mriqc.qc package
================

Module contents
---------------

.. automodule:: mriqc.qc
    :members:
    :undoc-members:
    :show-inheritance:


Submodules
----------

mriqc.qc.anatomical module
--------------------------

.. automodule:: mriqc.qc.anatomical
    :members:
    :undoc-members:
    :show-inheritance:

mriqc.qc.functional module
--------------------------

.. automodule:: mriqc.qc.functional
    :members:
    :undoc-members:
    :show-inheritance:


References
----------

    .. [Atkinson1997] Atkinson et al., *Automatic correction of motion artifacts
      in magnetic resonance images using an entropy
      focus criterion*, IEEE Trans Med Imag 16(6):903-910, 1997.
      doi:`10.1109/42.650886 <http://dx.doi.org/10.1109/42.650886>`_.

    .. [Giannelli2010] Giannelli et al., *Characterization of Nyquist ghost in
      EPI-fMRI acquisition sequences implemented on two clinical 1.5 T MR scanner
      systems: effect of readout bandwidth and echo spacing*. J App Clin Med Phy,
      11(4). 2010.
      doi:`10.1120/jacmp.v11i4.3237 <http://dx.doi.org/10.1120/jacmp.v11i4.3237>`_.

    .. [Jenkinson2002] Jenkinson et al., *Improved Optimisation for the Robust and
      Accurate Linear Registration and Motion Correction of Brain Images*.
      NeuroImage, 17(2), 825-841, 2002.
      doi:`10.1006/nimg.2002.1132 <http://dx.doi.org/10.1006/nimg.2002.1132>`_.

    .. [Mortamet2009] Mortamet B et al., *Automatic quality assessment in
      structural brain magnetic resonance imaging*, Mag Res Med 62(2):365-372,
      2009. doi:`10.1002/mrm.21992 <http://dx.doi.org/10.1002/mrm.21992>`_.

    .. [Nichols2013] Nichols, `Notes on Creating a Standardized Version of DVARS
      <http://www2.warwick.ac.uk/fac/sci/statistics/staff/academic-research/nichols/scripts/fsl/standardizeddvars.pdf>`_,
      2013.

    .. [Power2012] Poweret al., *Spurious but systematic correlations in
      functional connectivity MRI networks arise from subject motion*,
      NeuroImage 59(3):2142-2154,
      2012, doi:`10.1016/j.neuroimage.2011.10.018
      <http://dx.doi.org/10.1016/j.neuroimage.2011.10.018>`_.

    .. [QAP] `The QAP project
      <https://github.com/oesteban/quality-assessment-protocol/blob/enh/SmartQCWorkflow/qap/temporal_qc.py#L16>`_.
