help > RE: Sample data+output
Sep 18, 2019  12:09 PM | cccoleman
RE: Sample data+output
Can anyone who has been able to run the pipeline provide sample output messages and errors/warnings, if any?


We consistently  get Qt: XKEYBOARD and QMetaObject/QObject errors, but it works despite these.

When I run:
./Auto_EACSF --t1 /data/proj/app/pipeline/eacsf/Outputs/109956-100/ACPC109956-100.nii  --param /data/proj/app/pipeline/eacsf/config_17Aug2019.json --output_dir /data/proj/app/pipeline/eacsf/Outputs/109956-100

I get the following output:  

Qt: XKEYBOARD extension not present on the X server.
QMetaObject::connectSlotsByName: Connecting slot on_doubleSpinBox_TransformationStep_valueChanged() with the first of the following compatible signals: ("valueChanged(double)", "valueChanged(QString)")
QObject::connect: No such slot CSFWindow::prc_started()
QObject::connect: (receiver name: 'CSFWindow')
>>> Running main_script.py

>>> main_script.py : Running /data/proj/app/pipeline/eacsf/Outputs/109956-100/PythonScripts/rigid_align_script.py
>>> rigid_align_script.py : Running: /data/proj/app/pipeline/eacsf/Auto_EACSF_v1.4.1/bin/BRAINSFit --fixedVolume /data/proj/app/pipeline/eacsf/Atlases/TissueSegmentation_Atlases/1year-Average-IBIS-MNI-t1w.nrrd --movingVolume /data/proj/app/pipeline/eacsf/Outputs/109956-100/ACPC109956-100.nii --outputVolume /data/proj/app/pipeline/eacsf/Outputs/109956-100/RigidRegistration/ACPC109956-100_stx.nrrd --useRigid --initializeTransformMode useCenterOfHeadAlign --outputVolumePixelType short
Original Fixed image origin[0, 0, 0, 0]
TranformTypes: Rigid(1 of 1).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 7221032
833 ValidHistogramsEntries, 7221032 TotalFrequency
0.001 ---> 0
0.999 ---> 696
LowHigh Thresholds: [207,2147483647]
maxSIDirection = 109
Computing Sampled Distance Computations
ListSample TotalFrequency is 7261212
938 ValidHistogramsEntries, 7261212 TotalFrequency
0.001 ---> 0
0.999 ---> 861
LowHigh Thresholds: [289,2147483647]
maxSIDirection = 158
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x280c4b0)
RTTI typeinfo: itk::VersorRigid3DTransform
Reference Count: 2
Modified Time: 3593
Debug: Off
Object Name:
Observers:
none
Matrix:
1 -1.35745e-17 -2.88535e-18
1.38778e-17 0.978148 0.207912
-1.92593e-34 -0.207912 0.978148
Offset: [95.2278, 129.981, -80.1407]
Center: [-97.5, -121.105, 64.8263]
Translation: [95.2278, 146.106, -56.3782]
Inverse:
1 1.38778e-17 -1.92593e-34
-1.35745e-17 0.978148 -0.207912
-2.88535e-18 0.207912 0.978148
Singular: 0
Versor: [ -0.104528, -7.25312e-19, 6.90088e-18, 0.994522 ]
===============================================
=============================== ITKv4 Registration: Starting Transform Estimations for Rigid(1 of 1).===============================
0 -0.602821 [ -0.105378 0.00165885 -0.00179241 95.2205 146.065 -56.4048 ]
