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SNAKE-fMRI: Simulator from neuro-activation to K-space Exploration

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

Test deploy-docs HAL

python black ruff

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. See mri-nufft for details. SNAKE works best with a fast GPU NUFFT Backend such as cufinufft or gpuNUFFT

from PyPA (soon)

It is recommended to install the SNAKE toolkit on top of the core runtime (the toolkit contains reconstructors, statistical analysis tool and the CLI to run experiments).

pip install snake-fmri[toolkit]

Some Reconstructors requires extra dependencies such as pysap-fmri or patch-denoising

Development version

git clone [email protected]:paquiteau/snake-fmri 
cd snake-fmri 
pip install -e .[test,dev,doc,toolkit]

Getting Started

Documentation is available at https://paquiteau.github.io/snake-fmri

To get started, you can check the examples gallery: https://paquiteau/github.io/snake-fmri/examples