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MIC-DKFZ / LIDC-IDRI-processing

Scripts for the preprocessing of LIDC-IDRI data
MIT License
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Warnings and segmentation fault in MITK #24

Open EloySchultz opened 1 year ago

EloySchultz commented 1 year ago

I get the following output when from the lidc_data_to_nifti script. (from line 86). I do not see where I am going wrong...

/home/eloy/Desktop/LUNG_DATA/Phenotyping/MITK-2016.11.99_r5cccf9-linux64/MitkCLDicom2Nrrd.sh -i "/home/eloy/Desktop/LUNG_DATA/manifest-1600709154662/LIDC-IDRI/LIDC-IDRI-0332/1.3.6.1.4.1.14519.5.2.1.6279.6001.124508094927772723365648607398/1.3.6.1.4.1.14519.5.2.1.6279.6001.316900421002460665752357657094/1-011.dcm" -o "/home/eloy/Desktop/LUNG_DATA/NIFTI/Output_nifti/0332c/0332c_ct_scan.nrrd"
!Wed Aug  2 20:58:30 2023 
0.027! WARNING: In load_impl at /home/mgoetz/radiomics/mitk/Modules/CppMicroServices/core/src/util/usUtils.cpp:76 : libicuuc.so.52: cannot open shared object file: No such file or directory
!0.027! WARNING: In AutoLoadModulesFromPath at /home/mgoetz/radiomics/mitk/Modules/CppMicroServices/core/src/util/usUtils.cpp:176 : Auto-loading of module /home/eloy/Desktop/LUNG_DATA/Phenotyping/MITK-2016.11.99_r5cccf9-linux64/bin/MitkCore/libMitkDICOMReaderServices.so failed.
!0.044! WARNING: In load_impl at /home/mgoetz/radiomics/mitk/Modules/CppMicroServices/core/src/util/usUtils.cpp:76 : libicuuc.so.52: cannot open shared object file: No such file or directory
!0.044! WARNING: In AutoLoadModulesFromPath at /home/mgoetz/radiomics/mitk/Modules/CppMicroServices/core/src/util/usUtils.cpp:176 : Auto-loading of module /home/eloy/Desktop/LUNG_DATA/Phenotyping/MITK-2016.11.99_r5cccf9-linux64/bin/MitkCore/libMitkDicomRTIO.so failed.
!0.056! WARNING: In load_impl at /home/mgoetz/radiomics/mitk/Modules/CppMicroServices/core/src/util/usUtils.cpp:76 : libicuuc.so.52: cannot open shared object file: No such file or directory
!0.056! WARNING: In AutoLoadModulesFromPath at /home/mgoetz/radiomics/mitk/Modules/CppMicroServices/core/src/util/usUtils.cpp:176 : Auto-loading of module /home/eloy/Desktop/LUNG_DATA/Phenotyping/MITK-2016.11.99_r5cccf9-linux64/bin/MitkCore/libMitkCESTIO.so failed.
!0.057! WARNING: In load_impl at /home/mgoetz/radiomics/mitk/Modules/CppMicroServices/core/src/util/usUtils.cpp:76 : libicuuc.so.52: cannot open shared object file: No such file or directory
!0.057! WARNING: In AutoLoadModulesFromPath at /home/mgoetz/radiomics/mitk/Modules/CppMicroServices/core/src/util/usUtils.cpp:176 : Auto-loading of module /home/eloy/Desktop/LUNG_DATA/Phenotyping/MITK-2016.11.99_r5cccf9-linux64/bin/MitkCore/libMitkDiffusionCoreIO.so failed.
!0.059! WARNING: In load_impl at /home/mgoetz/radiomics/mitk/Modules/CppMicroServices/core/src/util/usUtils.cpp:76 : libicuuc.so.52: cannot open shared object file: No such file or directory
!0.059! WARNING: In AutoLoadModulesFromPath at /home/mgoetz/radiomics/mitk/Modules/CppMicroServices/core/src/util/usUtils.cpp:176 : Auto-loading of module /home/eloy/Desktop/LUNG_DATA/Phenotyping/MITK-2016.11.99_r5cccf9-linux64/bin/MitkCore/libMitkMultilabelIO.so failed.
!0.060! WARNING: In load_impl at /home/mgoetz/radiomics/mitk/Modules/CppMicroServices/core/src/util/usUtils.cpp:76 : libpng12.so.0: cannot open shared object file: No such file or directory
!0.060! WARNING: In AutoLoadModulesFromPath at /home/mgoetz/radiomics/mitk/Modules/CppMicroServices/core/src/util/usUtils.cpp:176 : Auto-loading of module /home/eloy/Desktop/LUNG_DATA/Phenotyping/MITK-2016.11.99_r5cccf9-linux64/bin/MitkCore/libMitkDiffusionIO.so failed.
Running Command Line Utility *Dicom Loader*
[0.061] DICOM Modality is CT
Segmentation fault (core dumped)

Please let me know what could be the issue. I do see that MITK is referring to /home/mgoetz which is of course not right, but I do not see a place where I can change these paths. To be clear, all paths in lidc_data_to_nifti.py have been configured properly.

ltmyr commented 7 months ago

Hello ! did you solve this issue ? (I have the same)