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

Setup Download and install the Fiji image viewer. This is the default image viewer used by SimpleITK. 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 root 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/SPIE2018_COURSE.git

Setup Create the virtual environment containing all packages required for the course: conda env create -f SPIE2018_COURSE/environment.yml Activate the virtual environment: On Windows: open the Anaconda Prompt (found under the Anaconda3 start menu) activate sitkpySPIE18. On Linux/Mac: on the command line source path_to_anaconda3/bin/activate sitkpySPIE18 Go over the setup notebook (requires internet connectivity): cd SPIE2018_COURSE jupyter notebook setup.ipynb

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.