20:28:12 daniel@sbia-pc66:~/SLICER/TRUNK/Slicer3/Modules/AtlasCreator$ python atlascreator.py -i /Users/daniel/Desktop/ATLASCREATORTEST/originals/ -s /Users/daniel/Desktop/ATLASCREATORTEST/segmentations -o /Users/daniel/Desktop/ATLASCREATORTEST/ --dynamic --meanIterations 2 -w -l "3 4 5 6 7 8 9 10 31 32" --debug --keepAligned AtlasCreator for 3D Slicer Version v0.21 Found 3D Slicer3 launcher at /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 Warning: The output directory (/Users/daniel/Desktop/ATLASCREATORTEST) already exists.. Warning: Using new output directory instead: /Users/daniel/Desktop/ATLASCREATORTEST6 Debug Mode is enabled! Adding module path: /Users/daniel/Downloads/Dumb/lib/Slicer3/Plugins:/Users/daniel/Slicer3daniel/16106/CMTK4Slicer Starting Slicer: /Users/daniel/SLICER/TRUNK/Slicer3-build [AtlasCreator 20:29:25] -------------------------------------------------------------------------------- [AtlasCreator 20:29:25] Starting Atlas Creator Normal Mode [AtlasCreator 20:29:25] Configuration for Atlas Creator: Original Images: ['/Users/daniel/Desktop/ATLASCREATORTEST/originals/case10.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/originals/case12.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/originals/case2.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/originals/case3.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/originals/case5.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/originals/case8.nrrd'] Segmentations: ['/Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case10.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case12.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case2.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case3.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case5.nrrd', '/Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case8.nrrd'] Output Directory: /Users/daniel/Desktop/ATLASCREATORTEST6/ Template Type: dynamic Dynamic Template Iterations: 2 Fixed Template Default Case: Labels: [32, 3, 4, 5, 6, 7, 8, 9, 10, 31] Toolkit: BRAINSFit Registration Type: Affine Save Transforms: 1 Delete Aligned Images: 0 Delete Aligned Segmentations: 0 Normalize Atlases: 0 Output Cast: Short [AtlasCreator 20:29:25] Entering Registration Stage.. [AtlasCreator 20:29:25] Found 3D Slicer launcher at /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 [AtlasCreator 20:29:25] DEBUG: The launchCommandPrefix is /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/ [AtlasCreator 20:29:25] Dynamic registration with 2 iterations [AtlasCreator 20:29:25] Starting iteration 1... Background level guess : first place: 4 (11.4145%) second place: 5 (11.2047%) Guessed background level: 4 [AtlasCreator 20:29:38] DEBUG: Guessing background value: 4.0 Background level guess : first place: 4 (3.15972%) second place: 4 (2.98913%) Guessed background level: 4.5 [AtlasCreator 20:29:40] DEBUG: Guessing background value for template: 4.5 [AtlasCreator 20:29:40] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --movingVolume /Users/daniel/Desktop/ATLASCREATORTEST/originals/case10.nrrd --outputTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case10.mat --outputVolume /Users/daniel/Slicer3daniel/UFWnA_AtlasCreator/case10.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 4.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 435 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 300 LowHigh Thresholds: [0,62.3594,300] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 298 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 203 LowHigh Thresholds: [0,49.0104,203] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x102beb3b0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4059 Debug: Off Observers: none Matrix: 1 -1.38588e-17 -7.26307e-19 1.38778e-17 0.99863 0.052336 0 -0.052336 0.99863 Offset: [0.491295, 1.49026, -4.90864] Center: [-3.03604, -0.200909, 1.57021] Translation: [0.491295, 1.57271, -4.90028] Inverse: 1 1.38778e-17 0 -1.38588e-17 0.99863 -0.052336 -7.26307e-19 0.052336 0.99863 Singular: 0 Versor: [ -0.0261769, -1.81639e-19, 6.93652e-18, 0.999657 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. 0 -0.543889 [-0.0253332, -0.00254098, -0.000119945, 0.678237, 1.57813, -4.82961] 1 -0.538982 [-0.023003, 0.00110964, -0.00253016, 0.637522, 1.59886, -4.74121] 2 -0.543429 [-0.0207943, 0.00297823, -0.0063497, 0.589043, 1.61508, -4.6558] 3 -0.546977 [-0.0194297, 0.00331771, -0.00693037, 0.543512, 1.62954, -4.568] 4 -0.548546 [-0.0174829, 0.00249662, -0.00802534, 0.495187, 1.64544, -4.48204] 5 -0.550533 [-0.0158183, 0.00157182, -0.00986785, 0.441254, 1.66173, -4.39959] 6 -0.552834 [-0.0153953, 0.000941927, -0.0104028, 0.404327, 1.66873, -4.30694] 7 -0.554051 [-0.0149695, 0.000616634, -0.010363, 0.362011, 1.67339, -4.21646] 8 -0.555028 [-0.0143218, 4.89541e-05, -0.0103151, 0.328478, 1.67933, -4.12245] 9 -0.555885 [-0.0142687, 0.000412367, -0.0106833, 0.295322, 1.68383, -4.02822] 10 -0.556962 [-0.0139225, 0.000275476, -0.0105832, 0.27236, 1.68317, -3.9309] 11 -0.557893 [-0.0137787, 0.000568942, -0.0103446, 0.242464, 1.67952, -3.83555] 12 -0.558747 [-0.0142211, 8.89263e-05, -0.0100249, 0.216669, 1.67045, -3.73937] 13 -0.559497 [-0.0142015, -0.000277997, -0.010192, 0.181354, 1.66593, -3.64593] 14 -0.560333 [-0.0142916, -0.000729592, -0.0100022, 0.152259, 1.65718, -3.55066] 15 -0.561268 [-0.0140698, -0.00108632, -0.00973019, 0.12173, 1.64519, -3.4562] 16 -0.562196 [-0.0134376, -0.00140369, -0.00936534, 0.093869, 1.62854, -3.36162] 17 -0.563175 [-0.0127553, -0.00149283, -0.0089199, 0.076179, 1.61424, -3.26426] 18 -0.564219 [-0.0129756, -0.00152741, -0.00792494, 0.063303, 1.58366, -3.16995] 19 -0.564804 [-0.0131626, -0.000281426, -0.00751796, 0.0257551, 1.55844, -3.0808] 20 -0.565622 [-0.0123888, 0.000332539, -0.00682084, 0.000849964, 1.52957, -2.98838] 21 -0.566132 [-0.0114634, -0.00031045, -0.00754178, -0.00873162, 1.50272, -2.89257] 22 -0.567095 [-0.0109044, -0.000780904, -0.00629402, -0.0216681, 1.47201, -2.79833] 23 -0.567522 [-0.0111544, -0.00127458, -0.00702937, -0.0285799, 1.44805, -2.70151] 24 -0.567994 [-0.0107398, -0.0011661, -0.00693208, -0.037093, 1.41109, -2.60899] 25 -0.568867 [-0.00969739, -0.00157727, -0.00638038, -0.0487414, 1.37991, -2.51472] 26 -0.5702 [-0.00873326, -0.00237867, -0.00696266, -0.0630882, 1.34592, -2.42182] 27 -0.571866 [-0.00789198, -0.00250626, -0.00763822, -0.0787828, 1.31696, -2.32742] 28 -0.573692 [-0.0075472, -0.00211664, -0.00724518, -0.107947, 1.28294, -2.23803] 29 -0.575161 [-0.00773482, -0.00276869, -0.0074744, -0.119591, 1.25163, -2.14379] 30 -0.576185 [-0.00690562, -0.00183366, -0.00724948, -0.142926, 1.23124, -2.04874] 31 -0.577721 [-0.00649928, -0.00168976, -0.00660432, -0.150065, 1.19975, -1.95411] 32 -0.578875 [-0.00592494, -0.000770244, -0.00619271, -0.161446, 1.16465, -1.8612] 33 -0.579465 [-0.00635264, -0.000926126, -0.00610421, -0.159383, 1.12287, -1.77037] 34 -0.58055 [-0.00513434, -0.000668282, -0.00617195, -0.165602, 1.08872, -1.67662] 35 -0.581763 [-0.00576983, -0.00104941, -0.0055039, -0.166532, 1.03876, -1.59003] 36 -0.583621 [-0.00444365, -0.00163951, -0.00579288, -0.182026, 0.992771, -1.50264] 37 -0.584751 [-0.00360972, -0.00216424, -0.0055866, -0.193481, 0.949952, -1.41302] 38 -0.586464 [-0.00449462, -0.00217023, -0.00569839, -0.203916, 0.902046, -1.32589] 39 -0.587604 [-0.00277539, -0.00222783, -0.00470495, -0.198095, 0.85869, -1.23605] 40 -0.590941 [-0.00421947, -0.00334328, -0.00596565, -0.208851, 0.813298, -1.14771] 41 -0.589682 [-0.00300833, 0.000245167, -0.00289533, -0.205574, 0.770012, -1.05815] 42 -0.594866 [-0.00176585, -0.00294287, -0.00343244, -0.174062, 0.726161, -0.97427] 43 -0.598276 [-0.00238529, -0.000180055, -0.00331014, -0.19449, 0.673995, -0.89163] 44 -0.597364 [0.00135175, -0.00409305, -0.00269566, -0.16069, 0.6263, -0.81123] 45 -0.599623 [-0.000253676, 0.00157917, -0.0040443, -0.205975, 0.563446, -0.749163] 46 -0.595951 [1.99949e-05, -0.00758976, -0.00414636, -0.151961, 0.481324, -0.750456] 47 -0.588182 [-0.000733385, 0.00297771, -0.00411904, -0.208098, 0.417453, -0.702288] 48 -0.5945 [-0.00143968, -0.00297272, -0.00250065, -0.136232, 0.367027, -0.656046] 49 -0.602693 [-0.00236678, 0.00374617, -8.58564e-05, -0.158877, 0.29316, -0.594211] 50 -0.594327 [-0.00115142, -0.00213216, -0.000413184, -0.0847401, 0.250509, -0.543811] 51 -0.605619 [-0.00229432, 0.00577011, -0.000221932, -0.0934781, 0.19056, -0.465871] 52 -0.588487 [0.000388215, -0.00387686, -0.000810173, -0.00349078, 0.162294, -0.439396] 53 -0.597814 [-0.000271071, 0.00117362, -0.0002486, -0.0386498, 0.140098, -0.413587] 54 -0.609021 [-0.00084301, -0.000417909, -0.000185736, -0.0141733, 0.125442, -0.372665] 55 -0.607571 [-0.00113895, 0.000353355, -0.000193047, -0.0141805, 0.115188, -0.323755] 56 -0.60805 [-0.000902645, -0.000113206, -0.00023893, -0.00446664, 0.106677, -0.275464] 57 -0.607514 [-0.000215435, 0.000349156, -0.000175209, -0.00458644, 0.0992934, -0.22604] 58 -0.608917 [-0.000324757, -0.000417226, -0.000124561, 0.00289899, 0.0876731, -0.178013] 59 -0.60687 [-0.000196501, 0.00151654, -5.91115e-05, -0.0090725, 0.0768651, -0.130845] 60 -0.605197 [-0.000139099, -0.00369194, -0.000116475, 0.0270788, 0.0667183, -0.0995151] 61 -0.593346 [-0.000132211, -0.000512449, 3.38668e-05, 0.00366562, 0.0631318, -0.0946744] 62 -0.603608 [-0.000163771, 0.00145919, -1.86757e-05, -0.0101798, 0.0573622, -0.075067] 63 -0.603383 [-0.000106235, -0.000138729, -6.47874e-05, 0.000631355, 0.0554798, -0.0700084] 64 -0.60116 [-7.88027e-05, 0.000471925, -6.99195e-06, -0.00382279, 0.0515482, -0.0590793] 65 -0.601795 [-4.1941e-05, -0.00057467, -6.75465e-05, 0.00308816, 0.0475742, -0.0496828] 66 -0.60101 [-5.7815e-05, 0.00014149, -3.03305e-05, -0.00213621, 0.0463809, -0.0468041] 67 -0.599741 [-3.69482e-05, 2.52357e-05, -1.75328e-05, -0.00154844, 0.0437379, -0.0411761] 68 -0.598716 [-2.67713e-05, 0.000185689, -2.79124e-06, -0.00288861, 0.0409502, -0.0357547] 69 -0.599027 [-1.58226e-05, -9.72578e-05, -1.71624e-05, -0.00121006, 0.0379864, -0.0305452] 70 -0.597994 [-9.02136e-06, 0.000439608, 1.2744e-05, -0.00511981, 0.0354094, -0.0265478] Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 71 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1 -2.54959e-05 0.000879215 2.548e-05 1 1.80539e-05 -0.000879216 -1.80315e-05 1 Offset = [-0.00650666, 0.0354584, -0.0292202] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. 0 -0.595704 [0.00193476, -0.0208481, -0.00251427, 0.187268, 0.0357778, 0.00346992, 1.0145, 1.00462, 0.99931] 1 -0.559018 [0.000736648, -0.0113612, -0.00257218, 0.103232, 0.00696381, -0.0381805, 1.01526, 1.00219, 0.998548] 2 -0.57719 [-0.000273801, 7.66621e-06, -0.00025049, 0.0118336, -0.00132102, -0.0702661, 1.01425, 1.00154, 0.996523] 3 -0.58665 [0.00342811, 0.00133359, -0.000283908, -0.00957381, 0.0212479, -0.162716, 1.0023, 1.00072, 1.01326] 4 -0.595843 [0.00116732, -0.00227205, 0.000129029, 0.0275572, -2.04128e-05, -0.138754, 1.00154, 1.00078, 1.00867] 5 -0.596398 [0.000767513, 0.000365219, -0.000112732, 0.00818432, -0.00147114, -0.124026, 1.00177, 1.00079, 1.00728] 6 -0.596885 [0.00052478, -0.000856305, -9.9012e-05, 0.0177834, -0.00335958, -0.101346, 1.00077, 1.0003, 1.00454] 7 -0.600625 [0.000343896, 0.00113822, -0.000210857, 0.00381361, -0.00534713, -0.0812537, 1.00089, 1.00019, 1.00208] 8 -0.60039 [0.000130028, -0.00158777, -0.00016144, 0.0214225, -0.00507181, -0.0644643, 1.00083, 1.00023, 1.00034] 9 -0.598131 [0.00015188, 0.00015975, -0.000183726, 0.0098993, -0.00361979, -0.0614527, 1.001, 1.0003, 1.00014] 10 -0.59755 [0.000163332, -0.000195158, -0.000106182, 0.0129686, -0.00187711, -0.0563575, 1.00081, 1.00039, 0.99988] 11 -0.597042 [0.000170207, 0.000441936, -8.6784e-05, 0.010096, 0.000971595, -0.0517716, 1.00077, 1.00054, 0.999747] Stop condition from optimizer.VersorTransformOptimizer: Step too small after 12 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1.00077 0.000173718 0.000883843 -0.000173418 1.00054 -0.00034049 -0.000883902 0.000340337 0.999747 Offset = [0.011083, 0.00108809, -0.0539891] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. 