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Add Docker for PyRadiomics-dcm Labs #527

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merged 4 commits into from Sep 25, 2019
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JoostJM
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@JoostJM JoostJM commented Sep 4, 2019

Add docker, based on PyRadiomics:CLI docker and latest QIICR/dcmqi docker image to containerize DICOM -> DICOM workflow

- Based on Docker file for PyRadiomics CLI, and copy required applications from the qiicr/dcmqi docker (segimage2itkimage and tid1500writer)
- Update PyRadiomics CLI dockerfile to include bzip2-devel, which is needed to run pandas

- Fix bug in pyradiomics-dcm.py: when using dcm2niix as converter, the expected filename should be included in the commandline arguments
Setup PyRadiomics from the build context instead of cloning & installing it.
@JoostJM
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JoostJM commented Sep 4, 2019

Additionally updates the CLI dockerfile in 2 respects:

  • Build PyRadiomics from the build context instead of cloning it from git. This ensures the correct version of PyRadiomics is used when building the docker.
  • Include bzip2-devel before compiling Python. This is required to build module bz2, which in turn is required by pandas, which is used in the labs docker.

Include the resources folder and example parameters as well.
@JoostJM JoostJM merged commit 7bab402 into AIM-Harvard:master Sep 25, 2019
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