Cholesterol-transporter ApoE4 is involved in lipid metabolism and is associated with neurodegenerative diseases. Studies show, functional connectivity(FC) in ApoE4 mice is significantly deviating from ApoE3 and Wild-Type(WT). Underlining cause of these differences are less explored. Since myelin is mostly comprised of cholesterol, we investigated if a change in white matter integrity(WMI) could have contributed to the FC changes. FC and WMI in ApoE4 are distinctively different from ApoE3 and WT as shown by our results. Our results within the auditory cortex show that an increase in FA in ApoE4 is associated with a decrease of FC in the region.