254175154792)
(-60.161182115745525, -96.26417089047455, -46.77178485621309)
(-60.15797668523136, -96.31019288390807, -47.30102796087826)
(-60.1547712547172, -96.3562148773416, -47.8302710655434)
(-60.15156582420303, -96.40223687077513, -48.35951417020857)
(-60.148360393688876, -96.44825886420865, -48.88875727487374)
(-60.14515496317471, -96.49428085764218, -49.41800037953891)
(-60.14194953266055, -96.54030285107571, -49.94724348420408)
(-60.13874410214638, -96.58632484450922, -50.47648658886925)
(-60.135538671632226, -96.63234683794275, -51.00572969353442)
(-60.13233324111806, -96.67836883137628, -51.53497279819956)
(-60.1291278106039, -96.7243908248098, -52.06421590286473)
(-60.12592238008974, -96.77041281824333, -52.5934590075299)
(-60.122716949575576, -96.81643481167686, -53.12270211219507)
(-60.11951151906141, -96.86245680511038, -53.65194521686024)
(-60.11630608854725, -96.90847879854391, -54.18118832152541)
(-60.11310065803309, -96.95450079197744, -54.71043142619055)
(-60.109895227518926, -97.00052278541096, -55.23967453085572)
(-60.10668979700476, -97.04654477884449, -55.76891763552089)
(-60.1034843664906, -97.09256677227802, -56.29816074018606)
(-60.10027893597644, -97.13858876571155, -56.82740384485123)
(-60.097073505462276, -97.18461075914507, -57.3566469495164)
(-60.09386807494811, -97.2306327525786, -57.885890054181544)
(-60.09066264443395, -97.27665474601213, -58.415133158846714)
(-60.08745721391979, -97.32267673944565, -58.944376263511884)
(-60.08425178340563, -97.36869873287918, -59.473619368177054)
(-60.08104635289146, -97.41472072631271, -60.002862472842224)
(-60.077840922377305, -97.46074271974624, -60.532105577507394)
(-60.07463549186314, -97.50676471317976, -61.061348682172564)
(-60.07143006134898, -97.55278670661329, -61.590591786837706)
(-60.06822463083481, -97.59880870004682, -62.119834891502876)
(-60.065019200320656, -97.64483069348034, -62.649077996168046)
(-60.06181376980649, -97.69085268691387, -63.178321100833216)
(-60.05860833929233, -97.7368746803474, -63.707564205498386)
(-60.05540290877816, -97.78289667378093, -64.23680731016356)
(-60.052197478264006, -97.82891866721445, -64.7660504148287)
(-60.04899204774984, -97.87494066064798, -65.29529351949387)
(-60.04578661723568, -97.9209626540815, -65.82453662415904)
(-60.04258118672152, -97.96698464751503, -66.35377972882421)
(-60.039375756207356, -98.01300664094856, -66.88302283348938)
(-60.03617032569319, -98.05902863438209, -67.41226593815455)
(-60.03296489517903, -98.10505062781561, -67.94150904281969)
(-60.02975946466487, -98.15107262124914, -68.47075214748486)
(-60.026554034150706, -98.19709461468267, -68.99999525215003)
(-60.02334860363654, -98.2431166081162, -69.5292383568152)
(-60.02014317312238, -98.28913860154972, -70.05848146148037)
(-60.01693774260822, -98.33516059498325, -70.58772456614554)
(-60.01373231209406, -98.38118258841678, -71.11696767081071)
(-60.01052688157989, -98.4272045818503, -71.64621077547585)
(-60.00732145106573, -98.47322657528383, -72.17545388014102)
(-60.00411602055157, -98.51924856871736, -72.70469698480619)
(-60.00091059003741, -98.56527056215089, -73.23394008947136)
(-59.99770515952324, -98.61129255558441, -73.76318319413653)
(-59.994499729009085, -98.65731454901794, -74.2924262988017)
(-59.99129429849492, -98.70333654245147, -74.82166940346684)
(-59.98808886798076, -98.749358535885, -75.35091250813201)
(-59.98488343746659, -98.79538052931852, -75.88015561279718)

Last, loop the third index:

fixed_image = sitk.ReadImage(names)
shape = fixed_image.GetSize()
for i in range(shape[2]):
    pos = fixed_image.TransformIndexToPhysicalPoint((0, 0, i))
    print(pos)

and the information is:

