In brain morphometry studies using magnetic resonance imaging, several scans with a range of contrasts are often collected. The images may be locally distorted due to imperfect shimming in regions where magnetic susceptibility changes rapidly, and all scans may not be distorted in the same way. In multispectral studies it is critical that the edges of structures align precisely across all contrasts. The MPRAGE (MPR) sequence has excellent contrast properties for cortical segmentation, while multiecho FLASH (MEF) provides better contrast for segmentation of subcortical structures. Here, a multiecho version of the MPRAGE (MEMPR) is evaluated using SIENA and FreeSurfer. The higher bandwidth of the MEMPR results in reduced distortions that match those of the MEF while the SNR is recovered by combining the echoes. Accurate automatic identification of cortex and thickness estimation is frustrated by the presence of dura adjacent to regions such as the entorhinal cortex. In the typical MPRAGE protocol, dura and cortex are approximately isointense. However, dura has substantially smaller T2* than cortex. This information is represented in the multiple echoes of the MEMPR. An algorithm is described for correcting cortical thickness using T2*. It is shown that with MEMPR, SIENA generates more reliable percentage brain volume changes and FreeSurfer generates more reliable cortical models. The regions where cortical thickness is affected by dura are shown. MEMPR did not substantially improve subcortical segmentations. Since acquisition time is the same for MEMPR as for MPRAGE, and it has better distortion properties and additional T2* information, MEMPR is recommended for morphometry studies.