Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
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README.rst

mriqc: image quality metrics for quality assessment of MRI

MRIQC is developed by the Poldrack Lab at Stanford University for use at the Center for Reproducible Neuroscience (CRN), as well as for open-source software distribution.

Available in OpenNeuro! https://circleci.com/gh/poldracklab/mriqc/tree/master.svg?style=svg Documentation Status https://api.codacy.com/project/badge/grade/fbb12f660141411a89ba1ae5bf873717 Latest Version Supported Python versions Development Status License

About

MRIQC extracts no-reference IQMs (image quality metrics) from structural (T1w and T2w) and functional MRI (magnetic resonance imaging) data.

MRIQC is an open-source project, developed under the following software engineering principles:

  1. Modularity and integrability: MRIQC implements a nipype workflow to integrate modular sub-workflows that rely upon third party software toolboxes such as FSL, ANTs and AFNI.
  2. Minimal preprocessing: the MRIQC workflows should be as minimal as possible to estimate the IQMs on the original data or their minimally processed derivatives.
  3. Interoperability and standards: MRIQC follows the the brain imaging data structure (BIDS), and it adopts the BIDS-App standard.
  4. Reliability and robustness: the software undergoes frequent vetting sprints by testing its robustness against data variability (acquisition parameters, physiological differences, etc.) using images from OpenfMRI. Its reliability is permanently checked and maintained with CircleCI.

MRIQC is part of the MRI image analysis and reproducibility platform offered by the CRN. This pipeline derives from, and is heavily influenced by, the PCP Quality Assessment Protocol.

Citation

When using MRIQC, please include the following citation:

Esteban O, Birman D, Schaer M, Koyejo OO, Poldrack RA, Gorgolewski KJ; MRIQC: Advancing the Automatic Prediction of Image Quality in MRI from Unseen Sites; PLOS ONE 12(9):e0184661; doi:10.1371/journal.pone.0184661.

Support and communication

The documentation of this project is found here: http://mriqc.readthedocs.io/.

Users can get help using the mriqc-users google group.

All bugs, concerns and enhancement requests for this software can be submitted here: https://github.com/poldracklab/mriqc/issues.

Authors

Oscar Esteban, Krzysztof F. Gorgolewski. Poldrack Lab, Psychology Department, Stanford University, and Center for Reproducible Neuroscience, Stanford University.

Thanks

  • The QAP developers (C. Craddock, S. Giavasis, D. Clark, Z. Shezhad, and J. Pellman) for the initial base of code which MRIQC was forked from.
  • W Triplett and CA Moodie for their initial contributions with bugfixes and documentation, and
  • J Varada for his contributions on the source code.

License information

We use the 3-clause BSD license; the full license is in the file LICENSE in the mriqc distribution.

All trademarks referenced herein are property of their respective holders.

Copyright (c) 2015-2017, the mriqc developers and the CRN. All rights reserved.