Metadata-Version: 2.1
Name: phys2cvr
Version: 0.15.0
Summary: Python library to generate regressors for and compute Cerebrovascular Reactivity and lag maps.
Home-page: https://github.com/smoia/phys2cvr
Author: Stefano Moia
Maintainer: Stefano Moia
Maintainer-email: s.moia@bcbl.eu
License: Apache-2.0
Download-URL: https://github.com/smoia/phys2cvr
Description: <a name="readme"></a>
        <!-- <img alt="Phys2BIDS" src="https://github.com/physiopy/phys2bids/blob/master/docs/_static/phys2bids_logo1280×640.png" height="150"> -->
        
        phys2cvr
        ========
        
        [![Latest version](https://img.shields.io/pypi/v/phys2cvr?style=flat&logo=pypi)](https://pypi.org/project/phys2cvr/)
        [![Latest DOI](https://zenodo.org/badge/357980417.svg)](https://zenodo.org/badge/latestdoi/357980417)
        [![Licensed Apache 2.0](https://img.shields.io/github/license/smoia/phys2cvr?style=flat)](https://github.com/smoia/phys2cvr/blob/master/LICENSE)
        
        [![Auto Release](https://img.shields.io/badge/release-auto.svg?colorA=888888&colorB=9B065A&label=auto)](https://github.com/intuit/auto)
        [![Supports python version](https://img.shields.io/pypi/pyversions/phys2cvr?style=shield&logo=python)](https://pypi.org/project/phys2cvr/)
        
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        A python-based tool to generate regressor for and/or estimate CVR maps and their lag.
        
        **The project is currently under development stage alpha**.
        Any suggestion/bug report is welcome! Feel free to open an issue.
        
        This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
        
        Documentation
        =============
        
        Full documentation coming soon!
        
        Cite
        ----
        
        If you use `phys2cvr` in your work, please cite either the all-time Zenodo DOI [![general Zenodo DOI](https://zenodo.org/badge/110845855.svg)](https://zenodo.org/badge/latestdoi/110845855) or the Zenodo DOI related to the version you are using.
        Please cite the following paper(s) too:
        >Moia, S., Stickland, R. C., Ayyagari, A., Termenon, M., Caballero-Gaudes, C., & Bright, M. G. (2020). Voxelwise optimization of hemodynamic lags to improve regional CVR estimates in breath-hold fMRI. In 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC) (pp. 1489–1492). Montreal, QC, Canada: IEEE. https://doi.org/10.1109/EMBC44109.2020.9176225
        
        If you are using the `--brightspin` configuration option:
        >Moia, S., Termenon, M., Uruñuela, E., Chen, G., Stickland, R. C., Bright, M. G., & Caballero-Gaudes, C. (2021). ICA-based denoising strategies in breath-hold induced cerebrovascular reactivity mapping with multi echo BOLD fMRI. NeuroImage, 233, 117914. https://doi.org/10.1016/j.neuroimage.2021.117914
        
        If you are using the `--brightspin-clinical` configuration option:
        >Stickland, R. C., Zvolanek, K. M., Moia, S., Ayyagari, A., & Bright, M. G. (2021). A practical modification to a resting state fMRI protocol for improved characterization of cerebrovascular function. Supplementary Material. Neuroimage.
        
        If you are using the `--baltimore-lag` configuration option:
        >Liu, P., Li, Y., Pinho, M., Park, D. C., Welch, B. G., & Lu, H. (2017). Cerebrovascular reactivity mapping without gas challenges. NeuroImage, 146(November 2016), 320–326. https://doi.org/10.1016/j.neuroimage.2016.11.054
        
        If you are using the `--baltimore` configuration option, please cite only the Zenodo DOI and the last listed paper.
        
        Installation
        ------------
        
        Install on any `*nix` system using python and pip, or clone this repository and install locally (run setup.py or pip).
        `phys2cvr` supports python versions 3.6+. However, please note that no tests are currently run.
        
        ### Install with `pip` (recommended)
        
        :exclamation::exclamation::exclamation: Please note that some systems might require to use `pip3` instead of `pip`.
        
        #### Basic installation:
        For basic installation, simply run:
        ```bash
        pip install phys2cvr
        ```
        
        ### Clone from Github / install without `pip`
        
        :exclamation::exclamation::exclamation: Please note that `phys2cvr` is continuously deployed, i.e. the latest feature available are immediately released on PyPI.
        To install `phys2cvr` from Github, clone the repository first, then move to the cloned folder and run:
        ```bash
        python setup.py install
        ```
        
        Alternatively, `pip` can be used too:
        ```bash
        pip install .
        ```
        
        ### Developer installation
        
        To be sure you have everything installed to develop (and test) `phys2cvr`, **fork** `smoia/phys2cvr` to your repository, then clone it locally and move inside the cloned folder. Finally, install with `pip` using the developer mode and the `[all]` label:
        ```bash
        pip install -e .[all]
        ```
        
        
        Run/use `phys2cvr`
        ---------------
        
        You can run the `phys2cvr` workflow in a shell session (or in your code) - just follow the help:
        ```shell
        phys2cvr --help
        ```
        
        Alternatively, you can use phys2cvr as a module in a python session (or within your python script):
        ```python
        import phys2cvr as p2c
        
        p2c.__version__
        ```
        
        Full API coming soon.
        
        
        <!-- ## Contributors ✨
        
        Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)): -->
        
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        License
        -------
        
        Copyright 2021, Stefano Moia.
        
        Licensed under the Apache License, Version 2.0 (the "License");
        you may not use this file except in compliance with the License.
        You may obtain a copy of the License at
        
        http://www.apache.org/licenses/LICENSE-2.0
        
        Unless required by applicable law or agreed to in writing, software
        distributed under the License is distributed on an "AS IS" BASIS,
        WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
        See the License for the specific language governing permissions and
        limitations under the License.
        
Platform: OS Independent
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Provides: phys2cvr
Requires-Python: >=3.6.1
Description-Content-Type: text/markdown; charset=UTF-8
Provides-Extra: test
Provides-Extra: style
Provides-Extra: all
Provides-Extra: doc