0 -0.59872 [0.00156124, -0.0318315, -0.00158452, 0.16262, -0.0335082, 0.0510925, 0.99995, 1.00762, 1.01345, -0.000946919, -0.0177985, -0.00243746, -0.00287354, 0.0144689, -0.00147043] 1 -0.52499 [0.00036641, -0.0202435, -0.00348261, 0.0726411, -0.0544548, 0.0772684, 1.00493, 1.00661, 1.01365, 0.00265235, -0.00471707, -0.000860819, -0.00405057, 0.0162892, -0.00373625] 2 -0.558647 [-0.000695451, -0.00860258, -0.00330235, -0.00902211, -0.0602016, 0.0260437, 1.00958, 1.00622, 1.0127, 0.00291093, 0.00535023, -0.000455126, -0.00399029, 0.0148645, -0.00473234] 3 -0.585723 [-0.00041441, 0.0086081, 0.00529725, -0.0642898, -0.130554, 0.0404235, 1.00624, 0.999014, 1.00525, -0.00100721, 0.0143239, 0.00430199, -0.00444492, 0.00644559, -0.00485922] 4 -0.571134 [0.000972459, 0.00342028, 0.00403526, -0.0247648, -0.121463, 0.0141634, 1.00947, 1.00111, 1.00632, -0.000580769, 0.00921889, 0.0035299, -0.00513142, 0.00646226, -0.00414812] 5 -0.592334 [-0.000306466, -0.00214093, 0.00178254, 0.00800912, -0.152091, 0.0311887, 1.00961, 1.0023, 1.00486, -0.000844398, 0.0031827, 0.00103117, -0.00445769, 0.00599119, -0.00473291] 6 -0.598493 [0.000333673, -0.000366119, 0.000491561, 0.00391201, -0.133076, 0.0170849, 1.00741, 1.00223, 1.00467, -0.00209231, 0.00271232, -0.00150871, -0.00272285, 0.003745, -0.00236063] 7 -0.60486 [0.00109105, 0.00158432, -0.00046458, 0.0133499, -0.112121, 0.0123358, 1.00165, 1.00098, 1.00131, -0.00239762, 0.00306607, -0.00277677, -0.00201904, 0.00214285, -0.000901875] 8 -0.604953 [0.000244443, -0.0016973, -0.000561207, 0.0364257, -0.106775, 0.00999535, 1.00188, 1.00149, 1.00089, -0.00122049, 6.97789e-05, -0.00169198, -0.001524, 0.00243168, -0.00125642] 9 -0.602969 [0.000322209, 4.74224e-05, -0.000484027, 0.0248763, -0.104212, 0.00848137, 1.00178, 1.00151, 1.00081, -0.000955711, 0.000886217, -0.00134999, -0.00142702, 0.00150268, -0.00108159] 10 -0.603054 [0.000616322, 0.000332166, 1.91818e-05, 0.021331, -0.0947858, 0.00155814, 1.00042, 1.0014, 1.00077, -0.000575013, 1.16903e-05, -0.000464125, -0.00119025, 0.000343272, -0.000552008] 11 -0.602841 [-0.00103003, -0.00215068, -0.00115997, 0.0232761, -0.0854844, -0.00226909, 1.00107, 1.00135, 1.00038, 0.00121023, -0.00171581, 0.000143065, 0.000404027, 0.00110065, -0.000605066] 12 -0.602524 [-0.000333304, -0.000711078, -0.000916572, 0.0128203, -0.0804073, -0.00530574, 1.00133, 1.00141, 1.00065, 0.00102241, -0.00098625, 0.000197654, -9.77045e-06, 0.000392568, -0.000324201] 13 -0.604201 [0.00027465, 0.000579284, -0.000247077, 0.00238545, -0.0746984, -0.00711642, 1.0011, 1.00138, 1.00065, 0.000391113, -0.000126682, 0.000236459, -0.000320959, -3.8667e-05, -2.81515e-05] 14 -0.602673 [0.000325787, -0.000413777, -0.000153268, 0.00725282, -0.071643, -0.00827486, 1.00073, 1.00134, 1.00066, 0.000175067, -0.000679547, 0.000114803, -0.000387314, 0.000401835, -4.30252e-05] Stop condition from optimizer.VersorTransformOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1.00073 0.000481334 -0.0015072 -0.000192003 1.00134 -0.00103876 0.00122929 0.000608676 1.00066 Offset = [0.0119306, -0.0703257, -0.00545509] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. 0 -0.598718 [1.00002, -0.000151507, 0.0138615, 0.00169882, 1.00073, -0.00233083, -0.00666277, -0.00187276, 0.998554, -0.166734, 0.0240403, 0.00778296] 1 -0.577429 [1.00557, -0.000279642, 0.00696204, 0.000623704, 1.00357, -0.000320235, -0.00337824, 0.000826832, 1.00244, -0.0699824, 0.0133667, -0.01223] 2 -0.598722 [1.00017, -0.000364072, -0.000391765, -0.000253703, 0.99987, -0.00163809, 0.0028501, -0.000855688, 0.995415, 0.0253985, 0.0161235, 0.0143135] 3 -0.595818 [1.00232, 0.000716144, 0.000524414, 0.000641725, 1.00157, -0.000991947, 0.00073823, -0.000291834, 1.00161, 0.000850884, 0.017701, -0.0285938] 4 -0.601264 [0.998157, -0.000231306, -0.00100708, 7.83183e-05, 1.00052, -0.000313169, -0.000474604, 0.000133369, 0.998297, 0.0080659, 0.0130663, -0.00586941] 5 -0.59366 [1.00123, 0.000231428, 0.000105684, 0.000197737, 1.00118, -0.000385638, 0.000132842, 0.000147306, 0.999924, -0.00198884, 0.0137703, -0.012215] 6 -0.594931 [0.999634, 0.000273881, -0.000252933, 8.28665e-05, 1.00106, -0.000358816, 7.31264e-05, 0.000211605, 1.00095, 0.00309401, 0.016612, -0.0133916] Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 7 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.999634 0.000273881 -0.000252933 8.28665e-05 1.00106 -0.000358816 7.31264e-05 0.000211605 1.00095 Offset = [0.00243495, 0.017639, -0.0146109] Background level guess : first place: 3 (19.7612%) second place: 4 (17.1901%) Guessed background level: 3 [AtlasCreator 20:34:52] DEBUG: Guessing background value: 3.0 Background level guess : first place: 4 (3.15972%) second place: 4 (2.98913%) Guessed background level: 4.5 [AtlasCreator 20:34:53] DEBUG: Guessing background value for template: 4.5 [AtlasCreator 20:34:53] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --movingVolume /Users/daniel/Desktop/ATLASCREATORTEST/originals/case12.nrrd --outputTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case12.mat --outputVolume /Users/daniel/Slicer3daniel/UFWnA_AtlasCreator/case12.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 3.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 427 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 307 LowHigh Thresholds: [0,56.6562,307] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 298 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 203 LowHigh Thresholds: [0,49.0104,203] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x112500040) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4053 Debug: Off Observers: none Matrix: 1 0 0 0 1 0 0 0 1 Offset: [0.0692118, 0.911742, 1.5091] Center: [-3.03604, -0.200909, 1.57021] Translation: [0.0692118, 0.911742, 1.5091] Inverse: 1 0 0 0 1 0 0 0 1 Singular: 0 Versor: [ 0, 0, 0, 1 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1 0.000285644 -0.000213336 -0.00028551 1 0.00062935 0.000213516 -0.000629289 1 Offset = [0.0664267, 0.0382853, -0.0232711] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 61 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.998533 0.0011215 0.00282233 -0.00112362 0.998504 0.000750298 -0.00282148 -0.000753465 0.999827 Offset = [0.0198558, 0.0103364, -0.043988] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.992944 0.00420788 0.0066945 -0.000313199 0.998909 -0.000192358 -0.00115037 -0.00696997 0.998805 Offset = [0.164396, -0.0233992, -0.320684] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.991037 0.00182076 0.00577455 0.000365897 0.99887 0.000366747 -0.00130314 -0.00153073 1.00009 Offset = [0.218712, 0.0056608, -0.0291174] Background level guess : first place: 2 (12.1833%) second place: 3 (11.7794%) Guessed background level: 2 [AtlasCreator 20:40:04] DEBUG: Guessing background value: 2.0 Background level guess : first place: 4 (3.15972%) second place: 4 (2.98913%) Guessed background level: 4.5 [AtlasCreator 20:40:05] DEBUG: Guessing background value for template: 4.5 [AtlasCreator 20:40:05] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --movingVolume /Users/daniel/Desktop/ATLASCREATORTEST/originals/case2.nrrd --outputTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case2.mat --outputVolume /Users/daniel/Slicer3daniel/UFWnA_AtlasCreator/case2.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 2.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 430 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 284 LowHigh Thresholds: [0,58.2969,284] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 298 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 203 LowHigh Thresholds: [0,49.0104,203] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x112200a20) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4053 Debug: Off Observers: none Matrix: 1 0 0 0 1 0 0 0 1 Offset: [2.11005, -4.10756, -5.97351] Center: [-3.03604, -0.200909, 1.57021] Translation: [2.11005, -4.10756, -5.97351] Inverse: 1 0 0 0 1 0 0 0 1 Singular: 0 Versor: [ 0, 0, 0, 1 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.998304 0.0515529 -0.0270495 -0.0510237 0.998499 0.0199037 0.0280349 -0.0184898 0.999436 Offset = [2.17204, -4.62642, -5.39498] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.960685 0.0404249 -0.0422475 -0.0390284 0.902096 0.0333715 0.0435408 -0.0316655 0.967422 Offset = [1.66233, -4.94664, -4.57626] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 111 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.960933 0.0276462 -0.0338051 -0.0617494 0.894941 0.0139411 0.0166243 -0.0291337 0.968434 Offset = [1.66359, -5.20553, -4.5695] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 10 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.959407 0.0320426 -0.0290129 -0.0537121 0.895235 0.018442 0.0127166 -0.0369706 0.970253 Offset = [1.88038, -5.05059, -4.34273] Background level guess : first place: 3 (20.7696%) second place: 4 (17.3754%) Guessed background level: 3 [AtlasCreator 20:45:19] DEBUG: Guessing background value: 3.0 Background level guess : first place: 4 (3.15972%) second place: 4 (2.98913%) Guessed background level: 4.5 [AtlasCreator 20:45:20] DEBUG: Guessing background value for template: 4.5 [AtlasCreator 20:45:20] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --movingVolume /Users/daniel/Desktop/ATLASCREATORTEST/originals/case3.nrrd --outputTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case3.mat --outputVolume /Users/daniel/Slicer3daniel/UFWnA_AtlasCreator/case3.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 3.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 448 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 290 LowHigh Thresholds: [0,59.5312,290] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 298 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 203 LowHigh Thresholds: [0,49.0104,203] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x102bef3c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4053 Debug: Off Observers: none Matrix: 1 0 0 0 1 0 0 0 1 Offset: [-3.40029, 2.45858, 2.52436] Center: [-3.03604, -0.200909, 1.57021] Translation: [-3.40029, 2.45858, 2.52436] Inverse: 1 0 0 0 1 0 0 0 1 Singular: 0 Versor: [ 0, 0, 0, 1 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. 0 -0.541893 [0.00301153, -0.00102368, 0.000818768, -3.53019, 2.60438, 2.56707] 1 -0.532075 [0.00516723, -0.00367574, 0.00132191, -3.59485, 2.6274, 2.37934] 2 -0.535977 [0.00140519, -0.00871451, 0.00166042, -3.47017, 2.52202, 2.26449] 3 -0.54336 [0.00457768, -0.0115349, 0.00160151, -3.37175, 2.64359, 2.14015] 4 -0.543604 [-7.52884e-05, -0.0139227, 0.0012169, -3.27176, 2.51963, 2.01963] 5 -0.550998 [0.00434983, -0.0164413, 0.000625987, -3.20133, 2.67366, 1.91376] 6 -0.547761 [0.000802447, -0.0154181, 0.00118176, -3.13549, 2.55903, 1.76386] 7 -0.552721 [0.00549338, -0.0148636, 0.00141465, -3.08358, 2.70304, 1.6355] 8 -0.551679 [0.00375865, -0.0146371, 0.00214589, -3.04941, 2.6251, 1.58314] 9 -0.552323 [0.00188992, -0.0143992, 0.00225039, -3.009, 2.56599, 1.51343] 10 -0.55414 [0.00312242, -0.0148084, 0.00251504, -2.95969, 2.58661, 1.42896] 11 -0.554355 [0.00144558, -0.0151292, 0.00265909, -2.90797, 2.54798, 1.35266] 12 -0.556885 [0.0026341, -0.0159758, 0.00331458, -2.85118, 2.56924, 1.27321] 13 -0.55653 [0.00170369, -0.016261, 0.00328435, -2.79759, 2.53721, 1.19512] 14 -0.558215 [0.00248373, -0.0157109, 0.00332778, -2.74909, 2.53253, 1.10781] 15 -0.5587 [0.00260594, -0.0159221, 0.00344841, -2.70085, 2.49844, 1.02713] 16 -0.560009 [0.0022075, -0.0155518, 0.00345969, -2.66363, 2.45427, 0.945502] 17 -0.561577 [0.00289079, -0.0149287, 0.00401396, -2.61347, 2.41075, 0.870767] 18 -0.562298 [0.00237965, -0.0141575, 0.0049051, -2.55898, 2.34659, 0.816842] 19 -0.563721 [0.00226573, -0.0146276, 0.00528341, -2.50049, 2.28508, 0.763979] 20 -0.56481 [0.00102549, -0.0134878, 0.0058864, -2.46047, 2.20746, 0.715393] 21 -0.565954 [0.00129394, -0.0118141, 0.00563981, -2.43386, 2.13443, 0.652573] 22 -0.566744 [0.000533523, -0.0116818, 0.00694849, -2.40032, 2.0518, 0.607429] 23 -0.567385 [-0.000478115, -0.00992553, 0.0068186, -2.3718, 1.98254, 0.541293] 24 -0.568191 [-0.00101715, -0.00984114, 0.00634233, -2.32211, 1.94058, 0.465349] 25 -0.568894 [-0.00158812, -0.0103349, 0.00595725, -2.27365, 1.89841, 0.388732] 26 -0.569343 [-0.0011839, -0.0100026, 0.00531545, -2.22248, 1.8415, 0.324387] 27 -0.569872 [-0.00214468, -0.0103448, 0.00496193, -2.175, 1.76546, 0.280122] 28 -0.570144 [-0.00122558, -0.0112702, 0.00545182, -2.12817, 1.69097, 0.23268] 29 -0.57095 [-0.00171273, -0.0098144, 0.00500035, -2.09898, 1.60507, 0.190739] 30 -0.571774 [-0.00147822, -0.011444, 0.00604824, -2.05785, 1.52825, 0.141836] 31 -0.572989 [-0.0017593, -0.00968444, 0.00579233, -2.03236, 1.44034, 0.101714] 32 -0.573967 [-0.000616128, -0.0106783, 0.00639324, -2.00067, 1.36355, 0.0461468] 33 -0.574446 [-0.00210767, -0.00850527, 0.00528653, -1.98193, 1.26803, 0.0239882] 34 -0.575186 [-0.000323485, -0.00901028, 0.00569674, -1.92301, 1.22066, -0.0413637] 35 -0.575381 [-0.00143266, -0.0085264, 0.0048125, -1.86956, 1.14931, -0.0865711] 36 -0.576619 [-0.00256519, -0.00822402, 0.00370892, -1.78213, 1.10536, -0.106897] 37 -0.577787 [-0.00269036, -0.00971309, 0.00490863, -1.68773, 1.08848, -0.134982] 38 -0.577683 [-0.00260136, -0.00664596, 0.00338925, -1.63883, 1.00528, -0.160291] 39 -0.579064 [-0.0029056, -0.00935325, 0.00487708, -1.54131, 0.995001, -0.1789] 40 -0.578618 [-0.00183128, 0.000241105, 0.000880438, -1.51769, 0.900344, -0.185652] 41 -0.579089 [-0.00230514, 6.51403e-05, 0.0019019, -1.56203, 0.912232, -0.165956] 42 -0.576388 [-0.00201399, -0.00242145, 0.00488043, -1.54033, 0.918582, -0.158646] 43 -0.576142 [-0.00121889, -0.00311972, 0.00462343, -1.51553, 0.916305, -0.158988] 44 -0.577764 [-0.000663047, -0.00382048, 0.00438177, -1.49083, 0.913213, -0.157684] 45 -0.579026 [-0.000388854, -0.0043782, 0.00387718, -1.46696, 0.909256, -0.163772] 46 -0.5804 [-0.00014587, -0.00469328, 0.00355106, -1.44572, 0.905236, -0.176281] 47 -0.581264 [0.000182613, -0.00469716, 0.00346883, -1.42319, 0.904909, -0.187096] 48 -0.581362 [0.000675372, -0.00460996, 0.00335627, -1.40038, 0.904705, -0.197266] 49 -0.581159 [0.000855698, -0.00484994, 0.00322296, -1.37691, 0.905705, -0.205799] 50 -0.581401 [0.00100687, -0.00513272, 0.00304306, -1.35338, 0.907792, -0.213948] 51 -0.581647 [0.00120386, -0.00528108, 0.00278358, -1.32942, 0.912221, -0.219496] 52 -0.581743 [0.00159467, -0.00548728, 0.00253415, -1.30689, 0.92013, -0.226842] 53 -0.581389 [0.00206343, -0.00601524, 0.00206848, -1.28706, 0.929426, -0.238775] 54 -0.580766 [0.00207843, -0.00607247, 0.00119459, -1.27005, 0.944224, -0.249442] 55 -0.580696 [0.00230158, -0.00635623, 0.0014792, -1.2537, 0.962389, -0.254621] 56 -0.579791 [0.00155037, -0.00590958, 0.000752901, -1.23762, 0.981361, -0.2557] 57 -0.581203 [0.00185205, -0.00597306, 0.000965939, -1.23243, 1.00553, -0.259355] 58 -0.579839 [0.00200719, -0.00611316, 0.00120543, -1.22507, 1.02875, -0.264961] 59 -0.578858 [0.00167611, -0.00608217, 0.00101638, -1.21711, 1.05105, -0.272943] 60 -0.578938 [0.00156375, -0.00597277, 0.00111334, -1.2111, 1.07504, -0.276531] 61 -0.578454 [0.00144, -0.00594804, 0.00112585, -1.20668, 1.09933, -0.280463] 62 -0.577911 [0.00119209, -0.00596396, 0.00105788, -1.20278, 1.12381, -0.283726] 63 -0.577617 [0.000988413, -0.00593863, 0.00094789, -1.19834, 1.14772, -0.289483] 64 -0.577176 [0.000849533, -0.00594845, 0.000895646, -1.1954, 1.17184, -0.295369] 65 -0.576531 [0.000717319, -0.00592174, 0.000875147, -1.19236, 1.19586, -0.301574] 66 -0.575819 [0.000721603, -0.00599762, 0.00081166, -1.1915, 1.21948, -0.309738] 67 -0.574763 [0.000418462, -0.00591841, 0.000610211, -1.19032, 1.24117, -0.32208] 68 -0.574446 [0.000544693, -0.00618759, 0.00106958, -1.19747, 1.26501, -0.320021] 69 -0.573033 [-4.17916e-05, -0.00404606, -0.000778232, -1.21686, 1.26322, -0.334586] 70 -0.574536 [0.000485325, -0.00422078, -0.000510712, -1.21844, 1.27228, -0.326202] 71 -0.573438 [0.000670929, -0.00446385, -0.00012441, -1.21865, 1.28025, -0.316631] 72 -0.572722 [0.000654493, -0.00464787, -2.24144e-05, -1.22444, 1.28417, -0.306276] 73 -0.572492 [0.000424405, -0.00493415, 0.000105635, -1.22884, 1.28681, -0.294908] 74 -0.57273 [0.000190137, -0.00532779, 0.000474577, -1.23143, 1.29059, -0.283333] 75 -0.572777 [0.00060089, -0.00646439, 0.0010907, -1.23065, 1.29812, -0.273764] 76 -0.571617 [0.00019711, -0.00581813, 0.000624133, -1.2311, 1.29239, -0.275446] Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 77 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.999932 -0.00125054 -0.0116358 0.00124595 0.999999 -0.000401475 0.0116363 0.00038695 0.999932 Offset = [-1.21329, 1.2968, -0.239934] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. 0 -0.574765 [0.0194086, -0.00550323, 0.00360083, -1.40816, 1.32261, -0.266157, 0.935137, 0.956669, 1.00745] 1 -0.550597 [0.0106778, -0.0111047, 0.00826428, -1.5871, 1.28404, -0.19159, 0.949622, 0.970997, 1.00745] 2 -0.572447 [0.00137054, -0.0114662, 0.0100391, -1.75827, 1.20786, -0.125636, 0.960397, 0.979169, 1.00911] 3 -0.58463 [-0.00104778, -0.00843818, 0.00715965, -1.93116, 1.11344, -0.0935122, 0.964257, 0.985907, 1.00617] 4 -0.589266 [-0.000309198, -0.00925929, 0.00284548, -2.12906, 1.0913, -0.0810465, 0.967761, 0.995621, 1.00771] 5 -0.590658 [0.0022834, -0.013228, 0.00346783, -2.03375, 1.11326, -0.063008, 0.966072, 0.993738, 1.00456] 6 -0.590195 [1.1132e-05, -0.0141473, 0.00177924, -2.02729, 1.06467, -0.0708477, 0.96677, 0.993857, 1.00489] 7 -0.590169 [0.00420572, -0.0131741, 0.00144468, -2.0046, 1.0569, -0.0279274, 0.966209, 0.991069, 1.00474] 8 -0.589043 [0.00344616, -0.0132261, 0.00154876, -2.0206, 1.03785, -0.026075, 0.965932, 0.991383, 1.00496] 9 -0.589346 [0.00263431, -0.0134445, 0.00144791, -2.03393, 1.01677, -0.0260501, 0.965666, 0.991498, 1.00477] 10 -0.589576 [0.00206174, -0.0138164, 0.00130107, -2.04746, 0.995946, -0.0235295, 0.965518, 0.991472, 1.00457] 11 -0.589518 [0.00156153, -0.0141416, 0.0013117, -2.06079, 0.975144, -0.0198929, 0.965521, 0.99146, 1.00433] 12 -0.589597 [0.00146438, -0.014374, 0.00158514, -2.07515, 0.956607, -0.0112579, 0.965506, 0.991309, 1.00404] 13 -0.589556 [0.00164564, -0.0144385, 0.00176413, -2.09, 0.93761, -0.00469686, 0.965363, 0.991152, 1.00389] 14 -0.589439 [0.00154002, -0.0143736, 0.00188856, -2.1056, 0.918825, 0.000663726, 0.965159, 0.991234, 1.00388] 15 -0.58955 [0.00163518, -0.0144212, 0.00203648, -2.12206, 0.900543, 0.00508465, 0.964923, 0.991166, 1.00394] 16 -0.589593 [0.00174629, -0.0145884, 0.00207626, -2.13955, 0.883105, 0.00894967, 0.964681, 0.991157, 1.00391] 17 -0.589609 [0.00191507, -0.0147344, 0.00218011, -2.15863, 0.867376, 0.0125849, 0.964375, 0.991019, 1.00381] 18 -0.589652 [0.00196863, -0.0149629, 0.0020598, -2.17785, 0.852493, 0.0183683, 0.964102, 0.991054, 1.00367] 19 -0.589599 [0.00204454, -0.0151696, 0.00214573, -2.19843, 0.838844, 0.0222103, 0.963646, 0.991044, 1.00329] 20 -0.589614 [0.00200925, -0.0150386, 0.00219742, -2.21734, 0.827063, 0.0335446, 0.96328, 0.991052, 1.00318] 21 -0.589726 [0.0019505, -0.0151336, 0.00259049, -2.23431, 0.814421, 0.0468067, 0.962655, 0.990961, 1.00283] 22 -0.589853 [0.00191809, -0.0148783, 0.00277992, -2.25498, 0.80336, 0.0554678, 0.962416, 0.990992, 1.00253] 23 -0.590019 [0.00192328, -0.0146591, 0.00296521, -2.2775, 0.794924, 0.0622516, 0.962398, 0.99093, 1.00227] 24 -0.590168 [0.00191849, -0.014519, 0.00318943, -2.3007, 0.785636, 0.0629774, 0.962436, 0.990912, 1.00223] 25 -0.590348 [0.00199905, -0.014259, 0.00347718, -2.32487, 0.779578, 0.064799, 0.962752, 0.990939, 1.00223] 26 -0.590626 [0.00200431, -0.0142503, 0.00391603, -2.34776, 0.772092, 0.0714289, 0.963151, 0.990945, 1.00228] 27 -0.590888 [0.00174843, -0.0141416, 0.00404527, -2.36919, 0.763164, 0.0806641, 0.963644, 0.990964, 1.00217] 28 -0.590959 [0.00170586, -0.0143365, 0.004722, -2.39008, 0.751229, 0.0872892, 0.964253, 0.990888, 1.00173] 29 -0.591308 [0.000883656, -0.0143767, 0.00564665, -2.40797, 0.737746, 0.0980583, 0.96448, 0.991533, 1.00107] 30 -0.59176 [0.00172174, -0.013074, 0.00737828, -2.42602, 0.727363, 0.0852065, 0.966115, 0.992628, 1.00202] 31 -0.592147 [0.000272196, -0.0126736, 0.00688251, -2.44711, 0.715264, 0.0897698, 0.966625, 0.994116, 1.00241] 32 -0.592288 [0.000612151, -0.0128199, 0.00749311, -2.44209, 0.719013, 0.0790615, 0.966839, 0.994002, 1.00284] 33 -0.592258 [0.000317013, -0.0131912, 0.00762654, -2.43959, 0.721028, 0.0670356, 0.96713, 0.994214, 1.00329] 34 -0.592284 [0.000591988, -0.0128462, 0.00782784, -2.43945, 0.725695, 0.0554925, 0.967261, 0.994451, 1.00374] 35 -0.592268 [2.55801e-05, -0.013218, 0.00781904, -2.43123, 0.724763, 0.0462231, 0.967398, 0.994766, 1.00392] 36 -0.592297 [0.000303378, -0.012473, 0.00823285, -2.43373, 0.727278, 0.0343808, 0.967234, 0.99513, 1.00423] 37 -0.592389 [-0.000336607, -0.0125552, 0.00854181, -2.42633, 0.725214, 0.0246505, 0.967589, 0.995726, 1.00446] 38 -0.592419 [0.00036268, -0.0120852, 0.00867965, -2.42249, 0.725418, 0.0129307, 0.967562, 0.996665, 1.005] 39 -0.592476 [6.01973e-05, -0.0115566, 0.00878678, -2.41687, 0.723014, 0.00210511, 0.967284, 0.996748, 1.00473] 40 -0.592571 [0.00023412, -0.0114366, 0.00875044, -2.41087, 0.724763, -0.00871465, 0.967112, 0.996821, 1.00473] 41 -0.592587 [0.00012102, -0.0115801, 0.00865976, -2.40441, 0.725142, -0.0193937, 0.966817, 0.996738, 1.00469] 42 -0.592617 [0.000163877, -0.0113165, 0.00856794, -2.40232, 0.724046, -0.0316543, 0.966753, 0.996871, 1.00467] 43 -0.592615 [0.000261545, -0.0114672, 0.00842347, -2.40087, 0.72376, -0.0440541, 0.966484, 0.996752, 1.00485] 44 -0.592631 [-0.000223525, -0.0107764, 0.00786666, -2.40694, 0.718804, -0.0535667, 0.966275, 0.996849, 1.00433] 45 -0.592453 [-5.39972e-05, -0.011041, 0.00821199, -2.4018, 0.720847, -0.0563131, 0.965929, 0.996784, 1.00441] 46 -0.592661 [0.000206457, -0.0112405, 0.00843824, -2.40179, 0.723636, -0.0618401, 0.965751, 0.996843, 1.00466] 47 -0.592676 [0.000221, -0.01108, 0.00839117, -2.40631, 0.723512, -0.0661338, 0.965649, 0.99691, 1.00475] 48 -0.59267 [0.000159, -0.0109875, 0.00844562, -2.41135, 0.723176, -0.0698039, 0.965454, 0.996988, 1.00484] 49 -0.592673 [0.000149689, -0.0110116, 0.00848046, -2.4149, 0.724121, -0.0748532, 0.965249, 0.997102, 1.00493] 50 -0.592671 [0.00022654, -0.010938, 0.00845593, -2.41935, 0.726245, -0.0786723, 0.965052, 0.997163, 1.00498] 51 -0.592685 [0.00026248, -0.0109275, 0.00849218, -2.42443, 0.726885, -0.0822586, 0.964807, 0.997206, 1.00502] 52 -0.592694 [0.000250691, -0.0109331, 0.0084975, -2.43013, 0.727366, -0.0847506, 0.964594, 0.997277, 1.00498] 53 -0.592701 [0.000290005, -0.0109422, 0.00852486, -2.43569, 0.728195, -0.0874829, 0.964416, 0.997336, 1.00494] 54 -0.592704 [0.000297949, -0.0109461, 0.00852327, -2.44093, 0.72904, -0.0907787, 0.964267, 0.99741, 1.00494] 55 -0.592692 [0.000292567, -0.0110725, 0.0086002, -2.44622, 0.72988, -0.0939736, 0.963997, 0.997518, 1.00491] 56 -0.592707 [0.000364214, -0.0110524, 0.00862673, -2.4497, 0.733937, -0.0971926, 0.963695, 0.997594, 1.00504] 57 -0.592674 [0.000228308, -0.0108713, 0.00874669, -2.45387, 0.738358, -0.095923, 0.963299, 0.997727, 1.00516] Stop condition from optimizer.VersorTransformOptimizer: Step too small after 58 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.962909 -0.0174966 -0.0217365 0.0174867 0.997574 -0.000646748 0.0217445 0.000266396 1.00493 Offset = [-2.53587, 0.791976, -0.0375892] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. 0 -0.592728 [-0.00370434, -0.0115801, 0.00514078, -2.39038, 0.706578, 0.089826, 0.964861, 0.98969, 0.996494, -0.000523321, -0.00925335, -0.00424244, -0.000203412, -0.00877173, -0.00408326] 1 -0.589301 [0.00154686, -0.00799758, 0.00567876, -2.41999, 0.71622, -0.00389869, 0.965266, 0.991325, 1.00209, -0.00139268, -0.00534168, -0.00465635, -0.00589194, -0.00830277, -0.0045865] 2 -0.592531 [0.00721977, -0.0045441, 0.00271886, -2.39583, 0.748398, -0.00217373, 0.97163, 0.993308, 1.00585, -0.00332331, -0.0132133, -0.00925216, 0.00509766, -0.0192821, 0.0121446] 3 -0.58572 [0.00450126, -0.00798343, 0.00461836, -2.36646, 0.734669, 0.0343625, 0.96957, 0.992752, 1.00636, -0.00354257, -0.0154382, -0.00755517, 0.00493592, -0.0181004, 0.00927255] 4 -0.589841 [0.00638206, -0.00967553, 0.00485263, -2.33328, 0.747636, 0.0683695, 0.966645, 0.987949, 1.00454, -0.00341782, -0.0154912, -0.00731744, 0.00177679, -0.0165482, 0.00792482] 5 -0.589047 [0.00328413, -0.00859281, 0.00336505, -2.3167, 0.716307, 0.102527, 0.967006, 0.990905, 1.00643, -0.00195082, -0.0134663, -0.00729533, 0.00366146, -0.0155557, 0.00676361] 6 -0.590124 [0.00284071, -0.0105117, 0.00399978, -2.26987, 0.730287, 0.095385, 0.965147, 0.987368, 1.00453, -0.00267768, -0.0129069, -0.0074739, 0.000962806, -0.0131681, 0.00356726] 7 -0.592047 [-0.00131506, -0.00774941, 0.00532897, -2.24886, 0.69126, 0.0890863, 0.967814, 1.00363, 1.0124, -0.00415098, -0.00744672, -0.00741573, 0.0048366, -0.0102588, 0.00339892] 8 -0.589956 [0.00083862, -0.00846747, 0.00269831, -2.22772, 0.674795, 0.0494282, 0.965365, 0.999518, 1.00158, -0.00169629, -0.0101427, -0.0076794, 0.00414587, -0.0124331, 0.00491991] 9 -0.599858 [-0.00135412, -0.00768727, 0.00239244, -2.22144, 0.626635, 0.0389551, 0.965448, 0.99895, 1.00185, -0.00248231, -0.009292, -0.00873261, 0.0066807, -0.0123562, 0.00524291] 10 -0.591163 [-0.00194403, -0.00681785, 0.00547906, -2.19655, 0.624144, -0.00251772, 0.964478, 0.994975, 0.995598, -0.00348464, -0.0111762, -0.00674099, 0.0024977, -0.0152406, 0.0005425] 11 -0.592216 [-0.000447765, -0.00665971, 0.00524103, -2.20055, 0.606139, -0.0487381, 0.964958, 0.993736, 0.998933, -0.00314151, -0.0109711, -0.00665181, 0.00188117, -0.0151334, 0.00141459] 12 -0.591181 [-0.000280415, -0.00764159, 0.00498315, -2.22804, 0.583181, -0.082306, 0.966495, 0.988769, 1.00228, -0.000941987, -0.00724048, -0.00476102, 0.000516757, -0.0103704, 0.000194835] 13 -0.591883 [0.000347453, -0.00721918, 0.00527977, -2.24103, 0.604012, -0.0787948, 0.96614, 0.989346, 1.00104, -0.00162455, -0.0084689, -0.00515321, 4.55228e-06, -0.012044, 0.000321492] 14 -0.590312 [0.000358457, -0.00696256, 0.0059572, -2.24432, 0.621836, -0.0618839, 0.965712, 0.990096, 1.00034, -0.00273561, -0.00977537, -0.00559528, -0.000884847, -0.0136334, -0.000546546] 15 -0.588918 [0.00115009, -0.00782108, 0.00607389, -2.24745, 0.638243, -0.0435621, 