The resting-state functional magnetic resonance imaging (rs-fMRI) is an advanced imaging method with several benefits compared to functional magnetic resonance imaging (fMRI) techniques. Major benefits of rs-fMRI are easy receiving of the signal, needs minimum effort from the patient, and good at differentiating the functional areas in patients. Resting-state fMRI (rs-fMRI) identifies the amount of Blood Oxygen Level-called as BOLD. These are variations at frequencies smaller than 0.1 Hz to identify the functional variations of the brain. Usage of this BOLD level allows viewing resting-state networks (RSN). RSN are distinct areas of the brain which are spatially distributed and which confirm synchronous BOLD fluctuations at rest. In the pipeline for fMRI data, various preprocessing steps are carried out as a normal procedure for achieving a better quality of data. In this paper, these steps for preprocessing are altered/changed in the pipeline of CONN neuroimaging software, and its effects on graph theory outcomes are explored and discussed. © 2023 Seventh Sense Research Group®