nibetaseries 0.2.0

BetaSeries Correlations implemented in Nipype

NiBetaSeries is BIDS compatible application that calculates betaseries correlations. In brief, a beta coefficient is calculated for each trial (or event) resulting in a series of betas that can be used to correlate regions of interest with each other.

NiBetaSeries takes preprocessed data as input that satisfy the BIDS deriviatives 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 MNI space since currently no transformations are applied to the data. You can use any arbitrary atlas as long as it is in MNI space (the same space as the preprocessed data).

With NiBetaSeries you can receive:

• betaseries images (TODO)

• correlation matrices

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 code of conduct and contributing page.

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

• Free software: MIT license

Installation

pip install nibetaseries

Documentation

https://NiBetaSeries.readthedocs.io/

If you’re interested in contributing to this project, here are some guidelines for contributing. Another good place to start is by checking out the open issues.

Development

To run the all tests run:

tox

Note, to combine the coverage data from all the tox environments run:

Windows	set PYTEST_ADDOPTS=--cov-append tox
Other	PYTEST_ADDOPTS=--cov-append tox

0.2.0 (November 13, 2018)

• [MGT] simplify and create deployment (#79)

• [TST] Add more tests (#78)

• [ENH] Reword docs (#77)

• [ENH]: allow confounds to be none (#76)

• various fixes for a real dataset (#75)

• [FIX]: Find metadata (#74)

• [FIX] confound removal (#72)

• [WIP, FIX]: file logic (#71)

• [DOC] Added zenodo file (#70)

• [FIX]: ignore sourcedata and derivatives directories in layout (#69)

• Update CONTRIBUTING.rst (#66)

• Fix pull request template (#65)

• FIX: add CODEOWNERS file (#63)

• FIX: connect derivative outputs (#61)

• run versioneer install (#60)

• Fix issue #29: Add link to Zenodo DOI (#57)

• Fix issue #45: conform colors of labels (#56)

• fix links in readme.rst (#55)

• Added code of conduct (#53)

• Add link to contributing in README (#52)

• removed acknowledgments section of pull request template (#50)

• [TST]: Add functional test (#49)

• [FIX]: remove references to bootstrap (#48)

• FIX: test remove base .travis.yml (#47)

• removed data directory (#40)

• Add pull request template (#41)

• Update issue templates (#44)

• Update contributing (#43)

• README (where’s the beef?) (#37)

• change jdkent to HBClab (#38)

• [FIX]: pass tests (#14)

• [ENH]: improve docs (#13)

• add documentation (#11)

• FIX: add graph (#10)

• Refactor NiBetaSeries (#9)

• Refactor (#2)

0.1.0 (2018-06-08)

• First release on PyPI.