Dear CONN Community,

I am working with the extracted BOLD signal data that is output in the REX files after the set-up step in CONN, and I am hoping to get some clarification on what data are in these files.

1) For any given ROI of interest, are the BOLD signal values in the REX file confound corrected (movement, CSF, WM), or are they just raw values? My assumption is that they are raw but need to confirm this. 

2) In the WM and CSF ROI REX files there are 16 variables. The first appears to be the raw signal and the remaining 15 appear to be the CompCor values for the principle components. However, in the denoising step in CONN, both the WM and CSF show that only 5 confounding effects will be regressed. Does the CompCor method only use the first 5 principle components for denoising?  

3) Is there any data file that is output after set-up that contains data for the 12 movement confounding variables? If so, where would I find this?

Any input or guidance is much appreciated! Thank you for such a great toolbox!

Best Wishes,
Allison