From 5fe23ae0ced4cc983ba1a2c5bccb31a4ace8be07 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Wed, 11 Dec 2019 14:59:31 -0800 Subject: [PATCH] Apply suggestions from code review Co-Authored-By: Chris Markiewicz Co-Authored-By: James Kent --- docs/outputs.rst | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/docs/outputs.rst b/docs/outputs.rst index 92821c63f..78f608656 100644 --- a/docs/outputs.rst +++ b/docs/outputs.rst @@ -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 `__). + 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 `__). Surprisingly, `our simulations `__ (with thanks to JD. Kent) suggest that using the confounds as currently calculated by @@ -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 `_ + .. [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 + `_ + .. [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 `_