NiBetaSeries

NiBetaSeries: task related correlations in fMRI - Published in JOSS (2019)

https://github.com/hbclab/nibetaseries

Science Score: 98.0%

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
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 5 DOI reference(s) in README and JOSS metadata
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Academic publication links
Links to: joss.theoj.org, zenodo.org
✓
Committers with academic emails
7 of 29 committers (24.1%) from academic institutions
✓
Institutional organization owner
Organization hbclab has institutional domain (psychology.uiowa.edu)
✓
JOSS paper metadata
Published in Journal of Open Source Software

Keywords from Contributors

bids neuroimaging ecog eeg ieeg meg neuroscience electrocorticography electroencephalography magnetoencephalography

Last synced: 6 months ago · JSON representation

Repository

Nipype implementation of BetaSeries Correlations (Beta)

Basic Info

Host: GitHub
Owner: HBClab
License: mit
Language: Python
Default Branch: master
Homepage: https://nibetaseries.readthedocs.io
Size: 2.2 MB

Statistics

Stars: 34
Watchers: 3
Forks: 28
Open Issues: 48
Releases: 22

Created over 8 years ago · Last pushed over 2 years ago

Metadata Files

Readme Changelog Contributing License Code of conduct Codeowners Authors Zenodo

README.rst

.. _readme:

============
NiBetaSeries
============

If you are viewing this file on GitHub, please see our
`readthedocs page `_
for links to render properly.

.. start-badges

.. list-table::
    :stub-columns: 1

    * - docs
      - |docs| |joss|
    * - tests
      - | |travis| |circleci|
        | |codecov|
    * - binder
      - | |binder|
    * - package
      - | |version| |wheel| |supported-versions|
        | |supported-implementations| |zenodo|

.. |docs| image:: https://readthedocs.org/projects/nibetaseries/badge/?version=latest
    :alt: Documentation Status
    :target: https://nibetaseries.readthedocs.io/en/latest/?badge=latest

.. |zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.2552303.svg
   :target: https://zenodo.org/record/2552303#.XFBjwN-YU8p

.. |joss| image:: https://joss.theoj.org/papers/10.21105/joss.01295/status.svg
   :target: https://doi.org/10.21105/joss.01295

.. |travis| image:: https://travis-ci.com/HBClab/NiBetaSeries.svg?branch=master
    :alt: Travis-CI Build Status
    :target: https://travis-ci.com/HBClab/NiBetaSeries

.. |codecov| image:: https://codecov.io/github/HBClab/NiBetaSeries/coverage.svg?branch=master
    :alt: Coverage Status
    :target: https://codecov.io/github/HBClab/NiBetaSeries

.. |circleci| image:: https://circleci.com/gh/HBClab/NiBetaSeries.svg?style=svg
    :alt: Circleci Build Status
    :target: https://circleci.com/gh/HBClab/NiBetaSeries

.. |binder| image:: https://mybinder.org/badge_logo.svg
    :target: https://mybinder.org/v2/gh/HBClab/NiBetaSeries/master?filepath=%2Fexamples

.. |version| image:: https://img.shields.io/pypi/v/nibetaseries.svg
    :alt: PyPI Package latest release
    :target: https://pypi.python.org/pypi/nibetaseries

.. |wheel| image:: https://img.shields.io/pypi/wheel/nibetaseries.svg
    :alt: PyPI Wheel
    :target: https://pypi.python.org/pypi/nibetaseries

.. |supported-versions| image:: https://img.shields.io/pypi/pyversions/nibetaseries.svg
    :alt: Supported versions
    :target: https://pypi.python.org/pypi/nibetaseries

.. |supported-implementations| image:: https://img.shields.io/pypi/implementation/nibetaseries.svg
    :alt: Supported implementations
    :target: https://pypi.python.org/pypi/nibetaseries


.. end-badges

What is NiBetaSeries?
---------------------
NiBetaSeries is BIDS_-compatible `application `_
that calculates betaseries correlations.
In brief, a beta coefficient (i.e., parameter estimate) is calculated
for each trial (or event) resulting in a series of betas ("betaseries")
that can be correlated across regions of interest.

Why should I use it?
--------------------
There are potential insights hidden in your task fMRI data.
Rest fMRI enjoys a multitude of toolboxes which can be applied to task fMRI
with some effort, but there are not many toolboxes that focus on making
betaseries.
Betaseries can then be used for correlations/classifications and
a multitude of other analyses.
While a couple alternatives exist (pybetaseries_ and BASCO_), NiBetaSeries
is the only application to interface with BIDS_ organized data with the goal
of providing a command-line application experience like fMRIPrep_.

What does NiBetaSeries give me?
-------------------------------
Currently NiBetaSeries returns the beta series images and optionally
symmetric z-transformed correlation matrices with an entry for each
parcel defined in the atlas.

.. note:: The betas (i.e., parameter estimates) are generated using either
    the "Least Squares Separate" or "Least Squares All" procedures.
    Please read the :ref:`betaseries` page for more background information.

What do I need to run NiBetaSeries?
-----------------------------------
NiBetaSeries takes BIDS_ and preprocessed data as input that satisfy the
`BIDS derivatives specification `_.
In practical terms, NiBetaSeries uses the output of fMRIPrep_,
a great BIDS-compatible preprocessing tool.
NiBetaSeries requires the input and the atlas to already
be in the same space (e.g., MNI space).
For more details, see :ref:`usage` and the tutorial
(:ref:`sphx_glr_auto_examples_plot_run_nibetaseries.py`)

Get Involved
------------
This is a very young project that still needs some tender loving care to grow.
That's where you fit in!
If you would like to contribute, please read our :ref:`code_of_conduct`
and contributing page (:ref:`contributing`).