(-61.007415771484375, -84.11436462402344, 92.94839477539062)
(-61.537387898868026, -84.11887861966818, 92.94557745809786)
(-62.06736002625167, -84.12339261531292, 92.94276014080509)
(-62.59733215363532, -84.12790661095767, 92.93994282351233)
(-63.12730428101897, -84.13242060660241, 92.93712550621956)
(-63.657276408402616, -84.13693460224714, 92.9343081889268)
(-64.18724853578627, -84.14144859789188, 92.93149087163404)
(-64.71722066316991, -84.14596259353662, 92.92867355434127)
(-65.24719279055357, -84.15047658918137, 92.9258562370485)
(-65.77716491793721, -84.15499058482611, 92.92303891975574)
(-66.30713704532086, -84.15950458047085, 92.92022160246297)
(-66.83710917270452, -84.1640185761156, 92.9174042851702)
(-67.36708130008816, -84.16853257176034, 92.91458696787744)
(-67.8970534274718, -84.17304656740507, 92.91176965058467)
(-68.42702555485546, -84.17756056304981, 92.90895233329192)
(-68.9569976822391, -84.18207455869455, 92.90613501599915)
(-69.48696980962275, -84.1865885543393, 92.90331769870639)
(-70.01694193700641, -84.19110254998404, 92.90050038141362)
(-70.54691406439005, -84.19561654562878, 92.89768306412086)
(-71.0768861917737, -84.20013054127352, 92.89486574682809)
(-71.60685831915734, -84.20464453691827, 92.89204842953532)
(-72.136830446541, -84.209158532563, 92.88923111224256)
(-72.66680257392464, -84.21367252820774, 92.88641379494979)
(-73.1967747013083, -84.21818652385248, 92.88359647765704)
(-73.72674682869194, -84.22270051949722, 92.88077916036427)
(-74.25671895607559, -84.22721451514197, 92.8779618430715)
(-74.78669108345923, -84.23172851078671, 92.87514452577874)
(-75.31666321084289, -84.23624250643145, 92.87232720848597)
(-75.84663533822653, -84.2407565020762, 92.8695098911932)
(-76.37660746561019, -84.24527049772092, 92.86669257390044)
(-76.90657959299384, -84.24978449336567, 92.86387525660767)
(-77.43655172037748, -84.25429848901041, 92.8610579393149)
(-77.96652384776112, -84.25881248465515, 92.85824062202214)
(-78.49649597514478, -84.2633264802999, 92.85542330472938)
(-79.02646810252843, -84.26784047594464, 92.85260598743662)
(-79.55644022991208, -84.27235447158938, 92.84978867014385)
(-80.08641235729573, -84.27686846723412, 92.84697135285109)
(-80.61638448467937, -84.28138246287885, 92.84415403555832)
(-81.14635661206302, -84.2858964585236, 92.84133671826555)
(-81.67632873944667, -84.29041045416834, 92.83851940097279)
(-82.20630086683032, -84.29492444981308, 92.83570208368002)
(-82.73627299421398, -84.29943844545782, 92.83288476638725)
(-83.26624512159762, -84.30395244110257, 92.8300674490945)
(-83.79621724898126, -84.30846643674731, 92.82725013180173)
(-84.32618937636491, -84.31298043239205, 92.82443281450897)
(-84.85616150374857, -84.31749442803678, 92.8216154972162)
(-85.38613363113221, -84.32200842368152, 92.81879817992343)
(-85.91610575851587, -84.32652241932627, 92.81598086263067)
(-86.44607788589951, -84.33103641497101, 92.8131635453379)
(-86.97605001328316, -84.33555041061575, 92.81034622804513)
(-87.5060221406668, -84.3400644062605, 92.80752891075237)
(-88.03599426805046, -84.34457840190524, 92.80471159345961)
(-88.5659663954341, -84.34909239754998, 92.80189427616685)
(-89.09593852281776, -84.35360639319471, 92.79907695887408)
(-89.6259106502014, -84.35812038883945, 92.79625964158132)
(-90.15588277758505, -84.3626343844842, 92.79344232428855)
(-90.68585490496869, -84.36714838012894, 92.79062500699578)
(-91.21582703235235, -84.37166237577368, 92.78780768970302)
(-91.745799159736, -84.37617637141842, 92.78499037241025)
(-92.27577128711964, -84.38069036706317, 92.78217305511748)
(-92.8057434145033, -84.38520436270791, 92.77935573782473)
