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.
- A working Python 3.10 environment or higher
- Optional: a working CUDA environment for NUFFT accelerations.
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 [email protected]/paquiteau/snake-fmri
cd snake-fmri
pip install -e .
After installation Snake-fMRI is available as the snkf
module:
import snkf
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).
3 CLI interfaces are able to use the configuration folder to perform differents task:
snkf-main
to do a full simulation + reconstruction + validation
The configuration are located in snkf/conf
and articulates over 3 main components:
- the simulation
- the reconstruction
- the validation via statistical analysis
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@unpublished{comby:hal-04533862,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},
}
SNAKE-fMRI is licensed under the MIT License. See the LICENSE file for more information.