Thanks!
-------
This project heavily leverages `nipype `_,
`nilearn `_, `pybids `_, and
`nistats `_ for development.
Please check out their pages and support the developers.

.. _BASCO: https://www.nitrc.org/projects/basco/
.. _pybetaseries: https://github.com/poldrack/pybetaseries
.. _BIDS: http://bids.neuroimaging.io/
.. _fMRIPrep: http://fmriprep.readthedocs.io/en/latest/

Owner

Name: Health, Brain, & Cognition Lab
Login: HBClab
Kind: organization

Website: https://psychology.uiowa.edu/health-brain-cognition-lab
Repositories: 3
Profile: https://github.com/HBClab

JOSS Publication

NiBetaSeries: task related correlations in fMRI

Published

September 19, 2019

DOI

10.21105/joss.01295

Volume 4, Issue 41, Page 1295

Authors

James D. Kent

Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, United states of America

Peer Herholz

Montréal Neurological Institute, McGill University Health Centre, Montreal, Quebec, Canada

Editor

Ariel Rokem

GitHub Events

Total

Issues event: 2
Watch event: 2
Issue comment event: 1

Last Year

Issues event: 2
Watch event: 2
Issue comment event: 1

Committers

Last synced: 7 months ago

All Time

Total Commits: 439
Total Committers: 29
Avg Commits per committer: 15.138
Development Distribution Score (DDS): 0.33

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
James Kent	j**t@u**u	294
arokem	a**m@g**m	67
Jake VanderPlas	j**p@u**u	9
Peer Herholz	h**r@g**m	7
Fred Mertz	m**f@b**e	6
Claudio Toro	c**o@b**u	5
Taylor Salo	t**6@f**u	5
Ben Cipollini	b**i@u**u	4
Andreas Mayer	a**m@g**m	4
Christopher Holdgraf	c**f@g**m	4
Krista DeStasio	k**o@g**m	4
Yaroslav Halchenko	d**n@o**m	4
rxqx	r**g@u**u	3
beckmart	r**n@g**m	3
Janelle Liu	j**u@g**m	3
Greg Wilson	g**n@t**m	3
RaginSagan	b**e@g**m	2
zkhan12	3****2	1
Samuel Nastase	s**e@g**m	1
Pranesh S	4****p	1
Nate Vack	n**k@f**t	1
Matteo Visconti di Oleggio Castello	m****c	1
Mark Mandel	m****1	1
Kristian Eschenburg	k**b@u**u	1
Ilkay Isik	i**k@g**m	1
Ignacio	i**o@d**m	1
Alec Trievel	a**l@g**m	1
Andrew Nelson	a**f@g**m	1
Asier Erramuzpe	a**e@g**m	1

Committer Domains (Top 20 + Academic)

uw.edu: 2 despegar.com: 1 freshforever.net: 1 third-bit.com: 1 uoregon.edu: 1 onerussian.com: 1 ucsd.edu: 1 fiu.edu: 1 bu.edu: 1 bargle.argle: 1 uiowa.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 65
Total pull requests: 36
Average time to close issues: 14 days
Average time to close pull requests: 2 days
Total issue authors: 13
Total pull request authors: 3
Average comments per issue: 1.75
Average comments per pull request: 1.0
Merged pull requests: 34
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 0
Average comments per issue: 1.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

jdkent (38)
LilianYou (6)
mbpincus (5)
PeerHerholz (5)
limbicode214 (2)
michaelmack (2)
kateiyas (1)
eahorwath (1)
csiyer (1)
Tsjitsjikow (1)
sjw42 (1)
poldrack (1)
KMIsenburg (1)
TamerGezici (1)

Pull Request Authors

jdkent (33)
PeerHerholz (2)
yarikoptic (1)

Top Labels

Issue Labels

enhancement (9) help wanted (6) bug (5) feature (5) question (5) documentation (4) good first issue (2) Hacktoberfest (1)

Pull Request Labels

hacktoberfest-accepted (1) enhancement (1) help wanted (1)

Packages

Total packages: 2
Total downloads:
- pypi 35 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 22
Total maintainers: 2

pypi.org: nibetaseries

BetaSeries Correlations implemented in Nipype

Homepage: https://github.com/HBClab/NiBetaSeries
Documentation: https://nibetaseries.readthedocs.io/
License: MIT License
Latest release: 0.6.0
published almost 6 years ago

Versions: 20
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 35 Last month

Rankings

Forks count: 7.5%

Dependent packages count: 10.1%

Stargazers count: 11.8%

Average: 17.8%

Dependent repos count: 21.5%

Downloads: 38.3%

Maintainers (1)

jdkent

Last synced: 6 months ago

spack.io: py-nibetaseries

BetaSeries Correlations implemented in Nipype.

Homepage: https://github.com/HBClab/NiBetaSeries
License: []
Status: removed
Latest release: 0.6.0
published almost 4 years ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Forks count: 18.1%

Stargazers count: 23.5%

Average: 24.7%

Dependent packages count: 57.3%

Maintainers (1)

adamjstewart

Last synced: 6 months ago

NiBetaSeries

Science Score: 98.0%

Keywords from Contributors

Repository

Basic Info

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Metadata Files

README.rst

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JOSS Publication

NiBetaSeries: task related correlations in fMRI

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Editor

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pypi.org: nibetaseries

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spack.io: py-nibetaseries

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