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Short Description
The MRI Quality Control Protocol of the Stanford CRN
Full Description

mriqc: image quality metrics for quality assessment of MRI

This pipeline 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

The package provides a series of image processing workflows to extract and
compute a series of NR (no-reference), IQMs (image quality metrics) to be
used in QAPs (quality assessment protocols) for MRI (magnetic resonance imaging).

This open-source neuroimaging data processing tool is being developed as a
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>_.

This tool extracts a series of IQMs from structural and functional MRI data.
It is also scheduled to add diffusion MRI to the target imaging families.

External Dependencies

mriqc is implemented using nipype, but it requires some other neuroimaging
software tools:

  • FSL <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>_.
  • The N4ITK bias correction tool released with ANTs <http://stnava.github.io/ANTs/>_.
  • AFNI <https://afni.nimh.nih.gov/>_.

These tools must be installed and their binaries available in the
system's $PATH.

Installation

The mriqc is packaged and available through the PyPi repository.
Therefore, the easiest way to install the tool is: ::

pip install mriqc

Execution and the BIDS format

The mriqc workflow takes as principal input the path of the dataset
that is to be processed.
The only requirement to the input dataset is that it has a valid BIDS (Brain Imaging Data Structure) <http://bids.neuroimaging.io/>_ format.
This can be easily checked online using the
BIDS Validator <http://incf.github.io/bids-validator/>_.

Example command line: ::

mriqc -i ~/Data/bids_dataset -o out/ -w work/

Support and communication

The documentation of this project is found here: http://mriqc.readthedocs.org/en/latest/.

If you have a problem or would like to ask a question about how to use mriqc,
please submit a question to NeuroStars.org with an mriqc tag.
NeuroStars.org is a platform similar to StackOverflow but dedicated to neuroinformatics.

All previous mriqc questions are available here:
http://neurostars.org/t/mriqc/

To participate in the mriqc development-related discussions please use the
following mailing list: http://mail.python.org/mailman/listinfo/neuroimaging
Please add [mriqc] to the subject line when posting on the mailing list.

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, Craig A. Moodie, William Triplett.
Poldrack Lab, Psychology Department, Stanford University,
and Center for Reproducible Neuroscience, Stanford University.

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) 2015-2016, the mriqc developers and the CRN.
All rights reserved.

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