1 -0.603753 [ -0.105203 0.00102208 -0.00383934 95.2108 146.017 -56.417 ]
2 -0.604963 [ -0.106355 0.00190251 -0.00412827 95.1937 145.971 -56.4248 ]
3 -0.604965 [ -0.106331 0.000573846 -0.002693 95.1733 145.941 -56.3906 ]
4 -0.604794 [ -0.104333 0.00362968 -0.00580743 95.154 145.897 -56.3836 ]
5 -0.602395 [ -0.10557 0.00132302 -0.00317764 95.1511 145.92 -56.3848 ]
6 -0.605469 [ -0.106042 0.00133856 -0.00347975 95.1466 145.909 -56.3832 ]
7 -0.605626 [ -0.106007 0.00156685 -0.00351755 95.1388 145.904 -56.3747 ]
8 -0.605657 [ -0.106383 0.000939925 -0.00323028 95.131 145.902 -56.3653 ]
9 -0.605509 [ -0.105906 0.00173338 -0.00378766 95.1322 145.89 -56.365 ]
10 -0.605563 [ -0.10622 0.00132545 -0.00335345 95.1297 145.895 -56.3636 ]
11 -0.605665 [ -0.106104 0.00142704 -0.00345414 95.1293 145.892 -56.3642 ]
12 -0.605681 [ -0.106067 0.00145339 -0.00342412 95.1281 145.889 -56.3648 ]
13 -0.605681 [ -0.106074 0.00143538 -0.00338464 95.1266 145.887 -56.3651 ]
14 -0.605682 [ -0.106061 0.00144564 -0.00338462 95.1253 145.884 -56.3655 ]
15 -0.605673 [ -0.106072 0.00143996 -0.00335695 95.1239 145.881 -56.3656 ]
16 -0.605667 [ -0.106071 0.00144602 -0.00334996 95.1226 145.878 -56.3657 ]
17 -0.605671 [ -0.106079 0.00144623 -0.00333095 95.1212 145.875 -56.3657 ]
18 -0.605685 [ -0.106085 0.00145119 -0.00331819 95.1198 145.872 -56.3657 ]
19 -0.605689 [ -0.106094 0.00145508 -0.0033022 95.1185 145.87 -56.3656 ]
20 -0.605693 [ -0.106102 0.0014597 -0.00328748 95.1171 145.867 -56.3655 ]
21 -0.605685 [ -0.10611 0.00146389 -0.00327158 95.1157 145.864 -56.3654 ]
22 -0.605701 [ -0.106119 0.00146863 -0.00325476 95.1144 145.861 -56.3653 ]
23 -0.605706 [ -0.106127 0.00147395 -0.00323716 95.1131 145.858 -56.3652 ]
24 -0.605706 [ -0.106137 0.00147915 -0.00321972 95.1118 145.856 -56.3651 ]
25 -0.60571 [ -0.106147 0.00148424 -0.00320012 95.1105 145.853 -56.3651 ]
26 -0.605711 [ -0.106157 0.00148976 -0.00317902 95.1092 145.85 -56.3651 ]
27 -0.6057 [ -0.106168 0.00149572 -0.00315661 95.108 145.847 -56.3652 ]
28 -0.605688 [ -0.106179 0.00150234 -0.00313281 95.1068 145.844 -56.3653 ]
29 -0.605689 [ -0.10619 0.00150862 -0.00310764 95.1055 145.841 -56.3656 ]
30 -0.605675 [ -0.106201 0.00151431 -0.00308208 95.1043 145.838 -56.3659 ]
31 -0.605675 [ -0.106214 0.00152058 -0.00305632 95.1031 145.836 -56.3663 ]
32 -0.605673 [ -0.106227 0.00152499 -0.00303145 95.1019 145.833 -56.3669 ]
33 -0.605673 [ -0.106237 0.00152693 -0.00300814 95.1008 145.83 -56.3675 ]
34 -0.605674 [ -0.106246 0.00152702 -0.00298646 95.0997 145.827 -56.3683 ]
35 -0.60568 [ -0.106255 0.00152637 -0.00296702 95.0987 145.824 -56.3691 ]
36 -0.605686 [ -0.106263 0.00152555 -0.00295226 95.0977 145.821 -56.37 ]
37 -0.605703 [ -0.106274 0.00152509 -0.00293636 95.0967 145.819 -56.3709 ]
38 -0.605705 [ -0.106284 0.00152427 -0.00292218 95.0957 145.816 -56.3719 ]
