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Co-Authored-By: Chris Markiewicz <markiewicz@stanford.edu>
Co-Authored-By: James Kent <james-kent@uiowa.edu>
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3 people committed Dec 11, 2019
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Expand Up @@ -420,12 +420,12 @@ 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's cleaned-data (``~desc-smoothAROMAnonaggr_bold.nii.gz``),
If you are already using AROMA-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>`__).
Additionally, as per [Hallquist2013]_ and [Lindquist2019]_, when using AROMA-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
Expand Down Expand Up @@ -521,6 +521,11 @@ See implementation on :mod:`~fmriprep.workflows.bold.confounds.init_bold_confs_w
NeuroImage. 2013. doi:`10.1016/j.neuroimage.2013.05.116
<https://doi.org/10.1016/j.neuroimage.2013.05.116>`_
.. [Lindquist2019] Lindquist, MA, Geuter, S, and Wager, TD, Caffo, BS,
Modular preprocessing pipelines can reintroduce artifacts into fMRI data.
Human Brain Mapping. 2019. doi: `10.1002/hbm.24528
<https://doi.org/10.1002/hbm.24528>`_
.. [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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