0.965853, 0.991404, 1.00082, -0.00360689, -0.0108057, -0.00633332, -0.000991507, -0.0137889, 0.000131268] 16 -0.591486 [-0.00117945, -0.0078671, 0.00601625, -2.25808, 0.639158, -0.0218671, 0.965193, 0.991349, 0.999223, -0.00397951, -0.0124839, -0.00677941, -0.00170426, -0.0154942, -0.0029014] 17 -0.59263 [4.51872e-06, -0.00773115, 0.00613599, -2.26196, 0.640793, -0.0332948, 0.965047, 0.99085, 0.999473, -0.00404366, -0.0123313, -0.00672869, -0.00154453, -0.0154596, -0.00155658] 18 -0.589076 [0.00165854, -0.00762273, 0.00598721, -2.26902, 0.647953, -0.0396242, 0.964907, 0.990804, 1.0004, -0.0040587, -0.0121876, -0.00689352, -0.00146003, -0.0153908, 0.000178765] 19 -0.591781 [0.000986319, -0.00771032, 0.00588908, -2.27005, 0.647503, -0.0336956, 0.964854, 0.991033, 1.00024, -0.00411888, -0.0122888, -0.00705143, -0.00159368, -0.0154176, -0.000629035] 20 -0.588618 [0.000783759, -0.00784078, 0.00565711, -2.27366, 0.650322, -0.0295414, 0.96453, 0.991236, 1.00011, -0.00412204, -0.0123384, -0.00728971, -0.00170982, -0.0153476, -0.000952137] 21 -0.587202 [0.00114636, -0.00782242, 0.0054273, -2.27678, 0.655578, -0.0286721, 0.96423, 0.991113, 1.00007, -0.00396105, -0.0123739, -0.0073646, -0.00179321, -0.0154034, -0.000673694] 22 -0.588759 [0.000828638, -0.00786271, 0.00542212, -2.27648, 0.658976, -0.0235036, 0.964079, 0.991169, 1.00001, -0.00404021, -0.012527, -0.00745176, -0.00193176, -0.0155246, -0.00113004] 23 -0.586631 [0.00131085, -0.00772186, 0.005194, -2.27944, 0.66434, -0.0237697, 0.963877, 0.99113, 1.00009, -0.003912, -0.0123836, -0.00755552, -0.00199276, -0.0155192, -0.000710418] 24 -0.589104 [0.000915346, -0.00788769, 0.00520801, -2.27757, 0.667628, -0.0189109, 0.963851, 0.991242, 1.00013, -0.00402189, -0.0125518, -0.00765257, -0.00215488, -0.0155275, -0.00126908] 25 -0.586493 [0.00153325, -0.00785398, 0.00503561, -2.27866, 0.673575, -0.01961, 0.963888, 0.99114, 1.00027, -0.00394714, -0.0124478, -0.00775235, -0.0022329, -0.0154486, -0.000731458] Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.963714 -0.014042 -0.0281396 0.00229434 0.991084 -0.00537835 0.000274117 0.0022558 1.00014 Offset = [-2.34746, 0.687195, -0.0185479] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. 0 -0.585314 [0.951778, -0.0142169, -0.0254429, 0.00191374, 0.989265, -0.0108938, -0.00229617, -0.0301167, 0.995612, -2.20238, 0.657368, 0.161111] 1 -0.575844 [0.95561, -0.0134338, -0.023297, 0.00357374, 0.992102, -0.000749684, -0.000908842, -0.0141683, 1.00274, -2.25646, 0.733005, 0.130885] 2 -0.586572 [0.955349, -0.0165581, -0.0250529, 0.00454726, 0.984662, -0.00146347, -0.000174192, -0.0081795, 0.998681, -2.25019, 0.738647, 0.031858] 3 -0.588703 [0.962217, -0.0175173, -0.0248697, 0.0051075, 0.996728, -0.00106623, 0.00145673, -0.0100939, 1.0024, -2.28682, 0.715516, 0.0520782] 4 -0.593356 [0.96274, -0.015467, -0.0243487, 0.00801478, 0.992725, -0.00192231, 0.00173265, -0.0102511, 1.00059, -2.28913, 0.706386, 0.0296502] 5 -0.59006 [0.963014, -0.0164495, -0.0246992, 0.00808561, 0.991003, -0.00200846, 0.00216669, -0.0106968, 0.999862, -2.28194, 0.698644, 0.00710357] 6 -0.589457 [0.963212, -0.0192954, -0.0261901, 0.00717865, 0.990528, -0.00235958, 0.00257757, -0.0115349, 0.999751, -2.26848, 0.699156, -0.013656] 7 -0.588529 [0.961933, -0.0222174, -0.0282935, 0.0066861, 0.990667, -0.00200354, 0.00272164, -0.00972143, 1.00116, -2.26613, 0.702044, -0.0379644] 8 -0.588654 [0.962442, -0.0216929, -0.0279407, 0.00689588, 0.990225, -0.00280202, 0.00339419, -0.0106273, 1.0002, -2.27947, 0.694432, -0.0575964] 9 -0.588568 [0.964129, -0.0238169, -0.03081, 0.00513414, 0.994426, -0.00273523, 0.00476497, -0.00665782, 1.00468, -2.28677, 0.694338, -0.0799054] 10 -0.589969 [0.962494, -0.0225428, -0.0308329, 0.00628201, 0.99091, -0.0037332, 0.00494226, -0.00593827, 1.0029, -2.2989, 0.696424, -0.101138] 11 -0.589008 [0.962627, -0.0226218, -0.0316292, 0.00549194, 0.99155, -0.00324084, 0.00536364, -0.00404613, 1.00203, -2.3078, 0.699073, -0.124211] 12 -0.588282 [0.962232, -0.0222527, -0.0326293, 0.00538767, 0.990207, -0.00246034, 0.00482074, -0.00176559, 1.00028, -2.33026, 0.702204, -0.134127] 13 -0.586767 [0.962436, -0.0218617, -0.0328848, 0.00535695, 0.99027, -0.00225371, 0.00421898, -0.00111138, 1.00008, -2.34061, 0.700257, -0.111479] 14 -0.586122 [0.96264, -0.0215588, -0.0332899, 0.00540938, 0.990283, -0.00212511, 0.00325831, -0.0005905, 0.999906, -2.34833, 0.697806, -0.0878598] 15 -0.585076 [0.962739, -0.021334, -0.033513, 0.00538833, 0.990267, -0.00215261, 0.00232261, -0.000346924, 0.999622, -2.35196, 0.695819, -0.0632273] 16 -0.583882 [0.962863, -0.0210028, -0.0334655, 0.00530597, 0.990216, -0.0022509, 0.00163092, 4.29612e-05, 0.999728, -2.35377, 0.693672, -0.0384014] 17 -0.582745 [0.963042, -0.0208176, -0.0334543, 0.00506349, 0.990055, -0.00262865, 0.00116789, 5.2946e-05, 0.999623, -2.35236, 0.690777, -0.01362] 18 -0.581985 [0.963271, -0.0205206, -0.0334323, 0.00460113, 0.990141, -0.00295111, 0.000853886, 0.000306286, 1.00036, -2.34369, 0.68999, 0.00979153] 19 -0.581671 [0.961257, -0.0201549, -0.0340449, 0.00390988, 0.989075, -0.00380557, 0.000181488, -0.00100301, 0.994918, -2.32192, 0.685829, 0.0195418] 20 -0.586565 [0.96369, -0.0197188, -0.032421, 0.00399551, 0.992671, -0.00320464, 0.000954941, 0.00108758, 1.00311, -2.32903, 0.688544, 0.017495] 21 -0.586615 [0.962634, -0.0196521, -0.0326984, 0.0041783, 0.991036, -0.00381034, 0.000728885, 0.000235965, 0.999805, -2.32673, 0.687502, 0.0215803] Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.962634 -0.0196521 -0.0326984 0.0041783 0.991036 -0.00381034 0.000728885 0.000235965 0.999805 Offset = [-2.39278, 0.704369, 0.0241466] Background level guess : first place: 3 (19.8423%) second place: 4 (17.4266%) Guessed background level: 3 [AtlasCreator 20:50:34] DEBUG: Guessing background value: 3.0 Background level guess : first place: 4 (3.15972%) second place: 4 (2.98913%) Guessed background level: 4.5 [AtlasCreator 20:50:35] DEBUG: Guessing background value for template: 4.5 [AtlasCreator 20:50:35] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --movingVolume /Users/daniel/Desktop/ATLASCREATORTEST/originals/case5.nrrd --outputTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case5.mat --outputVolume /Users/daniel/Slicer3daniel/UFWnA_AtlasCreator/case5.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 3.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 477 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 303 LowHigh Thresholds: [0,58.4062,303] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 298 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 203 LowHigh Thresholds: [0,49.0104,203] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x102beb3b0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4068 Debug: Off Observers: none Matrix: 0.99863 0.0520493 0.0054706 -0.052336 0.993159 0.104385 -8.67362e-19 -0.104528 0.994522 Offset: [1.70827, -0.193445, -14.8566] Center: [-3.03604, -0.200909, 1.57021] Translation: [1.71057, 0.13073, -14.8442] Inverse: 0.99863 -0.052336 -8.67362e-19 0.0520493 0.993159 -0.104528 0.0054706 0.104385 0.994522 Singular: 0 Versor: [ -0.052318, 0.00137, -0.0261411, 0.998287 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 44 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.998702 0.00468774 0.0507158 -0.0100276 0.994363 0.105554 -0.0499351 -0.105926 0.993119 Offset = [1.63355, 1.60817, -12.3282] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 222 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.990055 -0.00348448 0.0431251 5.98305e-05 1.00714 0.0791596 -0.0432656 -0.0790829 0.940896 Offset = [1.04325, 1.92437, -10.1347] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.994516 -0.00642819 0.0554976 -0.00879404 1.00004 0.0732147 -0.0427452 -0.0372777 0.943425 Offset = [1.48434, 0.854814, -9.52036] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.99289 -0.00691509 0.0611725 -0.0168654 1.00337 0.0747154 -0.046846 -0.0408707 0.933627 Offset = [1.91557, 0.999298, -9.64697] Background level guess : first place: 2 (11.5244%) second place: 3 (11.1119%) Guessed background level: 2 [AtlasCreator 20:56:32] DEBUG: Guessing background value: 2.0 Background level guess : first place: 4 (3.15972%) second place: 4 (2.98913%) Guessed background level: 4.5 [AtlasCreator 20:56:33] DEBUG: Guessing background value for template: 4.5 [AtlasCreator 20:56:33] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --movingVolume /Users/daniel/Desktop/ATLASCREATORTEST/originals/case8.nrrd --outputTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case8.mat --outputVolume /Users/daniel/Slicer3daniel/UFWnA_AtlasCreator/case8.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 2.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 493 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 306 LowHigh Thresholds: [0,56.6719,306] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 298 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 203 LowHigh Thresholds: [0,49.0104,203] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x10f500e10) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4056 Debug: Off Observers: none Matrix: 0.99863 -0.0522642 0.00273905 0.052336 0.997261 -0.0522642 4.33681e-19 0.052336 0.99863 Offset: [1.96443, -0.409579, 15.894] Center: [-3.03604, -0.200909, 1.57021] Translation: [1.9834, -0.649989, 15.8814] Inverse: 0.99863 0.052336 4.33681e-19 -0.0522642 0.997261 0.052336 0.00273905 -0.0522642 0.99863 Singular: 0 Versor: [ 0.026168, 0.000685233, 0.026168, 0.999315 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 82 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.998451 -0.054553 0.0109474 0.0546204 0.998489 -0.00595322 -0.0106061 0.00654194 0.999922 Offset = [1.86532, -1.78993, 8.36222] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.932438 -0.0423454 0.000204016 0.0423456 1.01955 -0.000907514 -0.000165404 0.000915339 1.01067 Offset = [2.0681, -2.02826, 8.62623] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 47 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.925356 -0.0382766 0.00994697 0.0235251 1.00842 -0.00309055 -0.0313722 0.00815479 1.02404 Offset = [2.43421, -1.55114, 8.0959] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 18 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.922483 -0.0462342 0.00662027 0.021681 1.00812 0.000777518 -0.0254822 0.00032552 1.0266 Offset = [1.97758, -1.61007, 8.04244] [AtlasCreator 21:01:42] Waiting for Registration to complete.. [AtlasCreator 21:01:47] DEBUG: All outputs exist! [AtlasCreator 21:01:47] Starting iteration 2... Warning: In /Users/daniel/SLICER/TRUNK/Slicer3/Libs/MRML/vtkMRMLVolumeArchetypeStorageNode.cxx, line 478 vtkMRMLVolumeArchetypeStorageNode (0x13aac5ef0): WriteData: removing old version of file /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd Background level guess : first place: 4 (11.4145%) second place: 5 (11.2047%) Guessed background level: 4 [AtlasCreator 21:01:59] DEBUG: Guessing background value: 4.0 Background level guess : first place: 4 (3.48106%) second place: 3 (3.37968%) Guessed background level: 4 [AtlasCreator 21:02:01] DEBUG: Guessing background value for template: 4.0 [AtlasCreator 21:02:01] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --movingVolume /Users/daniel/Desktop/ATLASCREATORTEST/originals/case10.nrrd --outputTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case10.mat --outputVolume /Users/daniel/Slicer3daniel/O6ZqLzAtlasCreator/case10.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 4.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 435 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 300 LowHigh Thresholds: [0,62.3594,300] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 341 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 1 0.999 ---> 224 LowHigh Thresholds: [1,52.1003,224] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x102bef3c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4053 Debug: Off Observers: none Matrix: 1 0 0 0 1 0 0 0 1 Offset: [1.01922, 1.09135, -5.31489] Center: [-3.56396, 0.280455, 1.98482] Translation: [1.01922, 1.09135, -5.31489] Inverse: 1 0 0 0 1 0 0 0 1 Singular: 0 Versor: [ 0, 0, 0, 1 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. 