39 -0.605694 [ -0.106296 0.00152252 -0.00290811 95.0947 145.813 -56.3728 ]
40 -0.605682 [ -0.106307 0.0015215 -0.00289481 95.0937 145.81 -56.3737 ]
41 -0.605679 [ -0.106318 0.00152029 -0.00288238 95.0927 145.807 -56.3747 ]
42 -0.605676 [ -0.106328 0.0015191 -0.00287064 95.0917 145.805 -56.3756 ]
43 -0.605672 [ -0.10634 0.00151809 -0.00285955 95.0907 145.802 -56.3765 ]
44 -0.605666 [ -0.106353 0.00151685 -0.00284907 95.0897 145.799 -56.3774 ]
45 -0.60566 [ -0.106367 0.00151583 -0.00284007 95.0888 145.796 -56.3783 ]
46 -0.605658 [ -0.106382 0.00151522 -0.00283176 95.0879 145.793 -56.3791 ]
47 -0.605647 [ -0.106397 0.00151421 -0.00282379 95.0871 145.79 -56.38 ]
48 -0.605647 [ -0.106413 0.00151328 -0.00281711 95.0863 145.787 -56.3808 ]
49 -0.605634 [ -0.10643 0.00151197 -0.00281109 95.0856 145.784 -56.3816 ]
50 -0.605636 [ -0.106448 0.00151046 -0.00280581 95.0849 145.781 -56.3824 ]
51 -0.605648 [ -0.106465 0.00150902 -0.00280133 95.0843 145.778 -56.3833 ]
52 -0.605637 [ -0.106483 0.00150827 -0.00279771 95.0838 145.776 -56.3841 ]
53 -0.605635 [ -0.106501 0.00150863 -0.00279452 95.0832 145.773 -56.385 ]
54 -0.605631 [ -0.106519 0.00150906 -0.00279194 95.0828 145.77 -56.3859 ]
55 -0.605625 [ -0.106536 0.00150912 -0.00279059 95.0824 145.767 -56.3868 ]
56 -0.605632 [ -0.106552 0.00150885 -0.00279007 95.082 145.764 -56.3877 ]
57 -0.60563 [ -0.106569 0.00150754 -0.00279114 95.0818 145.761 -56.3886 ]
58 -0.605634 [ -0.106585 0.00150488 -0.00279386 95.0817 145.758 -56.3896 ]
59 -0.605639 [ -0.106603 0.0015011 -0.00279823 95.0817 145.755 -56.3905 ]
60 -0.605645 [ -0.106622 0.00149672 -0.00280444 95.0818 145.752 -56.3916 ]
61 -0.605649 [ -0.106641 0.00149188 -0.00281193 95.0819 145.749 -56.3926 ]
62 -0.605653 [ -0.10666 0.00148647 -0.00282019 95.0822 145.746 -56.3937 ]
63 -0.605632 [ -0.106675 0.00148109 -0.00282944 95.0826 145.743 -56.3948 ]
64 -0.605613 [ -0.10669 0.00147633 -0.00283694 95.0831 145.74 -56.396 ]
65 -0.605618 [ -0.106706 0.00147217 -0.00284486 95.0836 145.737 -56.3973 ]
66 -0.605624 [ -0.106722 0.00146799 -0.00285201 95.0843 145.735 -56.3986 ]
67 -0.605629 [ -0.106738 0.00146443 -0.00285904 95.085 145.732 -56.3999 ]
68 -0.605633 [ -0.106754 0.00146222 -0.00286546 95.0857 145.729 -56.4013 ]
69 -0.605636 [ -0.106769 0.00146124 -0.00287096 95.0865 145.727 -56.4028 ]
70 -0.605625 [ -0.106783 0.00146064 -0.00287535 95.0874 145.724 -56.4044 ]
71 -0.605631 [ -0.106796 0.00146269 -0.00288022 95.0883 145.722 -56.4061 ]
72 -0.605648 [ -0.106806 0.00146633 -0.00288179 95.0891 145.719 -56.4078 ]
73 -0.605667 [ -0.106814 0.00147321 -0.00288282 95.09 145.717 -56.4097 ]
74 -0.605671 [ -0.10682 0.00148123 -0.00287961 95.0908 145.715 -56.4117 ]
75 -0.605675 [ -0.106824 0.00149257 -0.00287851 95.0915 145.712 -56.4139 ]
76 -0.605677 [ -0.106827 0.00150235 -0.00287314 95.0922 145.71 -56.4162 ]
