Metadata-Version: 2.1
Name: snake-fmri
Version: 0.1.0
Summary: A simulator and validator of fMRI reconstruction methods.
Author-email: Pierre-Antoine Comby <pierre-antoine.comby@cea.fr>
License: MIT License
        
        Copyright (c) 2022 Pierre-Antoine Comby
        
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Project-URL: Homepage, https://github.com/paquiteau/simfmri
Project-URL: Bug Reports, https://github.com/paquiteau/simfmri/issues
Project-URL: Source, https://github.com/paquiteau/simfmri
Keywords: simulation,fMRI
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Requires-Dist: pydantic
Requires-Dist: numpy
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Requires-Dist: nilearn
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Requires-Dist: seaborn
Requires-Dist: hydra-core
Requires-Dist: hydra-callbacks
Requires-Dist: hydra-colorlog
Requires-Dist: brainweb-dl
Requires-Dist: mri-nufft
Requires-Dist: pysap-fmri
Requires-Dist: modopt
Provides-Extra: dev
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Requires-Dist: pytest-sugar ; extra == 'test'
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<img align="left" width="33%" src="https://github.com/paquiteau/snake-fmri/blob/main/docs/images/logos/logo-snake_light.svg"> 
<h1> A Simulator from Neurovascular coupling to Acquisition of K-space data for Exploration of fMRI Technique </br></br></h1>


[![Test](https://github.com/paquiteau/snake-fmri/actions/workflows/test.yml/badge.svg)](https://github.com/paquiteau/snake-fmri/actions/workflows/test.yml)
[![deploy-docs](https://github.com/paquiteau/snake-fmri/actions/workflows/deploy-docs.yml/badge.svg)](https://paquiteau.github.io/snake-fmri)
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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. 

```bash
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:

```bash
git clone git@github.com/paquiteau/snake-fmri 
cd snake-fmri 
pip install -e .
```
After installation Snake-fMRI is available as the `snkf` module: 

``` python
import snkf

```

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

Don't hesitate to also check the [examples gallery (TBA)](https://paquiteau.github.io/snake-fmri).

# 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


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