BabelBrain v0.3.0

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.

Disclaimer

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

Hardware requirements

• A decent GPU (AMD, Nvidia or Apple Silicon). For AMD and Nvidia GPUs, 4 GB or more is highly recommended. For Apple Silicon, M1 Max/Ultra or M2 Max with 16 GB RAM or more is highly recommended. Intel-based Mac systems need a dedicated AMD GPU (internal or external). Intel-based iMac Pro and MacPro systems have internal GPUs suitable for sub 650 kHz simulations (i.e., Vega 56, Vega 64). An external GPU (i.e., AMD W6800 Pro) offers excellent performance and capability for high-frequency simulations.
• 16 GB RAM or more for main CPU memory for Intel-based systems.

Standalone application

Ready-to-use applications (no need for Python installation) for macOS and Windows are available in the Releases section.

• For macOS, download the correct DMG image according to your CPU architecture (Intel X64 or ARM64), and double-click the PKG installer. The first time you use you will be prompted to authorize to run and access directories.
• For Windows, download the MSI file and run the installer.

Note for Windows: CUDA 11.7 or up must be installed.

Instructions for use

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

Manual Installation for Development

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 recommended. - 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 installed

Recommended settings

• All OS: create a conda environment using the appropriate yaml file.

Running

If running from the GitHub source code, just change to the BabelBrain directory and execute

python BabelBrain.py

Building an standalone application

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

pyinstaller BabelBrain.spec --noconfirm

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

Citation

If you find BabelBrain useful for your research, please consider adding a citation to:
Pichardo S. BabelBrain: An Open-Source Application for Prospective Modeling of Transcranial Focused Ultrasound for Neuromodulation Applications.
IEEE Trans Ultrason Ferroelectr Freq Control. 2023 Jul;70(7):587-599.
doi: 10.1109/TUFFC.2023.3274046. Epub 2023 Jun 29. PMID: 37155375.

Version log

• 0.3.0 - Nov 5, 2023

  • New: Add checkboxes to hide marks on plots.
  • New: Replace labels in Step 3 with a table to organize better output metrics.
  • New: Add metrics in Step 3 of temperature and thermal dose at the target, which often does match the maximal temperature in the brain. Also, a metric of distance from maximal peak intensity in the brain to the target.
  • Fix an issue with display results in Step 3. Results were scaled to the intensity at the target instead of maximal intensity in the brain region, as done when calculating the required Isppa in water.
  • Fix an issue with the display results of the H317 Transducer.
  • Fix the remaining "bleeding" of the skin label in the brain region.
  • Fix NaN calculations when the target is accidentally in the brain region.
  • Fix passing version to macOS bundle.

• 0.2.9-b - Oct 14, 2023

  • macOS applications are now fully signed, and no more warnings from macOS Gatekeeper appear.
  • PKG installer in macOS DMG distribution files replaces the "drag" macOS app into the application.
  • Use of latest pyinstaller library (6.1.0) and new scripts to sign macOS applications.
  • Small fix for Step 3 the AllCombinations file that was not saving correctly an index based on the combinations of DC, PRF and duration.

• 0.2.9-a - Sep 21, 2023

  • Add fix for Apple Silicon systems with latest versions of MacOS. In some systems, occasional crashes were occurring. Fix was addressed at the underlying library at https://github.com/ProteusMRIgHIFU/py-metal-compute.
  • Address slow BHTE calculations in Step 3 in external AMD GPUs in Apple X64 system. Fix done in underlying library BabelViscoFDTD 1.0.1
  • Extra GPU optimizations in Step 1
  • Correct handling of dark mode display settings

• 0.2.9 - Aug 1, 2023

  • Add scrolling of imaging planes of acoustic fields in Step 2
  • Add the possibility in Step 2 of adjusting the positioning of the transducer to recreate the transducer pressed on the scalp. Use with caution. The processing will remove tissue layers. Limited to 10 mm.
  • Add multiple behind-the-scenes new GPU code to accelerate calculations for Step 1. Because now operations are float32, some very minor differences can be expected for the produced mask for simulations with previous versions.

• 0.2.7 - May 3, 2023

  • New devices as detailed in Schafer et al.
  • Option to show water-only modeling results added in Step 2
  • Adjustment of Z mechanical for CTX 500 device added for scenarios where a pad is added
  • New Nifti output (with extension _Sub_NORM.nii.gz) containing normalized pressure output (0 to 1.0) in the brain region. All other tissue regions are set to 0. This simplifies visualization and thresholding in tools such as fsleyes.

• 0.2.6 - Apr 8, 2023:

  • Windows standalone available
  • BUG fix: Issue #14 - Reduced precision with single Elem Tx with high F#
  • BUG fix: Issue #13 - Inadequate use of SimpleITK SetSpacing to create isotropic scans
  • Minor bugs for minimal requirements

• 0.2.5-1. March 15, 2023:

  • BUG fix: Issue #7 - Matplotlib backends are now included in macOS application
  • BUG fix: Remove CPU from engine

• 0.2.5 - Jan 10, 2023:

  • First public release