snake-fmri 0.1.0

A simulator and validator of fMRI reconstruction methods.

A Simulator from Neurovascular coupling to Acquisition of K-space data for Exploration of fMRI Technique

This package provides a simulation and reconstruction framework for fMRI data. It is designed to be used for benchmarking and testing of fMRI reconstruction methods.

Installation

Requirements

• A working Python 3.10 environment or higher
• Optional: a working CUDA environment for NUFFT accelerations.

Installation

To install SNAKE-fMRI, you can use pip.

pip install snake-fmri 
# Required for the reconstruction 
pip install git+github.com/pysap-fmri
# Recommended for the nufft acceleration 
pip install gpunufft # or cufinufft 

Or the latest version from the repository:

git clone [e-mail]/paquiteau/snake-fmri 
cd snake-fmri 
pip install -e .

After installation Snake-fMRI is available as the snkf module:

import snkf

Documentation

The documentation is available at https://paquiteau.github.io/snake-fmri/, our preprint (TBA) describe also the framework in details.

Don't hesitate to also check the examples gallery (TBA).

Running simulation and benchmarks

Available commands

3 CLI interfaces are able to use the configuration folder to perform differents task:

• snkf-main to do a full simulation + reconstruction + validation

Configurations Files

The configuration are located in snkf/conf and articulates over 3 main components:

• the simulation
• the reconstruction
• the validation via statistical analysis

License

SNAKE-fMRI is licensed under the MIT License. See the LICENSE file for more information.