The brain is an organ of interest in high-consequence infectious disease. Subtle blood-brain-barrier disruption and edema can be identified and quantified using T<sub>2</sub> relaxation time as a biomarker. Accuracy is required to correlate changes in imaging findings with biological processes and therapeutic effectiveness. Dual echo time Fluid-Attenuated Inversion Recovery images, which minimizes the partial volume effects from cerebrospinal fluid, can be used to quantify T<sub>2</sub> relaxation. This sequence also meets the acquisition time requirements of biosafety level-4 facilities, where cohorts of animals are imaged on a tight schedule until terminal stages, when the animals may not survive long scans. However, the echo time used to compute T<sub>2</sub> varies among slices due to k-space mapping in fast spin-echo sequence. Therefore, an effective echo time instead of the prescribed echo time should be considered. We hypothesize that accurate effective echo time can be estimated by optimization for each slice ordering. A longer and more accurate T<sub>2</sub>-weighted spin-echo (multiecho) sequence to compute T<sub>2</sub> maps from mono-exponential fitting was validated using gel phantoms and used as ground truth. A brain of a non-human primate was imaged in vivo using both T<sub>2</sub> sequences. T<sub>2</sub> maps were generated using both methods and a correction factor was computed by linear fitting for each set of echo times and slice ordering. The coefficient of variation within phantoms and the Pearson’s correlation coefficient between in vivo ground truth T<sub>2</sub> and each map were used to assess its accuracy and quality.