SPM vs. DPARSF: order of steps and how do I remove nuisance covariates before extracting seed time courses (is code accessible)?

Dear DPARSF team,

I have analysed my resting state data with two different approaches:

1. using the DPARSF toolbox

2. using in house scripts for Matlab/SPM. 

Interestingly the results are fairly the same expect that the t-values on group level are much higher in DPARSF (FWE .05 k10, tmax= 104,67,
(seed 51, 12, -27)) than for SPM (FWE .05 k10,  tmax=63.08(seed 51, 12, -27)).