(-93.33571554188694, -84.38971835835264, 92.77653842053196)
(-93.86568766927059, -84.39423235399738, 92.7737211032392)
(-94.39565979665423, -84.39874634964212, 92.77090378594643)
(-94.92563192403789, -84.40326034528687, 92.76808646865366)
(-95.45560405142155, -84.40777434093161, 92.7652691513609)
(-95.98557617880519, -84.41228833657635, 92.76245183406813)
(-96.51554830618883, -84.4168023322211, 92.75963451677536)
(-97.04552043357248, -84.42131632786584, 92.7568171994826)
(-97.57549256095612, -84.42583032351057, 92.75399988218985)
(-98.10546468833978, -84.43034431915531, 92.75118256489708)
(-98.63543681572344, -84.43485831480005, 92.74836524760431)
(-99.16540894310708, -84.4393723104448, 92.74554793031155)
(-99.69538107049073, -84.44388630608954, 92.74273061301878)
(-100.22535319787437, -84.44840030173428, 92.73991329572601)
(-100.75532532525801, -84.45291429737902, 92.73709597843325)
(-101.28529745264167, -84.45742829302377, 92.73427866114048)
(-101.81526958002533, -84.4619422886685, 92.73146134384771)
(-102.34524170740897, -84.46645628431324, 92.72864402655495)
(-102.87521383479262, -84.47097027995798, 92.7258267092622)
(-103.40518596217626, -84.47548427560272, 92.72300939196943)
(-103.9351580895599, -84.47999827124747, 92.72019207467666)
(-104.46513021694356, -84.48451226689221, 92.7173747573839)
(-104.99510234432721, -84.48902626253695, 92.71455744009113)
(-105.52507447171087, -84.4935402581817, 92.71174012279836)
(-106.05504659909451, -84.49805425382644, 92.7089228055056)
(-106.58501872647815, -84.50256824947117, 92.70610548821283)
(-107.1149908538618, -84.50708224511591, 92.70328817092006)
(-107.64496298124546, -84.51159624076065, 92.70047085362731)
(-108.1749351086291, -84.5161102364054, 92.69765353633454)
(-108.70490723601276, -84.52062423205014, 92.69483621904178)
(-109.2348793633964, -84.52513822769488, 92.69201890174901)
(-109.76485149078005, -84.52965222333962, 92.68920158445624)
(-110.29482361816369, -84.53416621898437, 92.68638426716348)
(-110.82479574554735, -84.5386802146291, 92.68356694987071)
(-111.35476787293099, -84.54319421027384, 92.68074963257794)
(-111.88474000031465, -84.54770820591858, 92.67793231528518)
(-112.4147121276983, -84.55222220156332, 92.67511499799242)
(-112.94468425508194, -84.55673619720807, 92.67229768069966)
(-113.47465638246558, -84.56125019285281, 92.66948036340689)
(-114.00462850984924, -84.56576418849755, 92.66666304611412)
(-114.53460063723288, -84.5702781841423, 92.66384572882136)
(-115.06457276461654, -84.57479217978702, 92.66102841152859)
(-115.59454489200019, -84.57930617543177, 92.65821109423582)
(-116.12451701938383, -84.58382017107651, 92.65539377694306)
(-116.65448914676747, -84.58833416672125, 92.65257645965029)
(-117.18446127415113, -84.592848162366, 92.64975914235754)
(-117.71443340153478, -84.59736215801074, 92.64694182506477)
(-118.24440552891843, -84.60187615365548, 92.644124507772)
(-118.77437765630208, -84.60639014930022, 92.64130719047924)
(-119.30434978368572, -84.61090414494495, 92.63848987318647)
(-119.83432191106937, -84.6154181405897, 92.6356725558937)
(-120.36429403845302, -84.61993213623444, 92.63285523860094)
(-120.89426616583667, -84.62444613187918, 92.63003792130817)
(-121.42423829322033, -84.62896012752392, 92.6272206040154)
(-121.95421042060397, -84.63347412316867, 92.62440328672265)
(-122.48418254798761, -84.63798811881341, 92.62158596942989)
(-123.01415467537126, -84.64250211445815, 92.61876865213712)
(-123.5441268027549, -84.64701611010288, 92.61595133484435)
(-124.07409893013856, -84.65153010574763, 92.61313401755159)
