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RadiologyFeatureExtraction

Requirements

  • A database in Common Data Model version 5 in one of these platforms: SQL Server, Oracle, PostgreSQL, IBM Netezza, Apache Impala, Amazon RedShift, or Microsoft APS.
  • R version 3.5.0 or newer
  • On Windows: RTools
  • Java (openjdk 1.8 recommended)
  • 25 GB of free disk space

See this video for instructions on how to set up the R environment on Windows.

Learning Requirements

  • Python 3
  • Minimum RAM (this is sampleCT data only): 16.0 GB (32.0 GB recommended)
  • Keras, Tensorflow

How to run

  1. In R, use the following code to install the dependencies:

    library(devtools)
    install_github("ohdsi/SqlRender", ref = "v1.5.2")
    install_github("ohdsi/DatabaseConnector", ref = "v2.2.0")
      
    #Install EBImage
    source("http://bioconductor.org/biocLite.R")
    biocLite("EBImage")

    If you experience problems on Windows where rJava can't find Java, one solution may be to add args = "--no-multiarch" to each install_github call, for example:

    install_github("ohdsi/SqlRender", args = "--no-multiarch")

    Alternatively, ensure that you have installed both 32-bit and 64-bit JDK versions, as mentioned in the video tutorial.

  2. If you want to use Sample CT provided by this project, please use the code below.

    load(file.path(getwd(), 'extra/sampleCT.rda'))

    Sample CT data is in nifti format, and both the image width and height are 128.

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