Best current fMRI preprocessing pipeline

What is the best currently pipeline for restingstate assuming I have everything in BIDS?

fMRIprep from fMRIPrep Demonstration — Andy’s Brain Book 1.0 documentation ( and then ICA-Aroma?

That depends on your data (is it high quality, how many subjects do you have, how long are your acquisitions?) and what you are planning on doing with it later (e.g. are you doing connectivity, or something else more complicated?).

fMRIPrep is minimal preprocessing, so there will be more steps afterwards that you may have to do, such as denoising and smoothing. Here is a good paper that discusses possible denoising strategies An evaluation of the efficacy, reliability, and sensitivity of motion correction strategies for resting-state functional MRI - PubMed. AROMA is among the pipelines that are evaluated.

If you are doing functional connectivity and want a more streamlined approach, then you may find XCP_D a good post processing option.


thanks Steven,

my goal is functional connectivity (building a connectome with Pearson correlation), I have many things in mind in terms of dataset, but generally small samples with decent acquisitions (3T). So if I understood well with AROMA and XCP_D you can do everything and you don’t need fMRIprep.

What’s more complicated than functional connectivity? Gradients?

XCP_D is a post-processing pipeline, which happens after fMRIPrep. See documentation here.