help > Sample data+output
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Sep 16, 2019  11:09 AM | Rikki Choi - Brigham Young University
Sample data+output
We have been running into multiple errors running the pipeline and have not been able to see successful results with our data. Can anyone who has been able to run the pipeline provide sample output messages and errors/warnings, if any?
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  
Sep 27, 2019  06:09 AM | Martin Styner
RE: Sample data+output
I just posted an example 1 year old case in the download section.

Re Qt: XKEYBOARD and QMetaObject/QObject: not sure, possible QT version issue, but as long as it works, you should be fine

Also, as mentioned in other posts, ABC will always yield an error that you can safely disregard (it can't find a file, which it then creates, this should not be an error and more be an FYI)

Martin
Sep 28, 2019  01:09 PM | petemade
RE: Sample data+output
Thank you for taking the time to provide the sample files with output! They have been both helpful and instructive!
Oct 2, 2019  08:10 PM | Rikki Choi - Brigham Young University
RE: Sample data+output
Thank you so much for the responses! We will put them into use!
Oct 15, 2019  10:10 AM | petemade
RE: Sample data+output
Hi,

When I ran the One-Year-Old-Example file through Auto_EACSF, I received an output image (see attached) that looked a little different from the provided output (so unsurprisingly, the stats on the files were also different). Thus, I was wondering what masks, templates, etc. were used as input for the One-Year-Old-Example.

Thanks,
Maddy
Oct 15, 2019  11:10 AM | Martin Styner
RE: Sample data+output
Hi Maddy, not sure whether the upload worked, but the nrrd file is all empty when I download it. 

In the json file in the 1year example (in the download section) you can see how I set those settings. You need to adjust the paths, but the templates and the corresponding atlases & templates are in the document section => Atlases 

Martin