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spichardo committed Apr 6, 2024
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Expand Up @@ -78,7 +78,8 @@ doi: [10.1109/TUFFC.2023.3274046](https://doi.org/10.1109/TUFFC.2023.3274046). E
- New: Possibility to update thermal profile in Step 3. The initial design of BabelBrain assumed that the parameters of the timing of LIFU exposures would vary little in a study. That is why it is asked as initial input when initiating BabelBrain. However, some users have expressed their need to have more flexibility to explore variated settings without having to restart BabelBrain. For this purpose, we added in Step 3 a new action button that can be used to load an updated version of the thermal profile file.
- New: Multi-point LIFU exposures. BabelBrain now offers the possibility to execute electronic steering over a list of points if a concave array is selected. In the first dialog, if any of the three concave arrays is selected (H317, I12378 and ATAC), the user can select a new profile definition specific to multi-point steering. You can consult an example in the [Profiles](https://github.com/ProteusMRIgHIFU/BabelBrain/blob/main/Profiles/MultiFocus_Profile1.yaml) subdirectory in BabelBrain. Coordinates in the profile are relative to the user-specified steering in Step 2. Be aware that the selected duty cycle for the thermal simulations is split among all multi-point entries. It is assumed that a single burst is applied per steering location, before steering to the next location. For example, if simulating three-point steering with a duty cycle of 30%, this implies that each point will represent 10% of the duty cycle.
- New: Examples for offline batch processing. We added a couple of Jupyter notebooks in the [OfflineBatchExamples](https://github.com/ProteusMRIgHIFU/BabelBrain/tree/main/OfflineBatchExamples) directory in the BabelBrain repository, along with a README file indicating steps to create an environment ready to run these examples. These notebooks can be very useful when running very large parametric studies. For example, the [CompareRayleightWithFDTD](https://github.com/ProteusMRIgHIFU/BabelBrain/tree/main/OfflineBatchExamples/CompareRayleightWithFDTD) case is the one we used to study the acoustic simulations in water-only conditions that facilitate reducing the computational costs in Step 2.
- Fix: Occasionally, Step 1 would produce incomplete tissue masks when using high PPW values (9 and higher) or with high frequency ( 1 MHz) when using Metal-based devices. The GPU filtering functions were rewritten to cover better these cases or at least provide a more meaningful error message to notify the users.
- Fix: Occasional mask generation issues with high-resolution conditions. In some cases, Step 1 would produce incomplete tissue masks when using high PPW values (9 and higher) or with high frequency ( 1 MHz) when using Metal-based devices. The GPU filtering functions were rewritten to cover better these cases or at least provide a more meaningful error message to notify the users.
- Fix: Enforce float type in profile files. Entries in thermal profiles such as duty cycle must be float values. Entries such as "1" should be "1.0". An error will be shown when loading profiles that do not adhere to this convention. This should imply minor changes to old profile files.
- 0.3.2 - March 3rd, 2024
- New: Full integration with Brainsight (Rogue Research) version 2.5.3 is now operational. In Brainsight, you need to start a new Simbnibs project and during the planning stage, a new "FUS" button in the Brainsight GUI can be used to invoke BabelBrain. Once simulations are completed, the results of the normalized transcranial simulation (normalized between 0 and 1 in the brain region) will be loaded automatically in Brainsight.
- New: Export of thermal maps into Nifti format. In Step 3, the current thermal simulation on display can now be exported in Nifti for inspection in neuronavigation and visualization software.
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