MATLAB code to replicate main results from "Functional ultrasound imaging of freely moving adult human neural activity through an acoustically transparent cranial prosthetic"

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Project Organization

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├── LICENSE
├── LICENSE.md                      <- license
├── README.md                       <- The top-level README for developers using this project
├── docs                            <- documentation 
├── +w2b                            <- window 2 the brain (w2b) package for commonly used functionality
├── acquisition                     <- sample acquisition code for fUSI
├── experiments                     <- source code for experiment specific scripts 
├── references                      <- data dictionaries, manuals, other explanatory materials
└── third-party                     <- third party submodules, repositories, functions, etc.

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Associated dataset

Available from CaltechData: Click here to download.

Packaged as .zip file in data hierarchy used by MATLAB functions. Once downloaded, extract contents from the .zip file.

├── human                                   Human data
|   └──S{*A}R{*B}.mat                       {*A} is the session number and {*B} is the run number.
├── in vitro                                In vitro data
|   └──In_vitro_Doppler_Data_STM.mat        Combined in vitro data
├── rodent                                  Rodent data
|   └──YYYYMMDD                             YYYY=Year, MM=Month, DD=Day
|       └──{Run name}                       
|           └──Dop.mat                      Doppler data
|           └──UF.mat                       Metadata

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Other information

Tested on MATLAB R2021a and R2023a on Windows 10, and MATLAB R2021b and R2022b on Mac Sonoma 14.1.2 Please send feedback and suggestions to: [email protected], [email protected], or [email protected]

Zenodo archive -

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In publications, please reference:

Rabut, C., Norman, S.L., Griggs, W.S., Russin, J.R., Jann, K., Christopoulos, V., Liu, C., Andersen, R.A., and Shapiro, M.G. Functional ultrasound imaging of freely moving adult human neural activity through an acoustically transparent cranial prosthetic. Science Translational Medicine. Accepted. (See BioRxiv version here)

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Getting set up

1. Clone the repository

   $ git clone https://github.com/wsgriggs2/window-to-the-brain

   note: If you are interested in contributing, please get in touch with the authors (Claire, Sumner, or Whitney). In the meantime, feel free to submit issues and/or feature requests.

2. Download paired dataset from CaltechData and unzip in a location that is convenient.

3. Run run_me_first.m within .\experiments. This will set up any necessary pathing.

4. Try out any of the scripts within the .\experiments folder!

Dependencies

This repository makes use of multiple MATLAB toolboxes including Bioinformatics Toolbox, Curve Fitting Toolbox, Image Processing Toolbox, Parallel Processing Toolbox, Signal Processing Toolbox, and Statistics and Machine Learning Toolbox.