(-124.60407105752222, -84.65604410139237, 92.61031670025882)
(-125.13404318490586, -84.66055809703711, 92.60749938296605)
(-125.66401531228951, -84.66507209268185, 92.60468206567329)
(-126.19398743967315, -84.6695860883266, 92.60186474838052)
(-126.72395956705681, -84.67410008397134, 92.59904743108775)
(-127.25393169444045, -84.67861407961608, 92.596230113795)
(-127.7839038218241, -84.68312807526081, 92.59341279650224)
(-128.31387594920776, -84.68764207090555, 92.59059547920947)
(-128.8438480765914, -84.6921560665503, 92.5877781619167)
(-129.37382020397504, -84.69667006219504, 92.58496084462394)
(-129.90379233135872, -84.70118405783978, 92.58214352733117)
(-130.43376445874236, -84.70569805348453, 92.5793262100384)
(-130.963736586126, -84.71021204912927, 92.57650889274564)
(-131.49370871350965, -84.71472604477401, 92.57369157545287)
(-132.0236808408933, -84.71924004041874, 92.57087425816012)
(-132.55365296827694, -84.72375403606348, 92.56805694086735)
(-133.08362509566058, -84.72826803170823, 92.56523962357458)
(-133.61359722304422, -84.73278202735297, 92.56242230628182)
(-134.14356935042787, -84.73729602299771, 92.55960498898905)
(-134.67354147781154, -84.74181001864245, 92.55678767169628)
(-135.20351360519518, -84.7463240142872, 92.55397035440352)
(-135.73348573257883, -84.75083800993194, 92.55115303711075)
(-136.2634578599625, -84.75535200557667, 92.54833571981798)
(-136.79342998734614, -84.75986600122141, 92.54551840252523)
(-137.3234021147298, -84.76437999686615, 92.54270108523247)
(-137.85337424211343, -84.7688939925109, 92.5398837679397)
(-138.38334636949708, -84.77340798815564, 92.53706645064693)
(-138.91331849688072, -84.77792198380038, 92.53424913335417)
(-139.44329062426436, -84.78243597944513, 92.5314318160614)
(-139.973262751648, -84.78694997508987, 92.52861449876863)
(-140.50323487903165, -84.7914639707346, 92.52579718147587)
(-141.03320700641532, -84.79597796637934, 92.5229798641831)
(-141.56317913379897, -84.80049196202408, 92.52016254689035)
(-142.0931512611826, -84.80500595766883, 92.51734522959758)
(-142.62312338856628, -84.80951995331357, 92.51452791230481)
(-143.15309551594993, -84.81403394895831, 92.51171059501205)
(-143.68306764333357, -84.81854794460305, 92.50889327771928)
(-144.21303977071722, -84.8230619402478, 92.50607596042651)
(-144.74301189810086, -84.82757593589253, 92.50325864313375)
(-145.2729840254845, -84.83208993153727, 92.50044132584098)
(-145.80295615286815, -84.83660392718201, 92.49762400854821)
(-146.3329282802518, -84.84111792282675, 92.49480669125546)
(-146.86290040763544, -84.8456319184715, 92.4919893739627)
(-147.39287253501908, -84.85014591411624, 92.48917205666993)
(-147.92284466240275, -84.85465990976098, 92.48635473937716)
(-148.4528167897864, -84.85917390540573, 92.4835374220844)
(-148.98278891717004, -84.86368790105047, 92.48072010479163)
(-149.5127610445537, -84.8682018966952, 92.47790278749886)
(-150.04273317193736, -84.87271589233994, 92.4750854702061)
(-150.572705299321, -84.87722988798468, 92.47226815291333)
(-151.10267742670464, -84.88174388362943, 92.46945083562056)
(-151.6326495540883, -84.88625787927417, 92.46663351832781)
(-152.16262168147193, -84.89077187491891, 92.46381620103504)
(-152.69259380885558, -84.89528587056365, 92.46099888374228)
(-153.22256593623922, -84.8997998662084, 92.45818156644951)
(-153.75253806362286, -84.90431386185313, 92.45536424915674)
(-154.28251019100654, -84.90882785749787, 92.45254693186398)
(-154.81248231839018, -84.91334185314261, 92.44972961457121)
(-155.34245444577383, -84.91785584878735, 92.44691229727844)
(-155.8724265731575, -84.9223698444321, 92.44409497998568)
