Hello!

I am very new to functional connectivity analysis and have two questions:

1) I am about to start resting state analysis and have read mixed inputs about whether to use or not use low-pass filter when analyzing resting state data. CONN has a default setting [0.008 0.09] for band pass filter that has been recommended to do denoising for resting state analysis. However, some publications such as from Smith et. al., 2013 (Resting-state fMRI in the Human Connectome Project) suggest not using low-pass filtering in cases where "multiple voxels'' timeseries are averaged together are less prone to the effects of thermal noise, and hence may be degraded, rather than improved, by any lowpass temporal filtering. Such analyses include: seed-based connectivity where the seed is an extended ROI and the data has been extensively spatially smoothed", which is the case in my condition. I was wondering if it would be a good idea to use [0.008 inf] for my resting state analysis?

2) My next question is about the role of the low pass filter in removing high frequency noise, such as cardiac effects and physiologic effects. So, if I dont use a low-pass filter, then I won''t be able to remove these physiological noise effects. So, I was wondering if I do choose to use [0.008 inf] as my band pass filter, how would I take care of these physiological effects? My TR is 0.662 for reference. Also would nyquist frequency play any role here in choosing the low-pass filter max value?

Thank you!