Questions about dummy scans and WM/CSF regression after tedana denoising

[Steven]

Hi @RongM and welcome to neurostars!

@RongM

I included the dummy_scans parameter in the tedana_workflow, but the output image still appears to have the same number of volumes as the original input.

The dummy_scans argument is not supposed to remove volumes. See here: Fmriprep --dummy-scans purpose? - #2 by effigies

@RongM

My understanding is that tedana performs TE-dependent denoising and separates BOLD-like from non-BOLD components. In that context, I am wondering whether WM- and CSF-related signals are already partly accounted for by tedana.

But tedana’s own docs also note an important limitation of spatial ICA: it is good at removing spatially localized noise, yet it can miss spatially diffuse noise spread across much of the brain. For that reason, the tedana docs explicitly describe additional post-processing to remove diffuse noise, and list methods such as GSR, MIR, and aCompCor among the approaches used after tedana. See here: tedana’s denoising approach — tedana 26.0.2 documentation

A 2023 comparison study reported that after applying ME-ICA, the data was best post-processed to remove spatially diffuse noise with a method such as aCompCor, and found ME-ICA + aCompCor highly effective: Comparing the efficacy of data-driven denoising methods for a multi-echo fMRI acquisition at 7T - ScienceDirect

It would still be wise to try both with and without additional denoising, and see if you get considerable improvement in QC-FC after including additional denoising.

Best,

Steven