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MIC-DKFZ / LIDC-IDRI-processing

Scripts for the preprocessing of LIDC-IDRI data
MIT License
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Help to guide me how to setup the MITK #19

Closed zuyuxin closed 3 years ago

zuyuxin commented 3 years ago

I downloaded the source codes and build them, I guess the MITK was not set up so that there cannot find the command 'MitkCLDicom2Nrrd -i ' and the errors below happended:

MitkCLDicom2Nrrd -i "datasets/LIDC-IDRI/raw_data/LIDC-IDRI-0101/1.3.6.1.4.1.14519.5.2.1.6279.6001.584233139051825667176600857752/01-01-2000/1.3.6.1.4.1.14519.5.2.1.6279.6001.340202188094259402036602717327/1.3.6.1.4.1.14519.5.2.1.6279.6001.238395483639894340551241543912.dcm" -o "datasets/LIDC-IDRI/nrrd/1.3.6.1.4.1.14519.5.2.1.6279.6001.584233139051825667176600857752a/1.3.6.1.4.1.14519.5.2.1.6279.6001.584233139051825667176600857752a_ct_scan.nrrd" Traceback (most recent call last): File "lidc_data_to_nifti.py", line 376, in parse_xml_file(xml_file) File "lidc_data_to_nifti.py", line 350, in parse_xml_file spacing, origin = get_spacing_and_origin(nrrd_file) File "lidc_data_to_nifti.py", line 97, in get_spacing_and_origin image=sitk.ReadImage(file) File "anaconda3/envs/venv/lib/python3.6/site-packages/SimpleITK/extra.py", line 346, in ReadImage return reader.Execute() File "anaconda3/envs/venv/lib/python3.6/site-packages/SimpleITK/SimpleITK.py", line 5779, in Execute return _SimpleITK.ImageFileReader_Execute(self) RuntimeError: Exception thrown in SimpleITK ImageFileReader_Execute: /tmp/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:97: sitk::ERROR: The file "datasets/LIDC-IDRI/nrrd/1.3.6.1.4.1.14519.5.2.1.6279.6001.584233139051825667176600857752a/1.3.6.1.4.1.14519.5.2.1.6279.6001.584233139051825667176600857752a_ct_scan.nrrd" does not exist.

please help me how to sovle it. I could not find the guides to setup the MITK on ubantu server.