Dear Sara,

I am sure you can combine preprocessing in SPM with the conn toolbox for denoising.

However, if you want to stay within the SPM framework completely, we have implemented a simple version of aCompCor in the PhysIO Toolbox (https://www.nitrc.org/projects/physio), which is integrated with the SPM Batch Editor. All you need to put there is a dependency on the warped white matter/CSF (wc2*,wc3*) tissue probability maps from unified segmentation to specify those as noise ROIs, and the warped (and realigned etc.) fMRI time series, from which the time series shall be extracted.

The help in the batch editor, after installing the toolbox, should give you more details. PhysIO is part of the TAPAS suite, and more info on it can be found in the README (https://github.com/translationalneuromod...).


All the best,
Lars