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SimpleITK Setup and Schedule

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Presentation on theme: "SimpleITK Setup and Schedule"— Presentation transcript:

1 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

2 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 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

3 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”’))

4 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.

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