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+https://github.com/paquiteau/pysap-fmri
# Recommended for the nufft acceleration 
pip install gpunufft # or cufinufft 

Or the latest version from the repository:

git clone git@github.com/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 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

Citing SNAKE-fMRI

If you use SNAKE-fMRI in your research, please cite the following paper:

Pierre-Antoine Comby, Alexandre Vignaud, Philippe Ciuciu. SNAKE-fMRI: A modular fMRI data simulator from the space-time domain to k-space and back. 2024. ⟨hal-04533862⟩

@unpublished{comby:hal-04533862,
  TITLE = {{SNAKE-fMRI: A modular fMRI data simulator from the space-time domain to k-space and back}},
  AUTHOR = {Comby, Pierre-Antoine and Vignaud, Alexandre and Ciuciu, Philippe},
  URL = {https://hal.science/hal-04533862},
  NOTE = {working paper or preprint},
  YEAR = {2024},
  MONTH = Mar,
  KEYWORDS = {fMRI ; Brain Imaging ; Accelerated sampling ; Compressed Sensing ; Simulation ; Open Source ; Python ; np ndarray , np newaxis] ; np ; ndarray , np ; newaxis]},
  PDF = {https://hal.science/hal-04533862/file/main.pdf},
  HAL_ID = {hal-04533862},
  HAL_VERSION = {v1},
}

License

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