(-156.40239870054114, -84.92688384007684, 92.44127766269293)
(-156.93237082792479, -84.93139783572158, 92.43846034540016)
(-157.46234295530843, -84.93591183136633, 92.43564302810739)
(-157.99231508269207, -84.94042582701105, 92.43282571081463)
(-158.52228721007572, -84.9449398226558, 92.43000839352186)
(-159.05225933745936, -84.94945381830054, 92.4271910762291)
(-159.582231464843, -84.95396781394528, 92.42437375893633)
(-160.11220359222665, -84.95848180959003, 92.42155644164356)
(-160.64217571961032, -84.96299580523477, 92.4187391243508)
(-161.17214784699397, -84.96750980087951, 92.41592180705804)
(-161.7021199743776, -84.97202379652425, 92.41310448976527)
(-162.23209210176128, -84.97653779216898, 92.41028717247251)
(-162.76206422914493, -84.98105178781373, 92.40746985517974)
(-163.29203635652857, -84.98556578345847, 92.40465253788697)
(-163.8220084839122, -84.99007977910321, 92.40183522059421)
(-164.35198061129586, -84.99459377474795, 92.39901790330144)
(-164.8819527386795, -84.9991077703927, 92.39620058600867)
(-165.41192486606315, -85.00362176603744, 92.39338326871591)
(-165.9418969934468, -85.00813576168218, 92.39056595142316)
(-166.47186912083043, -85.01264975732691, 92.38774863413039)
(-167.0018412482141, -85.01716375297165, 92.38493131683762)
(-167.53181337559775, -85.0216777486164, 92.38211399954486)
(-168.0617855029814, -85.02619174426114, 92.37929668225209)
(-168.59175763036507, -85.03070573990588, 92.37647936495932)
(-169.1217297577487, -85.03521973555063, 92.37366204766656)
(-169.65170188513235, -85.03973373119537, 92.37084473037379)
(-170.181674012516, -85.04424772684011, 92.36802741308102)
(-170.71164613989964, -85.04876172248484, 92.36521009578827)
(-171.2416182672833, -85.05327571812958, 92.3623927784955)
(-171.77159039466693, -85.05778971377433, 92.35957546120274)
(-172.30156252205057, -85.06230370941907, 92.35675814390997)
(-172.83153464943422, -85.06681770506381, 92.3539408266172)
(-173.3615067768179, -85.07133170070855, 92.35112350932444)
(-173.89147890420153, -85.0758456963533, 92.34830619203167)
(-174.42145103158518, -85.08035969199804, 92.3454888747389)
(-174.95142315896885, -85.08487368764277, 92.34267155744614)
(-175.4813952863525, -85.08938768328751, 92.33985424015339)
(-176.01136741373614, -85.09390167893226, 92.33703692286062)
(-176.54133954111978, -85.098415674577, 92.33421960556785)
(-177.07131166850343, -85.10292967022174, 92.33140228827509)
(-177.60128379588707, -85.10744366586648, 92.32858497098232)
(-178.13125592327071, -85.11195766151123, 92.32576765368955)
(-178.66122805065436, -85.11647165715597, 92.32295033639679)
(-179.191200178038, -85.1209856528007, 92.32013301910402)
(-179.72117230542167, -85.12549964844544, 92.31731570181125)
(-180.25114443280532, -85.13001364409018, 92.31449838451849)
(-180.78111656018896, -85.13452763973493, 92.31168106722573)
(-181.3110886875726, -85.13904163537967, 92.30886374993297)
(-181.84106081495628, -85.14355563102441, 92.3060464326402)
(-182.37103294233992, -85.14806962666916, 92.30322911534743)
(-182.90100506972357, -85.1525836223139, 92.30041179805467)
(-183.4309771971072, -85.15709761795863, 92.2975944807619)
(-183.96094932449085, -85.16161161360337, 92.29477716346913)
(-184.4909214518745, -85.16612560924811, 92.29195984617637)
(-185.02089357925814, -85.17063960489286, 92.2891425288836)
(-185.5508657066418, -85.1751536005376, 92.28632521159085)
(-186.08083783402543, -85.17966759618234, 92.28350789429808)
(-186.6108099614091, -85.18418159182708, 92.28069057700532)
(-187.14078208879275, -85.18869558747183, 92.27787325971255)
(-187.6707542161764, -85.19320958311656, 92.27505594241978)

