Hi Panos,

A value of 300 would mean 3 times the average BOLD signal (but since the average BOLD signal has been computed over a region that includes a lot of out-of-brain voxels, it is not all that meaningful).  Typically SPM defines the global BOLD signal through two steps: 1) compute a "preliminary" global BOLD signal by averaging across the entire image and find those voxels with average BOLD signal above 1/8th of this preliminary global BOLD signal value; 2) re-compute the global BOLD signal now averaging only over the voxels found in step (1). This procedure is the one that CONN will use for PSC-scaling if you select the "implicit" masking option (and the implicit mask will be defined as those voxels with average BOLD signal above 80% of the global BOLD signal). When you select the "explicit" masking option in CONN the global BOLD signal will instead be computed as the average BOLD signal across all voxels within the explicit mask (this is similar to the procedure used by FSL for PSC-scaling). The differences between these two procedures is often noticeable, and it creates quite a few complications when attempting to compare effect-sizes across studies. In any way, back to our case here, using PSC-scaling in CONN together with the "none" masking option would use the global BOLD value obtained in step (1) of the SPM procedure described above (simply the average BOLD signal across the entire image), which will typically result in a considerably understimated global BOLD signal value compared to the other two methods (in addition to making the procedure very sensible to other factors such as variations in FOV, etc.), so that is why I would probably recommend to use either implicit masking or no PSC-scaling in this case.  

And regarding (2), if skipping PSC-scaling, the BOLD signal of the denoised data will simply be in the same units as the original functional data (typically raw BOLD signal values are expressed in arbitrary units)

Hope this helps
Alfonso
Originally posted by Panos Fotiadis: