Ah thank you for the comprehensive walk through and commands. I failed to look originally at the errts.$subj files which do indeed contain the censored TR's, with zero values. I had orignally picked the errts.anaticor.$subj 3d+time file which does seem to just do away with TR's, which makes sense since its primarily for resting state, where time continuity is less important?
I'll try the normal errts output and compare it with a few errts.anaticor outputs and see if there is significance difference before moving forward
Thank you for the help,
John