Dear Georgia,

Did you check what is in CONN_x.Setup.rois.names ? Because it might contain the names of the white matter and CSF, if maybe you try to remove that, this might fix the issue.

Also make sure to set the following:

CONN_x.Setup.rois.add = 0;

If this does not fix the issue, then it might be that the WM and CSF denoising confounds might be hardcoded.

Hope this helps,
Best regards,
Stephen