which toolbox to use after fmriprep for denoising/detrending and constructing FC matrices?

I understand that the fmriprep preprocessed data will have to undergo detrending and denoising before i can apply a parcellation scheme to obtain the functional connectivity matrices.

Are there any toolbox that can perform all these? I’ve heard about xcpEngine and fmridenoise, but are there any others?

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Nilearn Nilearn: Statistical Analysis for NeuroImaging in Python — Machine learning for NeuroImaging

Nilearn can clean the images in the way you described and produce the matrices.