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.