0 -0.536761 [0.00202957, 0.00340452, -0.00225022, 0.884939, 1.20536, -5.40916] 1 -0.532442 [-0.000832612, 0.00614945, -0.0031629, 0.795099, 1.2522, -5.23692] 2 -0.538177 [-0.00122044, 0.00727633, -0.00365285, 0.746856, 1.30334, -5.0497] 3 -0.542552 [-0.00172009, 0.00650753, -0.00274624, 0.739414, 1.33331, -4.85211] 4 -0.546194 [-0.00094042, 0.00727816, -0.00283883, 0.72259, 1.39133, -4.66147] 5 -0.54712 [-0.00250582, 0.00767841, -0.00155048, 0.728574, 1.39478, -4.46163] 6 -0.552253 [0.000393619, 0.00669229, -0.00296705, 0.703178, 1.41591, -4.26449] 7 -0.552157 [-0.00358128, 0.00592744, -0.00116878, 0.723231, 1.39313, -4.06701] 8 -0.562097 [-0.00345206, 0.00517611, -0.00465118, 0.700316, 1.38853, -3.86851] 9 -0.566879 [-0.00653747, 0.00590252, -0.00699855, 0.675315, 1.33756, -3.6769] 10 -0.571951 [-0.00773767, 0.00495879, -0.00726667, 0.633895, 1.30844, -3.48344] 11 -0.575814 [-0.00820349, 0.0039333, -0.00725314, 0.588702, 1.28951, -3.28954] 12 -0.579454 [-0.00868093, 0.00411638, -0.00780675, 0.551955, 1.27875, -3.09325] 13 -0.582614 [-0.00809513, 0.0037967, -0.0079048, 0.505602, 1.26664, -2.89908] 14 -0.58653 [-0.00729196, 0.00314832, -0.00841306, 0.453369, 1.24009, -2.70787] 15 -0.590228 [-0.00594701, 0.00199295, -0.00871097, 0.405573, 1.20214, -2.51744] 16 -0.594568 [-0.00418324, 0.00148334, -0.00939913, 0.372816, 1.14608, -2.32831] 17 -0.597651 [-0.0032526, 0.00100913, -0.00908713, 0.338713, 1.07714, -2.14371] 18 -0.602104 [-0.00254569, 0.00127173, -0.0082484, 0.290711, 1.00844, -1.96213] 19 -0.606222 [0.00156416, 0.000862445, -0.00778953, 0.265955, 0.943743, -1.77469] 20 -0.606554 [-0.00835485, -0.00203553, -0.00812233, 0.218491, 0.843434, -1.60959] 21 -0.611672 [-0.00561544, 0.00127428, -0.00665479, 0.184701, 0.836916, -1.41278] 22 -0.620072 [-0.00141561, -0.00035548, -0.00456624, 0.178986, 0.80816, -1.21519] 23 -0.630377 [-0.00297752, -0.000696213, -0.00446943, 0.16499, 0.767544, -1.01989] 24 -0.635262 [-0.00115091, -9.20822e-06, -0.00258188, 0.132018, 0.710222, -0.831215] 25 -0.642401 [-0.00256328, -0.00249399, -0.00152812, 0.0701286, 0.609808, -0.669815] 26 -0.648181 [-0.00395394, 0.00667996, -0.000745558, -0.0276511, 0.532461, -0.514542] 27 -0.633636 [-0.000201275, -0.00442294, -0.00268476, 0.0866778, 0.477183, -0.36187] 28 -0.648775 [-0.0023178, 0.00639813, -0.00220047, -0.0305263, 0.352282, -0.260996] 29 -0.638178 [0.000920668, -0.00854802, -0.0025785, 0.103524, 0.250618, -0.15727] 30 -0.63069 [-0.000495587, 0.00621866, -0.0016301, -0.0351354, 0.132111, -0.0808114] 31 -0.635928 [0.000113507, -0.00315294, -0.00142898, 0.0551182, 0.105405, -0.0527379] 32 -0.648771 [6.16146e-05, 0.00241844, -0.000471346, 0.0101491, 0.0976758, -0.0357026] 33 -0.650877 [7.88115e-06, -0.000751566, -0.000513402, 0.032964, 0.0930606, -0.0291476] 34 -0.647573 [6.63977e-05, 0.000594537, -0.000228671, 0.0213442, 0.0912535, -0.0259258] 35 -0.646354 [3.71687e-05, -0.000273336, -0.00023295, 0.0262979, 0.0892063, -0.023221] Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1 0.00046588 -0.00054669 -0.000465921 1 -7.42101e-05 0.000546655 7.44648e-05 1 Offset = [0.0272515, 0.0876931, -0.0212933] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. 0 -0.642047 [0.00385709, 0.0212368, 0.00677336, -0.154794, 0.0684924, 0.0188559, 1.03254, 1.02399, 1.03558] 1 -0.608455 [0.00441454, 0.0151011, 0.00415851, -0.0664393, 0.0784003, -0.0245504, 1.03035, 1.02083, 1.03144] 2 -0.622404 [0.00579322, 0.00981216, 0.00254458, 0.0229161, 0.0935431, -0.0644962, 1.0272, 1.01657, 1.02572] 3 -0.633935 [0.00840072, 0.00583465, 0.000776542, 0.121155, 0.107347, -0.0634678, 1.02405, 1.01291, 1.02014] 4 -0.642122 [0.00434026, 0.00157113, -0.00485555, 0.215997, 0.0883887, -0.0795429, 1.01871, 1.00962, 1.01107] 5 -0.653317 [0.00220796, 0.00185824, -0.00464876, 0.303253, 0.0799253, -0.0318079, 1.01457, 1.00907, 1.01071] 6 -0.6557 [0.00390507, 0.000675531, -0.00255815, 0.283285, 0.12643, 0.0540723, 1.01401, 1.00771, 1.00558] 7 -0.657736 [0.00210392, 0.00103693, -0.00270214, 0.240083, 0.102066, 0.0527252, 1.01013, 1.00918, 1.0083] 8 -0.660975 [0.00127632, 0.00069848, -0.000637178, 0.195382, 0.0992452, 0.0739658, 1.00586, 1.00765, 1.00697] 9 -0.666303 [0.00132559, 0.000335591, -0.00107377, 0.179304, 0.100068, 0.120595, 1.00018, 1.00251, 1.0044] 10 -0.663046 [0.000188961, 0.000784817, 0.000111017, 0.130221, 0.0942236, 0.127199, 1.00084, 1.00249, 1.00338] 11 -0.657465 [0.000252566, -0.00162205, -0.000425034, 0.092106, 0.0888472, 0.0957964, 1.00005, 1.00145, 1.00088] 12 -0.650923 [0.000315101, 0.00249136, -0.000416775, 0.0465013, 0.0861485, 0.0772681, 1.00127, 1.00174, 1.00147] 13 -0.653069 [0.000234374, -0.0022694, -0.000125591, 0.067533, 0.0831734, 0.0681727, 1.00153, 1.00172, 1.0015] 14 -0.652516 [0.000268033, -0.000982034, -0.00018207, 0.0557105, 0.0821064, 0.0652262, 1.00162, 1.00169, 1.00146] 15 -0.652703 [0.000255545, 0.000152503, -0.000183611, 0.0444175, 0.0814401, 0.0604269, 1.00135, 1.00164, 1.00134] 16 -0.649135 [0.000175533, -0.000159373, -2.43091e-05, 0.0404463, 0.0799074, 0.0487138, 1.00071, 1.00158, 1.00136] 17 -0.647809 [0.000203037, 0.000319478, -5.72062e-05, 0.0323186, 0.0790501, 0.0393049, 1.00066, 1.00161, 1.00136] 18 -0.647377 [0.000172158, -0.00102563, -3.12995e-05, 0.0354693, 0.0768252, 0.0277237, 1.00062, 1.00166, 1.00134] 19 -0.650848 [0.000194379, -0.000284225, -6.98164e-05, 0.0294603, 0.0766514, 0.0268838, 1.00071, 1.00167, 1.00128] 20 -0.647836 [0.000196867, 0.000235134, -5.79995e-05, 0.0243677, 0.0761705, 0.0234465, 1.00069, 1.00168, 1.00124] Stop condition from optimizer.VersorTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1.00069 0.000116092 0.000470245 -0.000115906 1.00168 -0.000393761 -0.000470291 0.000393707 1.00124 Offset = [0.0258667, 0.0760664, 0.0192056] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. 0 -0.650874 [0.00402015, -0.0236554, -0.00228275, 0.18191, -0.0266161, -0.0188795, 1.00414, 1.00351, 1.00817, 0.00527345, -0.0162637, 0.00305703, -0.00588971, 0.00762652, -0.00206309] 1 -0.588482 [0.00551764, -0.0121267, -0.00377477, 0.094644, -0.0560175, 0.00874358, 1.01134, 1.00779, 1.01218, 0.00640007, -0.00539313, 0.00249754, -0.00703196, 0.00749456, -0.0016666] 2 -0.632172 [0.00296198, -0.000372505, -0.00462618, 0.00558407, -0.0627194, -0.0276273, 1.01473, 1.01079, 1.0128, 0.00802593, 0.00357003, 0.00319115, -0.00432643, 0.00481401, -0.00148091] 3 -0.656545 [0.00180731, -0.00275917, -0.00291324, 0.0434951, -0.0323949, -0.0195951, 1.01153, 1.00981, 1.00878, 0.00596391, 0.00125484, 0.0028955, -0.00299686, 0.00486656, -0.00133534] 4 -0.661583 [0.0030697, 0.00191972, -0.000122187, 0.0285498, -0.0175318, -0.0211303, 1.00645, 1.00852, 1.00759, 0.00278326, 0.00264819, 0.00253261, -0.00399386, 0.00153341, -0.00110034] 5 -0.664664 [0.0026503, 0.00107929, -0.0003393, 0.0366102, -0.0190883, -0.0119564, 1.00633, 1.00861, 1.00757, 0.00278687, 0.00180683, 0.00232255, -0.00354384, 0.00153305, -0.0010685] 6 -0.668819 [0.00219891, 0.000413177, -0.000458109, 0.0444279, -0.0186473, -0.00239906, 1.0059, 1.00859, 1.00739, 0.00287084, 0.00116244, 0.00229025, -0.00299602, 0.00155648, -0.000973056] 7 -0.671777 [0.00177911, 1.85174e-05, -0.000460152, 0.0531366, -0.0159266, 0.0060017, 1.00515, 1.00847, 1.00717, 0.00294069, 0.000675732, 0.00236061, -0.00252613, 0.0014655, -0.000924609] 8 -0.673671 [0.00138191, -0.000244144, -0.000188725, 0.0612377, -0.0130119, 0.0148903, 1.00412, 1.0082, 1.00667, 0.00282694, 0.000154085, 0.00252132, -0.00213956, 0.00120619, -0.000938222] 9 -0.674692 [0.00107203, -1.49217e-05, 0.000223986, 0.0611883, -0.0117142, 0.0269806, 1.0021, 1.0073, 1.00553, 0.00246031, -0.000231574, 0.00256981, -0.00165989, 0.000588689, -0.000774266] 10 -0.673544 [0.000859794, 0.000156954, 0.000344532, 0.0531586, -0.01513, 0.0356447, 1.00098, 1.00626, 1.00433, 0.00191462, -0.000398523, 0.00214407, -0.00117882, 0.000248745, -0.000510095] 11 -0.670132 [0.000402765, 0.000200366, 0.000369058, 0.0439487, -0.0177636, 0.0427726, 1.00011, 1.00453, 1.00165, 0.0010307, -0.000575146, 0.00128302, -0.000633539, 2.83601e-05, -0.000429008] 12 -0.658725 [0.000714341, -0.000114995, -0.000246343, 0.0356783, -0.0138434, 0.0345751, 1.00068, 1.00343, 1.00142, 0.000705098, -0.000347274, 0.000341489, -0.000747549, 0.000571337, -0.000232535] 13 -0.658795 [0.000141235, 0.00093361, 0.000276358, 0.0248078, -0.0135595, 0.0291179, 1.00059, 1.00279, 1.00134, 0.000241052, 1.84956e-05, 0.000400049, -0.000473882, -0.000112053, -0.000533331] 14 -0.655547 [0.000349874, -2.60523e-05, 0.000116074, 0.0302847, -0.0117829, 0.0279266, 1.00061, 1.00272, 1.0014, 0.000347363, -0.000572394, 0.000346385, -0.000564974, 0.000256676, -0.000415893] Stop condition from optimizer.VersorTransformOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1.00061 0.000115195 -0.000624417 0.000578516 1.00271 -0.00126473 0.000308862 0.000283849 1.0014 Offset = [0.0336612, -0.00797221, 0.0261668] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. 0 -0.650638 [1.00079, 0.00273474, 0.00671586, 0.000182442, 0.999988, -0.000692667, -0.00391101, 0.00150355, 0.999328, -0.14808, 0.0600906, -0.0261855] 1 -0.641003 [1.00494, 0.00214873, -0.00110236, -0.00094513, 1.00346, -0.000363408, -0.00053622, 0.000540238, 1.00417, -0.0496128, 0.049829, -0.0177533] 2 -0.666048 [0.974671, -0.00174175, 0.000736142, 0.00205318, 0.99211, -0.00260318, -0.00160193, 0.000186456, 0.97958, -0.0397129, 0.0536356, 0.0728214] 3 -0.550425 [1.02611, 0.00243256, 0.00249676, 0.00212665, 1.03277, 0.000336665, -0.00167654, -0.000402593, 1.01882, -0.0867399, 0.0708227, 0.113128] 4 -0.63083 [1.02336, 0.0049769, 0.00304834, 0.00357061, 1.02911, 0.000336793, -0.00156656, 0.00140103, 1.01587, -0.0436535, 0.0872168, 0.0948785] 5 -0.640682 [1.02139, 0.00722882, 0.00313605, 0.00452879, 1.02604, 8.95008e-05, -0.00145557, 0.00229214, 1.01297, -0.0124327, 0.105663, 0.0608723] 6 -0.646012 [1.01854, 0.00910925, 0.00218689, 0.00524616, 1.02151, -0.000415885, -0.00149893, 0.00262689, 1.00927, 0.0205173, 0.129385, 0.0325201] 7 -0.650512 [1.01502, 0.0101799, 0.000677211, 0.00580342, 1.01733, 8.87107e-05, -0.00177848, 0.0044717, 1.00883, 0.0596547, 0.151045, 0.0540054] 8 -0.655802 [1.00935, 0.0113466, 0.000569898, 0.00666552, 1.01452, 0.000539268, -0.0010302, 0.00649086, 1.00801, 0.0768435, 0.197469, 0.0527396] 9 -0.661722 [1.002, 0.00903516, 0.00131957, 0.00441225, 1.01346, 0.000565301, 0.00213602, 0.00696275, 1.00623, 0.0443304, 0.232353, 0.0648447] 10 -0.666721 [1.01258, 0.00843401, -0.00109464, 0.00111032, 1.01832, 0.00290603, -0.00148783, 0.00944319, 1.00726, 0.055654, 0.256439, 0.10501] 11 -0.655584 [1.00703, 0.00906024, -0.000362552, 0.00169482, 1.01507, 0.000585272, -0.00111136, 0.00791485, 1.00568, 0.0558934, 0.24249, 0.0855828] 12 -0.664171 [1.00388, 0.00990893, 0.000563653, 0.00229552, 1.01577, 0.000458976, 0.000545692, 0.00879698, 1.00689, 0.0469629, 0.25819, 0.0688081] 13 -0.66419 [1.00502, 0.010143, 0.000338989, 0.00227995, 1.01603, 0.000580795, 0.000617192, 0.00816102, 1.00556, 0.0498085, 0.255376, 0.0804948] 14 -0.664202 [1.0051, 0.0102892, 0.000295596, 0.00239266, 1.0162, 0.000760871, 0.000534182, 0.00845405, 1.00594, 0.0441425, 0.255413, 0.0779222] 15 -0.663666 [1.00523, 0.0102621, 0.000315015, 0.0024126, 1.01625, 0.000754314, 0.000595248, 0.00846898, 1.00599, 0.0382467, 0.253776, 0.0766595] 16 -0.66355 [1.00524, 0.0101999, 0.000243362, 0.00242715, 1.01624, 0.000748156, 0.000643387, 0.00841107, 1.00599, 0.0326177, 0.251341, 0.0754626] 17 -0.663607 [1.00531, 0.0102222, 0.000235892, 0.00252596, 1.01622, 0.000746831, 0.000647356, 0.00841623, 1.00602, 0.0266462, 0.250163, 0.0740483] 18 -0.663556 [1.00531, 0.0101158, -2.22168e-05, 0.00257712, 1.01621, 0.000748159, 0.0008344, 0.00834778, 1.00602, 0.0215835, 0.248857, 0.0706419] 19 -0.663667 [1.00545, 0.0102047, -0.000101969, 0.00272997, 1.01627, 0.000764726, 0.000829004, 0.00840171, 1.00614, 0.0155957, 0.250619, 0.0704826] 20 -0.663435 [1.00532, 0.0099382, -2.82439e-05, 0.00278395, 1.01604, 0.00076712, 0.00106833, 0.00829225, 1.00611, 0.00964126, 0.251699, 0.0719731] 21 -0.663844 [1.00559, 0.00998675, 4.81057e-06, 0.00288466, 1.01621, 0.000822164, 0.0010156, 0.00838924, 1.00637, 0.00582638, 0.255326, 0.0686334] 22 -0.663413 [1.00553, 0.00991384, 7.87712e-05, 0.00295532, 1.01601, 0.000668079, 0.00120035, 0.00824932, 1.00607, 0.000563353, 0.25799, 0.0666246] 23 -0.663653 [1.00579, 0.0098851, 1.50332e-05, 0.00306386, 1.01621, 0.000797652, 0.00120268, 0.0084353, 1.00656, -0.00257668, 0.261976, 0.0630336] 24 -0.663192 [1.00553, 0.0096552, 7.87897e-05, 0.00316544, 1.01559, 0.000571629, 0.00122944, 0.00786744, 1.00579, -0.00339898, 0.260052, 0.0572729] 25 -0.664281 [1.00577, 0.00976291, 0.000175376, 0.00326612, 1.016, 0.000831244, 0.001313, 0.0081973, 1.0064, -0.00219854, 0.264402, 0.0530444] 26 -0.6634 [1.00591, 0.00935477, -0.000168097, 0.00363309, 1.01599, 0.00101805, 0.00161432, 0.00730638, 1.00582, 0.00341793, 0.264365, 0.0506324] Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1.00591 0.00935477 -0.000168097 0.00363309 1.01599 0.00101805 0.00161432 0.00730638 1.00582 Offset = [0.0221879, 0.270807, 0.0427857] Background level guess : first place: 3 (19.7612%) second place: 4 (17.1901%) Guessed background level: 3 [AtlasCreator 21:07:15] DEBUG: Guessing background value: 3.0 Background level guess : first place: 4 (3.48106%) second place: 3 (3.37968%) Guessed background level: 4 [AtlasCreator 21:07:16] DEBUG: Guessing background value for template: 4.0 [AtlasCreator 21:07:16] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --movingVolume /Users/daniel/Desktop/ATLASCREATORTEST/originals/case12.nrrd --outputTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case12.mat --outputVolume /Users/daniel/Slicer3daniel/O6ZqLzAtlasCreator/case12.