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phys2cvr

python module to compute cerebrovascular reactivity mapping and other related maps

https://github.com/smoia/phys2cvr

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 8 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 5 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.7%) to scientific vocabulary

Keywords

cvr fmri hacktoberfest lagged-glm neuroimaging physiology python
Last synced: 6 months ago · JSON representation

Repository

python module to compute cerebrovascular reactivity mapping and other related maps

Basic Info
  • Host: GitHub
  • Owner: smoia
  • License: apache-2.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 1.06 MB
Statistics
  • Stars: 5
  • Watchers: 2
  • Forks: 18
  • Open Issues: 40
  • Releases: 49
Topics
cvr fmri hacktoberfest lagged-glm neuroimaging physiology python
Created almost 5 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License Zenodo

README.md

<!-- Phys2BIDS -->

phys2cvr

Latest version Release date Auto Release

Latest DOI Licensed Apache 2.0

Latest version Supports python version

All Contributors <!-- ALL-CONTRIBUTORS-BADGE:END -->

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 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 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, run the following commands from within the repository main folder: ```bash

Add upstream remote

git remote add upstream git@github.com:smoia/phys2cvr.git

Fetch everything, tags included

git fetch --all --tags

Checkout master (the main development branch) and make it track upstream

git checkout master git branch --set-upstream-to=upstream/master

!!! VERY IMPORTANT !!!

Set the default push to origin, in order NOT to push by mistake to upstream.

git config remote.pushDefault origin

Install package with pip using the developer mode and the [dev] label

You might need to use pip3 depending on how you set up your system

pip install -e .[dev] ``` If you make changes that you consider fundamental/interesting for the whole community, feel free to open a PR!

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):


Stefano Moia
💻 🤔 🚇 📆
Kristina Zvolanek
💻 🐛
Andrew Vigotsky
💻

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.

Owner

  • Name: Stefano Moia
  • Login: smoia
  • Kind: user
  • Location: Geneva
  • Company: EPFL

Postdoc researcher @ EPFL (MIP:lab), interested in neuroimaging and cerebral physiology. Co-founder and current PM of @physiopy.

GitHub Events

Total
  • Create event: 1
  • Release event: 1
  • Issues event: 1
  • Watch event: 1
  • Delete event: 1
  • Push event: 13
  • Pull request review event: 1
  • Pull request review comment event: 1
  • Pull request event: 4
  • Fork event: 2
Last Year
  • Create event: 1
  • Release event: 1
  • Issues event: 1
  • Watch event: 1
  • Delete event: 1
  • Push event: 13
  • Pull request review event: 1
  • Pull request review comment event: 1
  • Pull request event: 4
  • Fork event: 2

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 225
  • Total Committers: 5
  • Avg Commits per committer: 45.0
  • Development Distribution Score (DDS): 0.236
Top Committers
Name Email Commits
Stefano Moia s****a@b****u 172
Stefano Moia s****h@g****m 37
pre-commit-ci[bot] 6****]@u****m 10
Kristina Zvolanek k****k@u****u 5
DeepSource Bot b****t@d****o 1
Committer Domains (Top 20 + Academic)
deepsource.io: 1 u.northwestern.edu: 1 bcbl.eu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 45
  • Total pull requests: 80
  • Average time to close issues: 5 months
  • Average time to close pull requests: 27 days
  • Total issue authors: 5
  • Total pull request authors: 10
  • Average comments per issue: 0.13
  • Average comments per pull request: 0.45
  • Merged pull requests: 62
  • Bot issues: 0
  • Bot pull requests: 17
Past Year
  • Issues: 1
  • Pull requests: 4
  • Average time to close issues: 8 months
  • Average time to close pull requests: 9 months
  • Issue authors: 1
  • Pull request authors: 4
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.25
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • smoia (37)
  • CesarCaballeroGaudes (4)
  • kristinazvolanek (1)
  • srithetree (1)
  • farnazdelavari (1)
Pull Request Authors
  • smoia (49)
  • pre-commit-ci[bot] (18)
  • kristinazvolanek (7)
  • RazkinMalen (5)
  • merelvdthiel (3)
  • deepsource-autofix[bot] (2)
  • ccomellalue (1)
  • beccaclements99 (1)
  • AniqueSchuller (1)
  • snyk-bot (1)
Top Labels
Issue Labels
Enhancement (28) Documentation (4) Refactoring (4) Urgent (2) Testing (2)
Pull Request Labels
Internal (12) Documentation (8) Duplicate (6) Invalid (4) Minormod-breaking (3) Released (2) Refactoring (2) Outreach (2) Minormod (2) BugFIX (1) Majormod (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 92 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 48
  • Total maintainers: 1
pypi.org: phys2cvr

Python library to generate regressors for and compute Cerebrovascular Reactivity and lag maps.

  • Versions: 48
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 92 Last month
Rankings
Forks count: 9.1%
Dependent packages count: 10.1%
Downloads: 12.2%
Average: 15.2%
Dependent repos count: 21.5%
Stargazers count: 23.1%
Maintainers (1)
smoia
Last synced: 7 months ago

Dependencies

requirements.txt pypi
  • matplotlib >=3.1.1
  • nibabel *
  • numpy >=1.9.3
  • peakdet *
  • scipy *
.github/workflows/auto-release.yml actions
  • actions/checkout v2 composite
.github/workflows/python-publish.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
setup.py pypi