SimpleITK Setup and Schedule 1Hans J. Johnson, 2,4Bradley C. Lowekamp, 2,3Ziv Yaniv 1The University of Iowa 2National Institutes of Health 3TAJ Technologies Inc. 4MSC LLC

Setup Download and install the Fiji image viewer (Win: the user directory [C:\Users\your name\], Linux: ~/bin, Mac: /Applications). Download and install the Anaconda Python 3.6 version for your operating system. We assume it is installed in a directory named anaconda3. On Windows: open the Anaconda Prompt (found under the Anaconda3 start menu). On Linux/Mac: on the command line source path_to_anaconda3/bin/activate base Update the root anaconda environment and install the git version control system into it. conda update conda conda update anaconda conda install git Clone the repository: git clone https://github.com/SimpleITK/ISBI2018_TUTORIAL.git Create the virtual environment containing all packages required for the course: conda env create -f ISBI2018_TUTORIAL/python/environment.yml Activate the virtual environment (Win: open the Anaconda Prompt, Linux/Mac: commandline): conda activate sitkISBI18

Setup Continue with Python: On the command line: jupyter nbextension enable --py --sys-prefix widgetsnbextension Go over the setup notebook (requires internet connectivity): jupyter notebook ISBI2018_TUTORIAL/python/setup.ipynb Continue with R (only OS X and Linux), assumes CMake, git and a compiler are in your path: Install R on your machine. From the R prompt (appropriate number of parallel jobs, MAKEJ, depends on your specific machine): install.packages(c("devtools", "rPython", "plot3D", "tidyr", "ggplot2", "purrr")) devtools::install_github('IRkernel/IRkernel') IRkernel::installspec() devtools::install_github("SimpleITK/SimpleITKRInstaller", args=c('--configure-vars="MAKEJ=6”’))

Schedule [1:30PM- 2:00PM] history and overview of SimpleITK. [2:00PM- 2:30PM] spatial transformations. [2:30PM- 3:00PM] images and resampling. [3:15PM - 3:45PM] data augmentation for deep learning. [3:45PM - 4:30PM] basic registration. [4:30PM - 5:15PM] advanced registration. [5:15PM - 5:30PM] notebook development and testing, concluding remarks.