Hi Alfonso,

Thanks for implementing these great BIDS and fMRIprep import options, which works totally fine for me!

The thread with Adam was helpful for me to understand everything fully, but I have one remaining rather simple question.

After I used the fMRIprep import option, the unsmoothed images outputted by fMRIprep are now considered my primary dataset.

I would like to create smoothed images for seed-to-voxel connectivity analysis (which I can do in or outside CONN, no problem), and define the smoothed dataset as the secondary dataset, but this would be the opposite of CONN's defaults which considers smoothed images as the primary dataset.

Can I change this (smoothed images as the primary, unsmoothed as the secondary) after smoothing, within the same CONN project, to avoid confusion or having to adapt the defaults in later steps?

If I would smooth within CONN (using "apply single preprocessing step" from the functional tools menu in the functional screen of the setup tab), would you recommend the standard 'functional smoothing' option or the 'masked functional smoothing' option which seems to mask within gray matter only?

Thanks very much for your advice and help!

Best wishes,

Lukas