Reusable and configurable neuroimaging pipelines with Nipype.
Project description
# neuro_pypes
[](http://neuro-pypes.readthedocs.io) [](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 1.0.1
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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