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 3.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 427 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 307 LowHigh Thresholds: [0,56.6562,307] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 341 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 1 0.999 ---> 224 LowHigh Thresholds: [1,52.1003,224] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x102bef3c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4053 Debug: Off Observers: none Matrix: 1 0 0 0 1 0 0 0 1 Offset: [0.597135, 0.430377, 1.09449] Center: [-3.56396, 0.280455, 1.98482] Translation: [0.597135, 0.430377, 1.09449] Inverse: 1 0 0 0 1 0 0 0 1 Singular: 0 Versor: [ 0, 0, 0, 1 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. 0 -0.60984 [-0.00300709, -0.000304886, 0.000396831, 0.702013, 0.327042, 0.959268] 1 -0.60545 [-0.00059152, 0.00195399, -0.0011033, 0.788326, 0.241234, 0.80073] 2 -0.60562 [-0.00380463, 0.00778123, -0.000821842, 0.716616, 0.0773239, 0.712335] 3 -0.617456 [0.00070224, 0.00663965, -0.000887668, 0.662137, 0.0923317, 0.520709] 4 -0.612449 [-0.00692351, 0.00745549, -0.0011745, 0.606258, -0.0027698, 0.354584] 5 -0.622509 [-0.00439702, 0.00917554, -0.0019079, 0.530796, 0.00771183, 0.16977] 6 -0.625295 [0.00161323, 0.00318554, 0.000742009, 0.538775, -0.0164522, -0.0278061] 7 -0.617114 [-0.0134175, 0.00910696, -0.0031619, 0.503479, -0.100171, -0.00249999] 8 -0.618414 [-0.0100431, 0.00941735, -0.00225288, 0.501653, -0.0663573, -0.0386117] 9 -0.621801 [-0.0070307, 0.00826062, -0.000844034, 0.51741, -0.0282597, -0.0660104] 10 -0.625153 [-0.00566509, 0.00627977, -0.000102694, 0.547271, -0.0239759, -0.105566] 11 -0.627743 [-0.00552289, 0.00677551, -0.000830487, 0.527664, -0.0334804, -0.117693] 12 -0.627683 [-0.00516009, 0.00681789, -0.000809853, 0.515732, -0.046121, -0.135646] 13 -0.627992 [-0.00450617, 0.00666368, -0.000644983, 0.507362, -0.0626792, -0.152345] 14 -0.627982 [-0.00358124, 0.00634895, -0.000763546, 0.490153, -0.0753706, -0.165147] 15 -0.627008 [-0.00246286, 0.00597715, -0.00053492, 0.49078, -0.0631726, -0.164007] 16 -0.624496 [-0.00151828, 0.00591936, -0.00046621, 0.489794, -0.0508692, -0.163457] 17 -0.621265 [-0.00113853, 0.00562667, -0.000121995, 0.492378, -0.0395465, -0.158987] 18 -0.619577 [-0.00126505, 0.00535599, -0.000396802, 0.493088, -0.029751, -0.151297] 19 -0.620041 [-0.00111822, 0.00516469, -0.000262579, 0.495222, -0.0181843, -0.147101] 20 -0.619115 [-0.00165542, 0.00497417, -0.000611076, 0.50066, -0.00831846, -0.141852] 21 -0.621345 [9.44947e-05, 0.00557744, 2.96279e-05, 0.508634, 0.000456073, -0.141277] 22 -0.613199 [-0.000596521, 0.00550718, -0.000148472, 0.506556, -0.00361216, -0.13726] 23 -0.616338 [-0.00129021, 0.00536124, -0.000365661, 0.505542, -0.00841061, -0.133681] Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.999942 0.000717476 0.0107233 -0.000745145 0.999996 0.00257646 -0.0107214 -0.00258431 0.999939 Offset = [0.483851, -0.0161791, -0.171046] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. 0 -0.624586 [0.00111225, -0.00106968, -0.00169691, 0.348517, 0.0323672, -0.180155, 0.908703, 0.953374, 0.971438] 1 -0.576372 [-0.00346576, 0.00225827, -0.00251194, 0.313273, -0.00133002, -0.0944896, 0.917514, 0.959491, 0.97759] 2 -0.60033 [-0.00676538, 0.00677837, -0.00209883, 0.235502, 0.00592003, -0.0358273, 0.928762, 0.969398, 0.987951] 3 -0.628413 [-0.00879581, 0.015416, 0.0018902, 0.233859, 0.0365416, 0.0530323, 0.94973, 0.982295, 1.00133] 4 -0.657145 [-0.00892346, 0.0129067, 0.00563693, 0.318572, 0.0840827, 0.0746957, 0.951224, 0.984691, 1.00352] 5 -0.661639 [-0.00795446, 0.0112973, 0.0059069, 0.406691, 0.122475, 0.101214, 0.955874, 0.98796, 1.00687] 6 -0.664326 [-0.00833095, 0.0134234, 0.00557196, 0.47602, 0.116093, 0.172788, 0.957305, 0.989768, 1.00452] 7 -0.665153 [-0.00564802, 0.0119769, 0.00718808, 0.572467, 0.141392, 0.174224, 0.959938, 0.988644, 1.00431] 8 -0.665831 [-0.00987064, 0.0175772, 0.00163396, 0.666126, 0.166369, 0.190522, 0.963109, 0.990621, 1.00222] 9 -0.663184 [-0.00914066, 0.00801922, 0.00570004, 0.762898, 0.179954, 0.1938, 0.961891, 0.989208, 1.00387] 10 -0.66533 [-0.00526673, 0.0155416, -0.00258861, 0.738489, 0.18693, 0.157916, 0.964414, 0.989217, 1.00447] 11 -0.661918 [-0.0062815, 0.0123286, -0.000263036, 0.760645, 0.181623, 0.164072, 0.963694, 0.989244, 1.00375] 12 -0.666183 [-0.00447233, 0.0106657, 0.00173943, 0.777126, 0.191754, 0.149589, 0.963247, 0.988594, 1.00334] 13 -0.667574 [-0.00504463, 0.0100959, 0.00261637, 0.780561, 0.188163, 0.160783, 0.96286, 0.988534, 1.00269] 14 -0.667399 [-0.0054859, 0.00947941, 0.00341677, 0.785274, 0.177112, 0.163379, 0.962379, 0.988545, 1.00245] 15 -0.667155 [-0.00615201, 0.0101357, 0.00328756, 0.786555, 0.167999, 0.171624, 0.962375, 0.988709, 1.00248] 16 -0.667294 [-0.0063294, 0.0105595, 0.00348095, 0.781786, 0.160602, 0.18044, 0.962283, 0.9889, 1.00267] 17 -0.667197 [-0.00655672, 0.0108521, 0.00342819, 0.772754, 0.157479, 0.188457, 0.962278, 0.98912, 1.00252] 18 -0.667187 [-0.00676165, 0.0116732, 0.00419316, 0.764147, 0.148753, 0.187923, 0.96267, 0.989628, 1.00286] 19 -0.667048 [-0.00759029, 0.0129965, 0.0045129, 0.76076, 0.140724, 0.179633, 0.961673, 0.989159, 1.00239] 20 -0.666497 [-0.00715249, 0.013014, 0.00461163, 0.760492, 0.146616, 0.181488, 0.961694, 0.989204, 1.00255] 21 -0.666536 [-0.00671906, 0.013211, 0.00470051, 0.760447, 0.152177, 0.184149, 0.961936, 0.989419, 1.00261] 22 -0.666575 [-0.0065462, 0.0138522, 0.00466139, 0.763514, 0.151485, 0.189367, 0.96233, 0.989593, 1.00267] Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.961902 -0.00950294 0.0276398 0.00914022 0.989464 0.0132199 -0.0277619 -0.0129616 1.0022 Offset = [0.575541, 0.160776, 0.0896959] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. 0 -0.670785 [-0.0171583, 0.0142949, 0.000958846, 0.891324, 0.0190466, 0.255125, 0.957745, 0.984015, 0.987001, -0.00512721, 0.0105082, -0.00843985, -0.0126129, 0.0104742, -0.0228047] 1 -0.655497 [-0.0140475, 0.0121391, 0.00116394, 0.857298, 0.109585, 0.232939, 0.957539, 0.983423, 0.98979, -0.0050701, 0.00392484, -0.00844981, -0.0110587, 0.0059867, -0.0182074] 2 -0.663187 [-0.0107232, 0.0154851, -0.00133049, 0.771105, 0.15685, 0.220268, 0.958968, 0.983385, 0.994385, -0.00216412, 0.00530601, -0.00803348, -0.00958319, 0.00380482, -0.0135409] 3 -0.667867 [-0.0111066, 0.00902094, 0.00147721, 0.761473, 0.24137, 0.268541, 0.961826, 0.991161, 0.999538, -0.0065492, -0.00426019, -0.00993293, -0.00665445, 0.000548388, -0.0112257] 4 -0.664794 [-0.0055135, 0.0171414, -0.00378355, 0.723689, 0.230825, 0.285809, 0.961222, 0.986601, 1.00089, 0.000136709, 0.00245447, -0.0083949, -0.00560193, -0.00100172, -0.00453174] 5 -0.668018 [-0.00636359, 0.0137043, -0.00164629, 0.744732, 0.225802, 0.277485, 0.960865, 0.986936, 1.00187, -0.0020399, -0.00101989, -0.00846403, -0.00582482, -0.00102604, -0.00561698] 6 -0.671559 [-0.00735777, 0.0143965, -0.000910611, 0.743901, 0.214917, 0.282674, 0.961194, 0.986793, 1.00174, -0.00273911, -6.59348e-05, -0.00842861, -0.00536807, -0.000759631, -0.00615132] 7 -0.672288 [-0.00808119, 0.0132643, 0.00123119, 0.746812, 0.205227, 0.287069, 0.961115, 0.986558, 1.00373, -0.00449274, -4.05504e-05, -0.00805923, -0.00467188, 0.000369282, -0.00621303] 8 -0.67297 [-0.00824721, 0.0138514, 0.000931673, 0.738436, 0.197093, 0.283001, 0.961014, 0.986976, 1.00395, -0.00388873, 0.000614647, -0.00775729, -0.00414096, 0.000425025, -0.00586679] 9 -0.673017 [-0.00799864, 0.0138289, 0.000716703, 0.729702, 0.192209, 0.275567, 0.961124, 0.987051, 1.00413, -0.00342722, 0.000680723, -0.00751089, -0.00408325, 0.000498662, -0.00557167] 10 -0.673124 [-0.00820424, 0.0138254, 0.000366874, 0.720273, 0.18548, 0.270997, 0.96092, 0.987085, 1.0042, -0.00283266, 0.000803962, -0.0072689, -0.00391896, 0.000619552, -0.00562151] 11 -0.672949 [-0.00716087, 0.0123964, 0.00137142, 0.717622, 0.174533, 0.268322, 0.961764, 0.987009, 1.0056, -0.00340109, -8.54041e-05, -0.00685195, -0.00373262, 0.0011084, -0.0044252] 12 -0.673732 [-0.0079568, 0.0132042, 0.00111759, 0.722533, 0.166007, 0.261123, 0.961202, 0.987121, 1.00489, -0.0029528, 0.000814423, -0.00665682, -0.00328221, 0.00122417, -0.0047675] 13 -0.673402 [-0.00804366, 0.0135849, 0.0010655, 0.718567, 0.159277, 0.251449, 0.96091, 0.987422, 1.00467, -0.0023669, 0.000783207, -0.0061227, -0.00330325, 0.000815914, -0.00489006] 14 -0.673161 [-0.00805102, 0.0136647, 0.00111484, 0.714234, 0.155685, 0.240312, 0.960752, 0.987503, 1.00408, -0.00217717, 0.000718569, -0.00588327, -0.00335662, 0.00068865, -0.00494881] 15 -0.673031 [-0.00827122, 0.0135962, 0.00192166, 0.7062, 0.148574, 0.234311, 0.961158, 0.98789, 1.00385, -0.00261561, 0.000457207, -0.0054969, -0.00409796, 0.000495653, -0.00592275] 16 -0.673085 [-0.00707541, 0.0138073, 0.000953867, 0.69609, 0.15259, 0.22923, 0.961285, 0.987312, 1.00352, -0.00215897, 0.000911423, -0.00599974, -0.00420533, 0.000741228, -0.00480628] 17 -0.673155 [-0.00761877, 0.014065, 0.00177597, 0.687078, 0.150727, 0.237232, 0.961157, 0.987593, 1.00353, -0.00334088, 0.00171448, -0.00637097, -0.00336585, 0.00130696, -0.00450537] 18 -0.673238 [-0.00794745, 0.0138868, 0.000994661, 0.688628, 0.148477, 0.232022, 0.961031, 0.987993, 1.00362, -0.00236986, 0.00132999, -0.00618685, -0.00333903, 0.00108583, -0.0048192] 19 -0.672915 [-0.0076774, 0.013847, 0.00120378, 0.687275, 0.152323, 0.227354, 0.961008, 0.987928, 1.00373, -0.00260006, 0.00119016, -0.00620232, -0.00362747, 0.000987118, -0.0048375] 20 -0.673148 [-0.00762969, 0.0137626, 0.00122595, 0.682815, 0.152728, 0.223007, 0.961021, 0.987963, 1.00374, -0.0025551, 0.001294, -0.00613491, -0.00357447, 0.00117419, -0.00473982] 21 -0.673205 [-0.00754926, 0.0137259, 0.00136886, 0.677637, 0.153214, 0.219578, 0.961098, 0.988134, 1.00381, -0.0025735, 0.00142638, -0.0060103, -0.00348005, 0.00133991, -0.00457251] 22 -0.673301 [-0.00761061, 0.0135694, 0.0012832, 0.673798, 0.152563, 0.214761, 0.961401, 0.988311, 1.00344, -0.00227623, 0.00118727, -0.00580802, -0.00322317, 0.00125551, -0.00437941] 23 -0.673264 [-0.0074213, 0.0139244, 0.00146734, 0.670273, 0.149267, 0.210941, 0.961222, 0.988221, 1.00301, -0.00248703, 0.00150368, -0.00582564, -0.0034032, 0.00123626, -0.0043617] 24 -0.673152 [-0.0074593, 0.0138699, 0.00151693, 0.665768, 0.145062, 0.211691, 0.961517, 0.988351, 1.00319, -0.00248189, 0.00186588, -0.00576993, -0.00319983, 0.00164031, -0.00420359] 25 -0.673206 [-0.00678193, 0.0137196, 0.000562067, 0.660633, 0.143721, 0.212304, 0.961677, 0.987117, 1.00257, -0.00200446, 0.000742042, -0.00626368, -0.00335469, 0.000674382, -0.00363689] Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.9613 -0.00331456 0.0281704 -0.00532577 0.987025 0.010223 -0.0267692 -0.0171837 1.0021 Offset = [0.467725, 0.108088, 0.117551] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. 