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.

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.
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.