- 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.
- Python 3
- Minimum RAM (this is sampleCT data only): 16.0 GB (32.0 GB recommended)
- Keras, Tensorflow
How to run
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_githubcall, 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.
Sample CT data is in nifti format, and both the image width and height are 128.