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docs: address @jdkent's comments on ICA-AROMA and other confounds
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oesteban committed Dec 11, 2019
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Expand Up @@ -420,9 +420,17 @@ ICA-AROMA can be enabled with the flag ``--use-aroma``.
- ``aroma_motion_XX`` - the motion-related components identified by ICA-AROMA.

.. danger::
If you are already using ICA-AROMA cleaned data (``~desc-smoothAROMAnonaggr_bold.nii.gz``),
If you are already using ICA-AROMA's cleaned-data (``~desc-smoothAROMAnonaggr_bold.nii.gz``),
do not include ICA-AROMA confounds during your design specification or denoising procedure.

Additionally, as per [Hallquist2013]_, when using ICA-AROMA's cleaned-data most of the
confound regressors should be recalculated (this feature is a work-in-progress, follow up on
`#1905 <https://github.com/poldracklab/fmriprep/issues/1905>`__).
Surprisingly, `our simulations
<https://github.com/poldracklab/fmriprep-notebooks/blob/9933a628dfb759dc73e61701c144d67898b92de0/05%20-%20Discussion%20AROMA%20confounds%20-%20issue-817%20%5BJ.%20Kent%5D.ipynb>`__
(with thanks to JD. Kent) suggest that using the confounds as currently calculated by
*fMRIPrep* --before denoising-- would be just fine.

.. caution::
*Nonsteady-states* (or *dummy scans*) in the beginning of every run
are dropped **before** ICA-AROMA is performed.
Expand Down Expand Up @@ -509,6 +517,10 @@ See implementation on :mod:`~fmriprep.workflows.bold.confounds.init_bold_confs_w
Movement‐Related effects in fMRI time‐series. Magnetic Resonance in Medicine. 1996.
doi:`10.1002/mrm.191035031 <https://doi.org/10.1002/mrm.1910350312>`_
.. [Hallquist2013] Hallquist MN, Hwang K, Luna B. The Nuisance of Nuisance Regression.
NeuroImage. 2013. doi:`10.1016/j.neuroimage.2013.05.116
<https://doi.org/10.1016/j.neuroimage.2013.05.116>`_
.. [Muschelli2014] Muschelli J, Nebel MB, Caffo BS, Barber AD, Pekar JJ, Mostofsky SH,
Reduction of motion-related artifacts in resting state fMRI using aCompCor. NeuroImage. 2014.
doi:`10.1016/j.neuroimage.2014.03.028 <http://doi.org/10.1016/j.neuroimage.2014.03.028>`_
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