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Reusable and configurable neuroimaging pipelines with Nipype.

Project description

# neuro_pypes

[![Build Status](https://travis-ci.org/Neurita/pypes.svg?branch=master)](https://travis-ci.org/Neurita/pypes) [![ReadTheDocs](https://readthedocs.org/projects/neuro-pypes/badge/?version=latest)](http://neuro-pypes.readthedocs.io) [![DOI](https://zenodo.org/badge/46623736.svg)](https://zenodo.org/badge/latestdoi/46623736)

Reusable neuroimaging pipelines using [nipype](http://nipype.readthedocs.io/) and state-of-the-art neuroimaging preprocessing software.

The objectives of this projects are:

  • easy-to-use, complete, reusable, and configurable pre-processing pipelines, and
  • high-quality results with the minimum manual intervention in the images.

## Documentation

Please have a look at the documentation [here](http://neuro-pypes.readthedocs.io).

## Citation

If you use Pypes please cite it:

` Alexandre M. Savio, Michael Schutte, Manuel Graña and Igor Yakushev Pypes: Workflows for Processing Multimodal Neuroimaging Data Front. Neuroinform., April 2017, vol 11, 2017, pages 25 issn: 1662-5196 doi: 10.3389/finf.2017.00025 ` [https://doi.org/10.3389/fninf.2017.00025](https://doi.org/10.3389/fninf.2017.00025)

…or the BibTeX: ` @ARTICLE{10.3389/fninf.2017.00025, AUTHOR={Savio, Alexandre M. and Schutte, Michael and Graña, Manuel and Yakushev, Igor}, TITLE={Pypes: Workflows for Processing Multimodal Neuroimaging Data}, JOURNAL={Frontiers in Neuroinformatics}, VOLUME={11}, PAGES={25}, YEAR={2017}, URL={http://journal.frontiersin.org/article/10.3389/fninf.2017.00025}, DOI={10.3389/fninf.2017.00025}, ISSN={1662-5196} } ` Also consider citing [Nipype](http://nipype.readthedocs.io) and all the other open source tools you use.

## License

Licensed under the Apache License, Version 2.0.

Changelog

Version 1.1.2 (16.04.2018)

### Features:

  • Add –extra parameter to nitap motion for extra subject metadata.
  • Bump nipype version to 1.0.2. Few fixes included.

Version 1.1.1 (08.03.2018)

### Bugfixes:

  • Fix wrong import in cli/cli.py file.
  • Fix bugs in nitap plot command.

Version 1.1.0 (01.03.2018)

### Features:

  • Add nitap CLI with plot and motion subcommands.

### Docs:

  • Added a new section for the command line interface.

### Code changes:

  • Changed all import paths to absolute paths.
  • Line width changed to 120.
  • Many code style changes towards automatised lint checks.

Version 1.0.1

  • Bug fix: some wrong import names with the module name change.
  • Bug fix: added missing requirements.

Version 1.0.0

  • API break: Change module name from pypes to neuro_pypes.
  • Documentation update.

Version 0.3.5

  • Fix connection naming in the fMRI pipeline atlas output.

Version 0.3.4

  • Fix connection naming in the fMRI pipeline atlas output.

Version 0.3.3

  • Fix output renaming in SPM+DiReCT pipeline.
  • Add black_bg parameter to multi slices plotting functions.
  • Add motion_stats_sheet to fmri utils.
  • General fix on import ordering which was raising errors from new Nipype.

Version 0.3.2

  • Add atlas warping to fMRI pipeline.
  • Fixes in fMRI pipeline.

Version 0.3 - 0.3.1

  • Add motion statistics measures in DTI pipeline.
  • Improve documentation.
  • Add SPM+DiReCT option to anatomical preprocessing.
  • Add invoke examples in tasks.py.
  • Style and bug fixes.
  • Fix imports for latest nipype version.
  • Add plot_ortho_slices function to nilearn interface.

Version 0.2.0 - 0.2.1

  • Add mkdocs documentation and readthedocs setup.
  • Add registration options for PET and fMRI. Add options for this in config.
  • Add group template for fMRI and PET pipelines.
  • Add brain_mask output to anatomical MR pipeline.
  • Rename/re-structure fMRI pipeline and files.
  • Improve PET output file namings.
  • Add settings for Camino in config.
  • Fix bug in _get_n_slices in slicetime_params.
  • Bug fixes.

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