From all the printed position, I can not find the position which is the same with RadiAnt (-8.54, -83.67, 93.23).

However, if I just read one single

fixed_image = sitk.ReadImage(names[99])
pos = fixed_image.TransformIndexToPhysicalPoint((0, 0, 0))
print(pos)

and the result is:

(-8.5400607857625, -83.667478002813, 93.227306561284)

It really make me confuzed.

OK. Now I’m pretty sure I know what is the issue. I am 99% sure that your volume’s direction cosine matrix is not the identity (this is the direction of the axes along which the coordinates are given). Please print the cosine matrix fixed_image.GetDirection(). The matrix is given in row major order. If it is indeed not the identity then you are ok, there is no problem with reading the data in SimpleITK.

Yes, the direction is not the identity matrix. You mean that the SimpleITK would rotate the volume so that the direction change to be X (1, 0, 0), Y(0, 1, 0), Z(0, 0, 1)? But I have show the fixed_image = sitk.ReadImage(names[99]), and it is the same with the single image:

sitkImage = sitk.ReadImage(names[99])
Single99 = sitk.GetArrayFromImage(sitkImage)
sitkImage = sitk.ReadImage(names)
Volume99 = sitk.GetArrayFromImage(sitkImage[:, :, 99])
diff = Volume99 - Single99
print('the maximum difference: ',diff.max(), ' || the minimum difference: ', diff.min())

And printed information is:

the maximum difference:  0  || the minimum difference:  0

Since the image is the same, why the position is not the same?

More important, if I have the volume, how can I get the position that is the same as that from single dicom?

Hello @zhang-qiang-github,

Please familiarize yourself with the concept of an image as a spatial object, a fundamental principal of SimpleITK (Slide 7 in this ppt presentation should clarify things).

In SimpleITK an image is not an array of pixels, it exists somewhere in physical space. The subtraction of the intensity values you are performing treats the images as arrays and not as a physical object in 3D space.

If I have a volume:

sitkImage = sitk.ReadImage(names)

How can I obtain the position of 99-th image?

sitkImage.TransforIndexToPhysicalPoint((0, 0, 99))

The above code can not obtian the position of 99-th image.
That’s the problem I am faced.

sitkImage = sitk.ReadImage(names[99])
Single99 = sitk.GetArrayFromImage(sitkImage)
print('position of single dicom: ', sitkImage.TransformIndexToPhysicalPoint((0, 0, 0)))
sitkImage = sitk.ReadImage(names)
Volume99 = sitk.GetArrayFromImage(sitkImage[:, :, 99])
print('position of 99-th image from volume: ', sitkImage.TransformIndexToPhysicalPoint((0, 0, 99)))

The above code just is used to show that sitkImage.TransformIndexToPhysicalPoint((0, 0, 99)) can not return the correct position. Thus, how can I get the correct result?

Have you checked to see if you have uniforms spacing between your slices?

Yes, the spacing is almost the same.

pos = sitk.ReadImage(names[0]).TransformIndexToPhysicalPoint((0, 0, 0))
for i in range(1, len(names)):
    curPos = sitk.ReadImage(names[i]).TransformIndexToPhysicalPoint((0, 0, 0))
    spacing = np.linalg.norm(np.array(curPos) - np.array(pos))
    pos = curPos
    print(i, spacing)

The results is:

1 0.5299999872837455
2 0.5299999872847541
3 0.5299999872837454
4 0.5299999872847486
5 0.5299999872847402
6 0.529999987283754
7 0.5299999872847525
8 0.529999987283747
9 0.5299999872847474
10 0.5299999872847485
11 0.529999987283751
12 0.5299999872847486
13 0.5299999872837454
14 0.5299999872847486
15 0.5299999872847526
16 0.5299999872837469
17 0.5299999872847473
18 0.529999987283754
19 0.5299999872847402
20 0.529999987284754
21 0.5299999872837455
22 0.5299999872847557
23 0.5299999872837383
24 0.5299999872847612
25 0.5299999872847401
26 0.529999987283754
27 0.5299999872847402
28 0.5299999872837593
29 0.5299999872847403
30 0.5299999872837454
31 0.5299999872847486
32 0.5299999872847526
33 0.5299999872837469
34 0.5299999872847472
35 0.529999987283754
36 0.5299999872847402
37 0.529999987284754
38 0.5299999872837455
39 0.5299999872847557
40 0.5299999872837384
41 0.5299999872847612
42 0.5299999872847401
43 0.529999987283754
44 0.5299999872847401
45 0.5299999872837593
46 0.5299999872847401
47 0.5299999872847557
48 0.5299999872837385
49 0.5299999872847557
50 0.5299999872837509
51 0.5299999872847487
52 0.5299999872847401
53 0.529999987283754
54 0.5299999872847455
55 0.529999987283754
56 0.5299999872847436
57 0.5299999872847523
58 0.5299999872837472
59 0.5299999872847521
60 0.5299999872837456
61 0.5299999872847486
62 0.5299999872837506
63 0.5299999872847437
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74 0.5299999872847522
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84 0.5299999872847576
85 0.529999987283742
86 0.5299999872847521
87 0.529999987283742
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89 0.5299999872847436
90 0.5299999872837522
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92 0.5299999872837574
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100 0.529999987284344
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102 0.5299999872842429
103 0.5299999872843517
104 0.5299999872843433
105 0.5299999872843569
106 0.5299999872843443
107 0.5299999872843517
108 0.5299999872843426
109 0.5299999872843517
110 0.5299999872843485
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112 0.5299999872843434
113 0.5299999872843517
114 0.5299999872843486
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117 0.5299999872843517
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120 0.5299999872843435
121 0.5299999872843517
122 0.5299999872843485
123 0.5299999872843513
124 0.5299999872843434
125 0.5299999872843516
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140 0.5299999872847576
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145 0.5299999872847436
146 0.5299999872837523
147 0.5299999872847436
148 0.5299999872847541
149 0.5299999872837454
150 0.5299999872847522
151 0.529999987283742
152 0.5299999872847575
153 0.5299999872847437
154 0.5299999872837504
155 0.5299999872847437
156 0.5299999872837504
157 0.529999987284749
158 0.5299999872847523
159 0.5299999872837418
160 0.5299999872847437
161 0.5299999872837593
162 0.5299999872847401
163 0.529999987283754
164 0.5299999872847436
165 0.5299999872847541
166 0.5299999872837454
167 0.5299999872847523
168 0.529999987283742
169 0.5299999872847521
170 0.5299999872847492
171 0.5299999872837504
172 0.5299999872847436
173 0.5299999872837504
174 0.5299999872847491
175 0.5299999872847522
176 0.5299999872837418
177 0.5299999872847558
178 0.5299999872837438
179 0.5299999872847557
180 0.5299999872847402
181 0.5299999872837539
182 0.5299999872847456
183 0.529999987283754
184 0.5299999872847401
185 0.5299999872847557
186 0.5299999872837384
187 0.529999987284761
188 0.5299999872837454
189 0.5299999872847487
190 0.5299999872847402
191 0.5299999872837593
192 0.5299999872847474
193 0.5299999872837383
194 0.5299999872847557
195 0.5299999872837436
196 0.5299999872847557
197 0.5299999872847402
198 0.529999987283754
199 0.5299999872847402
200 0.5299999872837593
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202 0.5299999872847557
203 0.5299999872837454
204 0.5299999872847541
205 0.5299999872837454
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209 0.5299999872847474
210 0.529999987283747
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212 0.529999987284754
213 0.5299999872837454
214 0.5299999872847486
215 0.5299999872837454
216 0.5299999872847486
217 0.5299999872847527
218 0.5299999872837468
219 0.5299999872847474
220 0.5299999872837541
221 0.5299999872847454
222 0.5299999872847487
223 0.5299999872837454
224 0.5299999872847474
225 0.5299999872837522
226 0.5299999872847474
227 0.5299999872837469
228 0.5299999872847472
229 0.5299999872847487
230 0.5299999872837506
231 0.5299999872847486
232 0.5299999872837454
233 0.5299999872847486
234 0.5299999872847527
235 0.5299999872837468
236 0.5299999872847474
237 0.529999987283754
238 0.5299999872847455
239 0.5299999872847486