I am wondering if there is a command for extracting confidence intervals of my estimates (z-scores) using 3dttest ? thank you in advance!

Assume that 1) by “z-score” you mean Fisher-transformed z-score, and 2) you have the output from 3dttest++. To obtain the upper bound for the 95% confidence interval, get the degrees of freedom (DF) for the t-stat, and try

3dcalc -a myBeta -b myTstat -expr ‘a+fitt_p2t(0.05,DF)*a/b’ -prefix upperBound

Similarly for the lower bound

3dcalc -a myBeta -b myTstat -expr ‘a-fitt_p2t(0.05,DF)*a/b’ -prefix upperBound