Dear Willem,

The denoising looks fine to me. I guess you are working with healthy volunteers, and if you look at the machine parameters there might be some filters set (such as prescan normalize or hamming filter) which are partially correcting already a bit the connectivity, hence why you observe this. The filters might hide some of the connectivity, hence it's advised to disable these (except prescan normalize which allows for more homogenous subcortical voxels intensity and thus analysis).

So if you want to tweak further, you might want to have a look at your MRI machine's parameters, but otherwise I think the analysis should be fine as it is.

Hope this helps,
Best regards,
Stephen