Samuel Pichardo, Ph.D
Associate Professor
Radiology and Clinical Neurosciences, Hotchkiss Brain Institute
Cumming School of Medicine,
University of Calgary
[email protected]
www.neurofus.ca

GUI application for the modeling of transcranial ultrasound for neuromodulation applications BabelBrain is a frontend application specially designed to work in tandem with neuronavigation software to perform focused ultrasound research. BabelBrain uses BabelViscoFDTD extensively for calculations. BabelViscoFDTD is optimized for multiple GPU backends (Metal, OpenCL and CUDA). In its initial inception, BabelViscoFDTD is focused on MacOS systems based on Apple ARM64 processors. However, BabelViscoFDTD can run on any system (Mac, Linux, Windows) that has a decent GPU from NVidia or AMD.

This software is provided "as is" and it is intended exclusively for research purposes.

Ready-to-use applications (no need for Python installation) for MacOS are available in the Releases section. Download, open and drag "BabelBrain" into the Applications folder. The first time you use you will be prompted to authorize to run and access directories. You may also need to authorize it in the Security settings of MacOS.

Please consult the online manual for details on instructions for use.

If you prefer to run the code in a Python environment, the requirements are roughly a clean Python 3.9-3.10 environment, a healthy XCode installation in macOS, or CUDA (up to v11.8) + Visual Studio/gcc in Windows/Linux. Consult BabelViscoFDTD for details on what is needed for the FDTD solvers

• Python 3.9-3.10. Anaconda/miniconda is recommende. - if running in Apple new ARM64 processors (M1, M1 Max, etc.), be sure to use a native ARM64 version. Consult BabelViscoFDTD for further details.
• Blender
• FSL

Be sure FSL init scripts are properly activated in your .bash_profile or .zsh_profile.

macOS/Linux: Create first and activate a new environment with some basics libraries from Conda

conda create --name babel python=3.10 numpy scipy

activate babel

In Windows only, install cupy and numba from conda install -c conda-forge cupy numba

Install the rest of dependencies with either

pip install -r requirements_mac.txt or pip install -r requirements_linux.txt or pip install -r requirements_win.txt

If running from the Github source code, just change to the BabelBrain directory and run

python BabelBrain.py

A Pyinstaller specification file is ready for use. To build the MacOS application, just change to the BabelBrain directory and run

pyinstaller BabelBrain.spec

A new application ready to use will be created at BabelBrain/BabelBrain/dist/Babelbrain.app