| Name | snake-fmri JSON |
| Version |
0.1.0
JSON |
| download |
| home_page | None |
| Summary | A simulator and validator of fMRI reconstruction methods. |
| upload_time | 2024-04-12 10:20:44 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | MIT License Copyright (c) 2022 Pierre-Antoine Comby Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
simulation
fmri
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
<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>
[](https://github.com/paquiteau/snake-fmri/actions/workflows/test.yml)
[](https://paquiteau.github.io/snake-fmri)
[](httsp://arxiv.org)
[](https://pypi.org/project/snake-fmri)
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
<!--
# Citing SNAKE-fMRI
If you use SNAKE-fMRI in your research, please cite the following paper:
>
>
```
```
-->
# License
SNAKE-fMRI is licensed under the MIT License. See the LICENSE file for more information.
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"description": "<img align=\"left\" width=\"33%\" src=\"https://github.com/paquiteau/snake-fmri/blob/main/docs/images/logos/logo-snake_light.svg\"> \n<h1> A Simulator from Neurovascular coupling to Acquisition of K-space data for Exploration of fMRI Technique </br></br></h1>\n\n\n[](https://github.com/paquiteau/snake-fmri/actions/workflows/test.yml)\n[](https://paquiteau.github.io/snake-fmri)\n[](httsp://arxiv.org)\n\n[](https://pypi.org/project/snake-fmri)\n\n\n\n\n\nThis package provides a simulation and reconstruction framework for fMRI data. It is designed to be used for benchmarking and testing of fMRI reconstruction methods.\n\n\n# Installation\n## Requirements \n- A working Python 3.10 environment or higher \n- Optional: a working CUDA environment for NUFFT accelerations.\n\n## Installation\nTo install SNAKE-fMRI, you can use pip. \n\n```bash\npip install snake-fmri \n# Required for the reconstruction \npip install git+github.com/pysap-fmri\n# Recommended for the nufft acceleration \npip install gpunufft # or cufinufft \n```\n\nOr the latest version from the repository:\n\n```bash\ngit clone git@github.com/paquiteau/snake-fmri \ncd snake-fmri \npip install -e .\n```\nAfter installation Snake-fMRI is available as the `snkf` module: \n\n``` python\nimport snkf\n\n```\n\n# Documentation\nThe documentation is available at https://paquiteau.github.io/snake-fmri/, our [preprint (TBA)](XXXX) describe also the framework in details.\n\nDon't hesitate to also check the [examples gallery (TBA)](https://paquiteau.github.io/snake-fmri).\n\n# Running simulation and benchmarks \n## Available commands \n\n3 CLI interfaces are able to use the configuration folder to perform differents task: \n - `snkf-main` to do a full simulation + reconstruction + validation \n \n\n## Configurations Files\nThe configuration are located in `snkf/conf` and articulates over 3 main components: \n- the simulation\n- the reconstruction\n- the validation via statistical analysis\n\n\n<!--\n\n# Citing SNAKE-fMRI\nIf you use SNAKE-fMRI in your research, please cite the following paper:\n\n> \n> \n\n```\n```\n-->\n# License\nSNAKE-fMRI is licensed under the MIT License. See the LICENSE file for more information.\n",
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