Hi Maarten,

Thank you very much for your help. Now I think I understand. I don't know why the whole time I've been thinking that _Z maps contain Z scores and now I know that is why I had problems with thresholding (which is due to fact that correlation simply cannot be over 1). Also thank you for the advice on masks, it worked and now the nan problem is gone. So now, can I actually threshold individual 3D images too, by giving coefficient values that might be statistically significant as Z input in easythresh?

As to the seed, I created a seed on Broca's area using MNI coordinates from the paper I read on Broca's and Wernicke's areas, using 3dundump and MNI152_T1_3mm_brain template. Is it the right way? I looked through the individual 3D maps from my RSFC anlysis and it seems that the biggest coefficient values are about 0.6 to 0.65. 

Thanks,
Michal