0 -0.666208 [0.970883, -0.0108305, 0.0355657, -0.00218273, 0.998325, 0.00902947, -0.00647759, -0.0219892, 1.009, 0.833396, 0.102686, 0.124871] 1 -0.65232 [0.948215, -0.00755861, 0.0133002, 0.00238239, 0.979094, -0.00609808, -0.0165384, -0.0251775, 0.993605, 0.853206, 0.200771, -0.0424571] 2 -0.649267 [0.954424, -0.00562044, 0.0215442, 0.00298398, 0.985847, -0.000547299, -0.015928, -0.0249844, 0.998231, 0.771143, 0.16383, -0.0013199] 3 -0.662293 [0.963735, -0.00197598, 0.029104, 0.00429952, 0.975897, 0.00470953, -0.0144451, -0.0185199, 1.00091, 0.684846, 0.210104, 0.00732694] 4 -0.661613 [0.962241, -0.00557342, 0.0264401, 0.0022972, 0.983627, 0.00353497, -0.0157193, -0.0203736, 1.0021, 0.723619, 0.240097, 0.0055438] 5 -0.666372 [0.962423, -0.00477501, 0.024541, 0.00228852, 0.98371, 0.00458269, -0.01693, -0.0192169, 1.00268, 0.751101, 0.247425, 0.0465625] 6 -0.666953 [0.964303, -0.0046813, 0.0260354, 0.00179056, 0.983699, 0.00542859, -0.016851, -0.018833, 1.00294, 0.754539, 0.228824, 0.0927709] 7 -0.6675 [0.963768, -0.00367112, 0.0237109, 0.00146285, 0.984039, 0.00634793, -0.0161923, -0.0177582, 1.00396, 0.792615, 0.215674, 0.122214] 8 -0.667428 [0.965421, -0.00636852, 0.0238969, 0.000542651, 0.985031, 0.00766108, -0.0159905, -0.0170604, 1.00468, 0.808964, 0.191625, 0.162707] 9 -0.66794 [0.96392, -0.00343728, 0.0248787, 0.00195439, 0.985818, 0.00872841, -0.0161544, -0.016004, 1.00267, 0.77031, 0.196452, 0.193719] 10 -0.667399 [0.963657, -0.00498211, 0.023569, 0.0013321, 0.98721, 0.0078564, -0.0156595, -0.0157458, 1.00398, 0.791336, 0.200919, 0.181324] 11 -0.668339 [0.964319, -0.00494333, 0.0240511, 0.00138238, 0.98839, 0.00878679, -0.0157493, -0.0146191, 1.00396, 0.781349, 0.207719, 0.183789] 12 -0.668335 [0.963933, -0.00627235, 0.0229544, 0.00139157, 0.989494, 0.00831047, -0.0161714, -0.0145594, 1.00288, 0.786993, 0.218417, 0.185793] 13 -0.668455 [0.964041, -0.0056427, 0.0230575, 0.00153893, 0.989685, 0.00836494, -0.0162801, -0.0143645, 1.00274, 0.777664, 0.224486, 0.180149] 14 -0.668493 [0.964141, -0.00514937, 0.0230825, 0.00158401, 0.989905, 0.00826757, -0.0163282, -0.0143305, 1.00246, 0.771307, 0.230893, 0.171525] 15 -0.668587 [0.964186, -0.00486088, 0.0229741, 0.00157401, 0.990123, 0.00805165, -0.0162678, -0.0142706, 1.00231, 0.766542, 0.238076, 0.162485] 16 -0.668701 [0.964366, -0.00477208, 0.0229308, 0.00150659, 0.990538, 0.00774715, -0.0162222, -0.0144446, 1.00249, 0.764017, 0.246293, 0.153431] 17 -0.668888 [0.964406, -0.00467793, 0.0229213, 0.00140069, 0.99087, 0.00746835, -0.0161823, -0.0146841, 1.00269, 0.761235, 0.253286, 0.143466] 18 -0.668988 [0.964446, -0.00461742, 0.0228807, 0.00132765, 0.991132, 0.00723085, -0.0161658, -0.0148832, 1.00286, 0.759009, 0.260064, 0.133211] 19 -0.66902 [0.964466, -0.00461214, 0.0228478, 0.00125637, 0.991369, 0.00703546, -0.0161382, -0.0150972, 1.00295, 0.756461, 0.266329, 0.122706] 20 -0.668978 [0.964493, -0.00461761, 0.0228402, 0.00119652, 0.99159, 0.00688389, -0.0160983, -0.0152951, 1.00301, 0.754109, 0.272242, 0.111953] 21 -0.668916 [0.964524, -0.00463553, 0.0228504, 0.00114718, 0.99176, 0.00675923, -0.0160796, -0.0154543, 1.00304, 0.75155, 0.277556, 0.100935] 22 -0.66886 [0.964545, -0.00468171, 0.0228755, 0.00109516, 0.991902, 0.00663094, -0.0160869, -0.0156094, 1.00303, 0.748934, 0.282432, 0.0897301] 23 -0.668807 [0.964555, -0.00473033, 0.0228862, 0.00103784, 0.992034, 0.00652308, -0.0160812, -0.0157565, 1.00301, 0.747038, 0.286578, 0.0780934] 24 -0.668753 [0.964537, -0.0047531, 0.0228912, 0.000989395, 0.992143, 0.00642733, -0.0160786, -0.015924, 1.00296, 0.745348, 0.290266, 0.0662723] 25 -0.668709 [0.964499, -0.00479934, 0.0228967, 0.000942669, 0.992237, 0.00635373, -0.0160804, -0.0161035, 1.00289, 0.743564, 0.29345, 0.0543195] 26 -0.668664 [0.964455, -0.00484578, 0.0229016, 0.000906657, 0.992318, 0.00628364, -0.0160917, -0.0162878, 1.0028, 0.741688, 0.296149, 0.0422618] 27 -0.668632 [0.964409, -0.0048972, 0.022928, 0.000873218, 0.992356, 0.00620432, -0.0161165, -0.0164956, 1.00272, 0.739243, 0.29813, 0.030167] 28 -0.668617 [0.964376, -0.00494049, 0.0229416, 0.000816577, 0.992442, 0.00614885, -0.0161359, -0.0166839, 1.00268, 0.736661, 0.300482, 0.0181672] 29 -0.668575 [0.964328, -0.00497923, 0.0229578, 0.000768852, 0.992532, 0.00608804, -0.0161484, -0.0168821, 1.00263, 0.734847, 0.302129, 0.00591201] 30 -0.668521 [0.964293, -0.0050464, 0.0229977, 0.000702984, 0.992648, 0.00603402, -0.0161746, -0.0170725, 1.00255, 0.733056, 0.303483, -0.0063817] 31 -0.66844 [0.964238, -0.00511886, 0.0230249, 0.000640508, 0.992794, 0.00598248, -0.0161965, -0.0172027, 1.00243, 0.730936, 0.304303, -0.0186706] 32 -0.668338 [0.964171, -0.00515914, 0.0231383, 0.000592788, 0.992941, 0.00590917, -0.0161782, -0.0173702, 1.00232, 0.729427, 0.304754, -0.0310673] 33 -0.668229 [0.964102, -0.00525883, 0.023175, 0.000552089, 0.993101, 0.00581662, -0.0161666, -0.0175334, 1.00217, 0.727854, 0.30523, -0.0434548] 34 -0.668047 [0.964038, -0.00534731, 0.0232082, 0.000512808, 0.993263, 0.00576446, -0.0161465, -0.0176642, 1.00207, 0.725123, 0.305716, -0.0556401] 35 -0.667911 [0.96395, -0.0054169, 0.0232454, 0.000483155, 0.993395, 0.00570126, -0.0161499, -0.017767, 1.00197, 0.722263, 0.305827, -0.0678056] 36 -0.667803 [0.963882, -0.00548171, 0.0232882, 0.000448403, 0.993523, 0.0056773, -0.0161733, -0.0178787, 1.00182, 0.720311, 0.305827, -0.0801497] 37 -0.667682 [0.963811, -0.00552238, 0.0233201, 0.000424389, 0.993624, 0.0056319, -0.0162422, -0.0180059, 1.00165, 0.718211, 0.305893, -0.092469] 38 -0.667559 [0.96377, -0.00555255, 0.0233288, 0.000400955, 0.993705, 0.00559415, -0.0162708, -0.0181236, 1.00149, 0.717154, 0.3051, -0.104897] 39 -0.667458 [0.963769, -0.00559254, 0.0233515, 0.000371897, 0.993747, 0.00556773, -0.0162793, -0.0182472, 1.00134, 0.716075, 0.304029, -0.117302] 40 -0.667388 [0.963774, -0.00558849, 0.0233636, 0.000352223, 0.993788, 0.00554258, -0.0162663, -0.018333, 1.00113, 0.715227, 0.302918, -0.129722] 41 -0.667319 [0.963801, -0.00560927, 0.0233508, 0.000318149, 0.993784, 0.00549675, -0.0162391, -0.0184295, 1.00094, 0.714899, 0.301504, -0.142135] 42 -0.667272 [0.963809, -0.00563314, 0.0233619, 0.000278925, 0.993766, 0.00542148, -0.0161902, -0.0185459, 1.00075, 0.714921, 0.299253, -0.154428] 43 -0.667219 [0.963818, -0.00565403, 0.0233554, 0.000243504, 0.993765, 0.00535372, -0.016155, -0.0186494, 1.00052, 0.715587, 0.296872, -0.166679] 44 -0.667147 [0.963812, -0.00563446, 0.0233795, 0.000196456, 0.993765, 0.00528924, -0.0161234, -0.0187626, 1.00033, 0.716626, 0.294182, -0.178839] 45 -0.667108 [0.96377, -0.00563185, 0.0233615, 0.0001591, 0.993813, 0.00524171, -0.0161155, -0.0188528, 1.00018, 0.717785, 0.29163, -0.191019] 46 -0.667026 [0.96374, -0.00558965, 0.0233859, 0.00013741, 0.993871, 0.0052325, -0.0160674, -0.0189161, 1.00005, 0.719291, 0.288868, -0.203116] 47 -0.666951 [0.963724, -0.00559242, 0.0234255, 0.000116752, 0.993967, 0.00518155, -0.016052, -0.0189853, 0.99996, 0.722175, 0.285252, -0.214727] 48 -0.666825 [0.963784, -0.00554846, 0.023441, 8.78224e-05, 0.994079, 0.00513075, -0.0160794, -0.0189352, 0.999907, 0.724938, 0.280557, -0.225976] 49 -0.666717 [0.96373, -0.00550401, 0.023497, 6.08886e-05, 0.994103, 0.00501529, -0.016125, -0.0188892, 0.999873, 0.726902, 0.275305, -0.237147] 50 -0.666621 [0.963691, -0.005501, 0.0235481, 2.31293e-05, 0.994173, 0.00495864, -0.0160815, -0.0188094, 0.999791, 0.729963, 0.270276, -0.248172] 51 -0.666501 [0.963676, -0.00553299, 0.0236627, 1.06304e-05, 0.99421, 0.00484617, -0.0160217, -0.0187626, 0.999647, 0.734421, 0.264342, -0.258228] 52 -0.666398 [0.963681, -0.00555938, 0.0237719, -6.07522e-06, 0.994323, 0.00476421, -0.0159335, -0.0185909, 0.9995, 0.738997, 0.258399, -0.268223] 53 -0.666274 [0.963648, -0.00552414, 0.023853, 1.65025e-05, 0.994383, 0.00464629, -0.0158183, -0.0183588, 0.999284, 0.742337, 0.252412, -0.278668] 54 -0.666168 [0.96364, -0.0054145, 0.0239537, 9.36796e-05, 0.99453, 0.00447441, -0.0156951, -0.0181006, 0.999177, 0.745957, 0.245769, -0.28861] 55 -0.665959 [0.963701, -0.00546108, 0.0240398, 0.000114789, 0.994788, 0.00435435, -0.0155776, -0.0178317, 0.999125, 0.750205, 0.237951, -0.29738] 56 -0.665613 [0.963795, -0.00529446, 0.0240563, 0.000188091, 0.995058, 0.00407035, -0.0154878, -0.0176737, 0.99907, 0.752073, 0.228202, -0.304961] 57 -0.665141 [0.963981, -0.00521681, 0.0240601, 0.000219999, 0.995431, 0.00374809, -0.0153718, -0.017681, 0.99918, 0.754267, 0.216107, -0.307163] 58 -0.664432 [0.964135, -0.0050972, 0.0240795, 0.000261421, 0.995774, 0.00340201, -0.0153257, -0.0178657, 0.999355, 0.754226, 0.203818, -0.304957] 59 -0.663662 [0.964273, -0.00494392, 0.0241116, 0.000306549, 0.996156, 0.00311936, -0.015284, -0.0180911, 0.999606, 0.753682, 0.191991, -0.300995] 60 -0.662817 [0.964337, -0.00482487, 0.024146, 0.000337537, 0.996462, 0.00291248, -0.0152578, -0.0182664, 0.99981, 0.75301, 0.180298, -0.296653] 61 -0.662073 [0.964326, -0.00472457, 0.0241354, 0.000359531, 0.996689, 0.00273679, -0.0152534, -0.0184009, 0.999956, 0.75265, 0.168627, -0.292207] 62 -0.661429 [0.964229, -0.00464227, 0.0241195, 0.000375384, 0.99685, 0.00259031, -0.0152518, -0.0184929, 1.00005, 0.752763, 0.156908, -0.287868] 63 -0.660919 [0.964069, -0.00457514, 0.024103, 0.000391193, 0.996991, 0.00243799, -0.0152438, -0.0185627, 1.00015, 0.753307, 0.145132, -0.283724] 64 -0.660423 [0.963893, -0.0045441, 0.0241423, 0.000389176, 0.997109, 0.00229985, -0.0152234, -0.0186054, 1.0002, 0.754002, 0.133407, -0.279455] 65 -0.659969 [0.963712, -0.00455119, 0.0241596, 0.000364221, 0.997165, 0.00217622, -0.0152259, -0.0186291, 1.00024, 0.754292, 0.122122, -0.274091] 66 -0.659675 [0.963499, -0.0045462, 0.0241439, 0.000353897, 0.997196, 0.00207255, -0.0152286, -0.0186094, 1.00028, 0.755413, 0.11075, -0.269031] 67 -0.659455 [0.963309, -0.00451293, 0.0242022, 0.000362661, 0.997223, 0.00197087, -0.0151928, -0.018554, 1.00032, 0.756896, 0.0993174, -0.264205] 68 -0.659258 [0.963116, -0.00458451, 0.0241814, 0.000322528, 0.997257, 0.00189614, -0.0151617, -0.0183828, 1.00036, 0.759462, 0.0881688, -0.259176] 69 -0.659104 [0.962902, -0.00474221, 0.0242294, 0.000303198, 0.997216, 0.00176548, -0.0151833, -0.0182482, 1.0004, 0.759195, 0.0772488, -0.253108] 70 -0.659132 [0.962906, -0.00487946, 0.0242192, 0.000329336, 0.997287, 0.00168836, -0.0153377, -0.0179658, 1.00054, 0.757047, 0.0665086, -0.247097] 71 -0.658969 [0.962686, -0.00492932, 0.0243664, 0.000423784, 0.997239, 0.0014223, -0.0156297, -0.0176709, 1.00058, 0.75142, 0.0569824, -0.241309] 72 -0.659074 [0.962777, -0.00536793, 0.0244959, 0.000263491, 0.997428, 0.00163082, -0.0156733, -0.0173513, 1.00063, 0.748018, 0.0455658, -0.23758] 73 -0.658649 [0.962345, -0.00511269, 0.0243475, 0.000505411, 0.99712, 0.00106788, -0.0157675, -0.017284, 1.00035, 0.75205, 0.0472828, -0.233218] Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 74 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.962345 -0.00511269 0.0243475 0.000505411 0.99712 0.00106788 -0.0157675 -0.017284 1.00035 Offset = [0.570956, 0.0477722, -0.285257] Background level guess : first place: 2 (12.1833%) second place: 3 (11.7794%) Guessed background level: 2 [AtlasCreator 21:12:23] DEBUG: Guessing background value: 2.0 Background level guess : first place: 4 (3.48106%) second place: 3 (3.37968%) Guessed background level: 4 [AtlasCreator 21:12:25] DEBUG: Guessing background value for template: 4.0 [AtlasCreator 21:12:25] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --movingVolume /Users/daniel/Desktop/ATLASCREATORTEST/originals/case2.nrrd --outputTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case2.mat --outputVolume /Users/daniel/Slicer3daniel/O6ZqLzAtlasCreator/case2.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 2.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 430 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 284 LowHigh Thresholds: [0,58.2969,284] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 341 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 1 0.999 ---> 224 LowHigh Thresholds: [1,52.1003,224] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x10f300a20) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4068 Debug: Off Observers: none Matrix: 0.99863 0.0522642 0.00273905 -0.052336 0.997261 0.0522642 4.33681e-19 -0.052336 0.99863 Offset: [2.613, -4.87842, -6.37073] Center: [-3.56396, 0.280455, 1.98482] Translation: [2.63797, -4.58893, -6.38812] Inverse: 0.99863 -0.052336 4.33681e-19 0.0522642 0.997261 -0.052336 0.00273905 0.0522642 0.99863 Singular: 0 Versor: [ -0.026168, 0.000685233, -0.026168, 0.999315 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.997767 0.0619469 -0.024987 -0.0609261 0.997351 0.0397341 0.0273822 -0.038123 0.998898 Offset = [2.03836, -5.17354, -5.39751] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.961039 0.029543 -0.0304389 -0.0285809 0.903783 0.0315721 0.031344 -0.0306737 0.968873 Offset = [1.85056, -4.96361, -4.26412] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.958691 0.0305048 -0.0325896 -0.0585983 0.900451 0.0174489 0.0149378 -0.0367051 0.967522 Offset = [1.86933, -5.10885, -4.24769] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 10 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.958939 0.0308858 -0.0323933 -0.0565761 0.898287 0.017804 0.0128888 -0.0394251 0.967965 Offset = [1.9123, -5.034, -4.33981] Background level guess : first place: 3 (20.7696%) second place: 4 (17.3754%) Guessed background level: 3 [AtlasCreator 21:17:09] DEBUG: Guessing background value: 3.0 Background level guess : first place: 4 (3.48106%) second place: 3 (3.37968%) Guessed background level: 4 [AtlasCreator 21:17:11] DEBUG: Guessing background value for template: 4.0 [AtlasCreator 21:17:11] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --movingVolume /Users/daniel/Desktop/ATLASCREATORTEST/originals/case3.nrrd --outputTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case3.mat --outputVolume /Users/daniel/Slicer3daniel/O6ZqLzAtlasCreator/case3.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 3.