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SimpleITK R Notebooks

Setting Up an R Environment with Dependencies

  1. Install R on your machine.
  2. Install the Jupyter environment.
  3. Install the R kernel for Jupyter.
  4. Install the following R packages, at the R prompt: install.packages(c("reticulate", "scatterplot3d", "tidyr", "ggplot2", "xtable", "purrr")).

Install SimpleITK

A remotes based installer is available on github. It requires that you have the CMake tool and the git version control system installed on your machine.

A manual approach to compiling and installing SimpleITK with the R wrapping turned on is described here.

Downloading Data

The data is automatically downloaded to the "Data" directory when you execute the notebooks.

Alternatively, to download all the data before hand (assumes Python is available):

cd SimpleITK-Notebooks
./downloaddata.py Data/ Data/manifest.json

Working offline

In some situations, such as a tutorial session, you may not have internet access. This requires that you:

  1. Download the data in advance - see above.

View Static Converted Pages

Static views of all pages are available on the html site of this repository.