poldracklab / Mriqc
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mriqc: image quality metrics for quality assessment of MRI
MRIQC is developed by the Poldrack Lab at Stanford University <https://poldracklab.stanford.edu>
_ for use at the Center for Reproducible Neuroscience (CRN) <http://reproducibility.stanford.edu>
_, as well as
for open-source software distribution.
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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:
#. Modularity and integrability: MRIQC implements a
nipype <http://nipype.readthedocs.io>
_ workflow to integrate modular
sub-workflows that rely upon third party software toolboxes such as
FSL, ANTs and AFNI.
#. Minimal preprocessing: the MRIQC workflows should be as minimal as possible to estimate the IQMs on the original data or their minimally processed derivatives.
#. Interoperability and standards: MRIQC follows the the brain imaging data structure (BIDS) <http://bids.neuroimaging.io>
, and it adopts the BIDS-App <http://bids-apps.neuroimaging.io>
standard.
#. 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 <https://openfmri.org>
.
Its reliability is permanently checked and maintained with
CircleCI <https://circleci.com/gh/poldracklab/mriqc>
.
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 <http://preprocessed-connectomes-project.github.io/quality-assessment-protocol>
_.
Citation
.. topic:: 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 <https://doi.org/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 <https://groups.google.com/forum/#!forum/mriqc-users>
_.
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.
.. topic:: 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.