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 448 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 290 LowHigh Thresholds: [0,59.5312,290] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 341 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 1 0.999 ---> 224 LowHigh Thresholds: [1,52.1003,224] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x102beb3b0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4056 Debug: Off Observers: none Matrix: 0.99863 -0.052336 7.26307e-19 0.052336 0.99863 -1.38588e-17 0 1.38778e-17 1 Offset: [-2.86258, 2.16412, 2.10975] Center: [-3.56396, 0.280455, 1.98482] Translation: [-2.87237, 1.97721, 2.10975] Inverse: 0.99863 0.052336 0 -0.052336 0.99863 1.38778e-17 7.26307e-19 -1.38588e-17 1 Singular: 0 Versor: [ 6.93652e-18, 1.81639e-19, 0.0261769, 0.999657 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.999432 -0.0231344 -0.0244979 0.0228961 0.999688 -0.00996308 0.0247208 0.00939652 0.99965 Offset = [-2.77687, 0.587914, -0.0557447] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 56 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.95014 -0.0236113 -0.0356617 0.0235771 0.987573 -0.00137846 0.0356843 0.000536397 1.00205 Offset = [-3.08024, 1.16626, 0.509571] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.954511 -0.0248659 -0.0337018 0.00432806 0.99009 -0.00502656 0.000203035 -8.95525e-05 1.00055 Offset = [-2.83364, 0.757862, 0.0488222] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 11 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.955562 -0.024099 -0.0341992 0.00434602 0.98893 -0.00498486 0.000197084 1.71739e-05 0.999075 Offset = [-2.71678, 0.764924, 0.0632491] Background level guess : first place: 3 (19.8423%) second place: 4 (17.4266%) Guessed background level: 3 [AtlasCreator 21:22:02] DEBUG: Guessing background value: 3.0 Background level guess : first place: 4 (3.48106%) second place: 3 (3.37968%) Guessed background level: 4 [AtlasCreator 21:22:03] DEBUG: Guessing background value for template: 4.0 [AtlasCreator 21:22:03] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --movingVolume /Users/daniel/Desktop/ATLASCREATORTEST/originals/case5.nrrd --outputTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case5.mat --outputVolume /Users/daniel/Slicer3daniel/O6ZqLzAtlasCreator/case5.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 3.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 477 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 303 LowHigh Thresholds: [0,58.4062,303] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 341 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 1 0.999 ---> 224 LowHigh Thresholds: [1,52.1003,224] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x10f300a20) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4062 Debug: Off Observers: none Matrix: 1 -1.38018e-17 -1.45062e-18 1.38778e-17 0.994522 0.104528 0 -0.104528 0.994522 Offset: [2.23849, -0.556569, -15.2186] Center: [-3.56396, 0.280455, 1.98482] Translation: [2.23849, -0.350635, -15.2588] Inverse: 1 1.38778e-17 0 -1.38018e-17 0.994522 -0.104528 -1.45062e-18 0.104528 0.994522 Singular: 0 Versor: [ -0.052336, -3.63154e-19, 6.92938e-18, 0.99863 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 45 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.998608 -0.00147829 0.0527288 -0.00412107 0.994366 0.105925 -0.0525883 -0.105995 0.992975 Offset = [2.11237, 2.12204, -12.8411] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 97 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.99444 0.000138798 0.0597447 -0.0049677 1.00512 0.0806848 -0.0595379 -0.0808374 0.958137 Offset = [2.21881, 1.82607, -11.1025] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 50 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.990269 -0.0073211 0.0603864 -0.0191589 1.00352 0.0838841 -0.0473686 -0.0477285 0.942654 Offset = [1.91705, 1.22195, -9.88424] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.991746 -0.00550076 0.0627568 -0.0200454 1.00535 0.0810627 -0.0468557 -0.0433557 0.939277 Offset = [2.00488, 1.16461, -9.77065] Background level guess : first place: 2 (11.5244%) second place: 3 (11.1119%) Guessed background level: 2 [AtlasCreator 21:27:22] DEBUG: Guessing background value: 2.0 Background level guess : first place: 4 (3.48106%) second place: 3 (3.37968%) Guessed background level: 4 [AtlasCreator 21:27:23] DEBUG: Guessing background value for template: 4.0 [AtlasCreator 21:27:23] DEBUG: Register command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --movingVolume /Users/daniel/Desktop/ATLASCREATORTEST/originals/case8.nrrd --outputTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case8.mat --outputVolume /Users/daniel/Slicer3daniel/O6ZqLzAtlasCreator/case8.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 2.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 493 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 306 LowHigh Thresholds: [0,56.6719,306] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 341 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 1 0.999 ---> 224 LowHigh Thresholds: [1,52.1003,224] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x102beb3b0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4053 Debug: Off Observers: none Matrix: 1 0 0 0 1 0 0 0 1 Offset: [2.51132, -1.13135, 15.4668] Center: [-3.56396, 0.280455, 1.98482] Translation: [2.51132, -1.13135, 15.4668] Inverse: 1 0 0 0 1 0 0 0 1 Singular: 0 Versor: [ 0, 0, 0, 1 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 111 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.998565 -0.0530647 0.00723744 0.0531147 0.998564 -0.00691386 -0.00686017 0.00728835 0.99995 Offset = [2.34628, -2.33087, 7.86516] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.913439 -0.0501005 0.00585123 0.0500924 0.998609 0.00152938 -0.0059205 -0.00123433 1.02552 Offset = [2.00743, -2.1508, 8.10106] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.918386 -0.0472499 0.00289433 0.0208224 0.998022 0.00226229 -0.0250657 0.00330402 1.02381 Offset = [2.04552, -2.12589, 8.12555] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.918006 -0.0476174 0.00593471 0.0206792 0.998457 0.00517605 -0.024413 0.00142346 1.0245 Offset = [2.0135, -1.99528, 8.09157] [AtlasCreator 21:32:35] Waiting for Registration to complete.. [AtlasCreator 21:32:40] DEBUG: All outputs exist! [AtlasCreator 21:32:40] End of Dynamic registration.. [AtlasCreator 21:32:40] Saving template to /Users/daniel/Desktop/ATLASCREATORTEST6/template.nrrd [AtlasCreator 21:32:49] Entering Resampling Stage.. [AtlasCreator 21:32:49] Found 3D Slicer launcher at /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 [AtlasCreator 21:32:49] DEBUG: The launchCommandPrefix is /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/ Guessed background level: 0 [AtlasCreator 21:32:50] DEBUG: Guessing background value: 0.0 [AtlasCreator 21:32:50] DEBUG: Resample command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case10.nrrd --referenceVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --warpTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case10.mat --outputVolume /Users/daniel/Slicer3daniel/dHOIQSAtlasCreatorResampled/case10.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case10.nrrd Reference Volume: /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd Output Volume: /Users/daniel/Slicer3daniel/dHOIQSAtlasCreatorResampled/case10.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /Users/daniel/Desktop/ATLASCREATORTEST6/case10.mat ===================================================== Read ITK transform from text file: /Users/daniel/Desktop/ATLASCREATORTEST6/case10.mat Guessed background level: 0 [AtlasCreator 21:32:53] DEBUG: Guessing background value: 0.0 [AtlasCreator 21:32:53] DEBUG: Resample command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case12.nrrd --referenceVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --warpTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case12.mat --outputVolume /Users/daniel/Slicer3daniel/dHOIQSAtlasCreatorResampled/case12.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case12.nrrd Reference Volume: /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd Output Volume: /Users/daniel/Slicer3daniel/dHOIQSAtlasCreatorResampled/case12.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /Users/daniel/Desktop/ATLASCREATORTEST6/case12.mat ===================================================== Read ITK transform from text file: /Users/daniel/Desktop/ATLASCREATORTEST6/case12.mat Guessed background level: 0 [AtlasCreator 21:32:57] DEBUG: Guessing background value: 0.0 [AtlasCreator 21:32:57] DEBUG: Resample command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case2.nrrd --referenceVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --warpTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case2.mat --outputVolume /Users/daniel/Slicer3daniel/dHOIQSAtlasCreatorResampled/case2.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case2.nrrd Reference Volume: /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd Output Volume: /Users/daniel/Slicer3daniel/dHOIQSAtlasCreatorResampled/case2.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /Users/daniel/Desktop/ATLASCREATORTEST6/case2.mat ===================================================== Read ITK transform from text file: /Users/daniel/Desktop/ATLASCREATORTEST6/case2.mat Guessed background level: 0 [AtlasCreator 21:33:01] DEBUG: Guessing background value: 0.0 [AtlasCreator 21:33:01] DEBUG: Resample command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case3.nrrd --referenceVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --warpTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case3.mat --outputVolume /Users/daniel/Slicer3daniel/dHOIQSAtlasCreatorResampled/case3.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case3.nrrd Reference Volume: /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd Output Volume: /Users/daniel/Slicer3daniel/dHOIQSAtlasCreatorResampled/case3.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /Users/daniel/Desktop/ATLASCREATORTEST6/case3.mat ===================================================== Read ITK transform from text file: /Users/daniel/Desktop/ATLASCREATORTEST6/case3.mat Guessed background level: 0 [AtlasCreator 21:33:04] DEBUG: Guessing background value: 0.0 [AtlasCreator 21:33:04] DEBUG: Resample command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case5.nrrd --referenceVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --warpTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case5.mat --outputVolume /Users/daniel/Slicer3daniel/dHOIQSAtlasCreatorResampled/case5.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case5.nrrd Reference Volume: /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd Output Volume: /Users/daniel/Slicer3daniel/dHOIQSAtlasCreatorResampled/case5.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /Users/daniel/Desktop/ATLASCREATORTEST6/case5.mat ===================================================== Read ITK transform from text file: /Users/daniel/Desktop/ATLASCREATORTEST6/case5.mat Guessed background level: 0 [AtlasCreator 21:33:08] DEBUG: Guessing background value: 0.0 [AtlasCreator 21:33:08] DEBUG: Resample command: /Users/daniel/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /Users/daniel/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case8.nrrd --referenceVolume /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd --warpTransform /Users/daniel/Desktop/ATLASCREATORTEST6/case8.mat --outputVolume /Users/daniel/Slicer3daniel/dHOIQSAtlasCreatorResampled/case8.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /Users/daniel/Desktop/ATLASCREATORTEST/segmentations/case8.nrrd Reference Volume: /Users/daniel/Slicer3daniel/tmpMeanImage.nrrd Output Volume: /Users/daniel/Slicer3daniel/dHOIQSAtlasCreatorResampled/case8.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /Users/daniel/Desktop/ATLASCREATORTEST6/case8.mat ===================================================== Read ITK transform from text file: /Users/daniel/Desktop/ATLASCREATORTEST6/case8.mat [AtlasCreator 21:33:11] Entering Combine-To-Atlas Stage.. [AtlasCreator 21:33:13] Re-Casting atlas for label 32 to Short [AtlasCreator 21:33:15] Re-Casting atlas for label 3 to Short [AtlasCreator 21:33:18] Re-Casting atlas for label 4 to Short [AtlasCreator 21:33:20] Re-Casting atlas for label 5 to Short [AtlasCreator 21:33:22] Re-Casting atlas for label 6 to Short [AtlasCreator 21:33:25] Re-Casting atlas for label 7 to Short [AtlasCreator 21:33:27] Re-Casting atlas for label 8 to Short [AtlasCreator 21:33:30] Re-Casting atlas for label 9 to Short [AtlasCreator 21:33:32] Re-Casting atlas for label 10 to Short [AtlasCreator 21:33:35] Re-Casting atlas for label 31 to Short [AtlasCreator 21:33:36] Re-Casting atlas to Short [AtlasCreator 21:33:36] -------------------------------------------------------------------------------- [AtlasCreator 21:33:36] All Done, folks! [AtlasCreator 21:33:36] -------------------------------------------------------------------------------- Thread ID: -1