Hi Ben,

Here is what I think goes on under the hood (Dr. Alfonso can correct and/or add details):
The gray matter signal is band pass filtered and detrended. After that 16 principal components are extracted from the white matter and the CSF regions (these regions are saved as ROI files during the segmentation step; actually the files are eroded a few times before saving as ROIs). These, along with the six motion parameters, their first order derivatives, and other effects that you select in the denoising tab (for example, the main effect of the task), are regressed out from the signal of interest. You have the choice of deciding whether band pass and detrending happens before regression or simultaneously in the denoising tab.

These steps are performed before the first level modeling (i.e. the first level GLM is applied to already denoised data). Therefore, the same strategy can be applied to resting state: the GLM will have a single condition (called rest) in the first level.

I mentioned that Conn extracts 16 components; however, the default number of components that are regressed out are 5 (both for WM and CSF).

These components are saved here: /data/ROI_Subjectxxx_Sessionxxx.mat file. Once you load this variable into MATLAB, you will find a variable named data. The first cell has the overall GM signal while the second and the third one have the PCs from WM and CSF (you will notice that they have 16 columns). The rest of the cells correspond to signal (before denoising) across the ROIs that you have specified. The names variable in your workspace will tell you which cell corresponds to which ROI.


Hope that helps


Best
Pravesh