A simulator and validator of fMRI reconstruction methods.
Project description
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
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 git@github.com: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
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