77 -0.60568 [ -0.106827 0.00151721 -0.00287519 95.0929 145.709 -56.4186 ]
78 -0.605681 [ -0.106827 0.00152572 -0.00286536 95.0936 145.707 -56.4212 ]
79 -0.605685 [ -0.106824 0.00154596 -0.0028722 95.0942 145.705 -56.4238 ]
80 -0.605685 [ -0.106825 0.00155098 -0.00285526 95.0949 145.704 -56.4266 ]
81 -0.605689 [ -0.106821 0.0015763 -0.00286913 95.0955 145.703 -56.4292 ]
82 -0.605697 [ -0.106824 0.00157769 -0.0028464 95.0962 145.701 -56.4321 ]
83 -0.605714 [ -0.106821 0.0016077 -0.00286542 95.0968 145.7 -56.4348 ]
84 -0.605695 [ -0.106825 0.00160533 -0.00283813 95.0974 145.699 -56.4377 ]
85 -0.605714 [ -0.106822 0.00163902 -0.00286157 95.098 145.698 -56.4405 ]
86 -0.605721 [ -0.106825 0.00163407 -0.00282608 95.0986 145.697 -56.4434 ]
87 -0.605728 [ -0.10682 0.0016742 -0.00285501 95.0992 145.696 -56.4462 ]
88 -0.605726 [ -0.10683 0.00166332 -0.0028099 95.0996 145.695 -56.4492 ]
89 -0.605723 [ -0.106822 0.00171561 -0.00285499 95.1001 145.694 -56.452 ]
90 -0.605701 [ -0.106842 0.00168126 -0.0027802 95.1004 145.693 -56.4551 ]
91 -0.605705 [ -0.106812 0.00180421 -0.0029167 95.1008 145.691 -56.4577 ]
92 -0.605638 [ -0.106874 0.00165443 -0.00270362 95.1009 145.691 -56.4608 ]
93 -0.605702 [ -0.106802 0.00186061 -0.00296684 95.1009 145.69 -56.4604 ]
Stop condition from optimizer.RegularStepGradientDescentOptimizerv4: Step too small after 94 iterations. Current step (0.00078125) is less than minimum step (0.001).
/data/proj/app/pipeline/eacsf/Auto_EACSF_v1.4.1/bin/BRAINSFit : exit with success
>>> main_script.py : Finished running /data/proj/app/pipeline/eacsf/Outputs/109956-100/PythonScripts/rigid_align_script.py
>>> main_script.py : Running /data/proj/app/pipeline/eacsf/Outputs/109956-100/PythonScripts/make_mask_script.py
>>> make_mask_script.py : Running: /data/proj/app/pipeline/eacsf/Auto_EACSF_v1.4.1/bin/convertITKformats /data/proj/app/pipeline/eacsf/Outputs/109956-100/RigidRegistration/ACPC109956-100_stx.nrrd /data/proj/app/pipeline/eacsf/Outputs/109956-100/RigidRegistration/ACPC109956-100_stx.nii.gz
/data/proj/app/pipeline/eacsf/Auto_EACSF_v1.4.1/bin/convertITKformats : exit with success
>>> make_mask_script.py : Running: /data/proj/app/pipeline/eacsf/Auto_EACSF_v1.4.1/bin/ANTS 3 -m CC[/data/proj/app/pipeline/eacsf/Outputs/109956-100/RigidRegistration/ACPC109956-100_stx.nii.gz,/data/proj/app/pipeline/eacsf/Atlases/SkullStripping_Atlases/Colin27_T1.nrrd,1,4] -i 100x50x25 -o /data/proj/app/pipeline/eacsf/Outputs/109956-100/SkullStripping/ACPC109956-100_stx_Colin27_ -t SyN[0.25] -r Gauss[3,0]



..... lots more  

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TitleAuthorDate
Rikki Choi Sep 16, 2019
petemade Oct 15, 2019
Martin Styner Oct 15, 2019
Rikki Choi Oct 2, 2019
RE: Sample data+output
cccoleman Sep 18, 2019
Martin Styner Sep 27, 2019
petemade Sep 28, 2019