Whole brain and deep gray matter structure segmentation: Quantitative comparison between MPRAGE and MP2RAGE sequences

Amgad Droby*, Avner Thaler, Nir Giladi, R. Matthew Hutchison, Anat Mirelman, Dafna Ben Bashat, Moran Artzi

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Objective T1-weighted MRI images are commonly used for volumetric assessment of brain structures. Magnetization prepared 2 rapid gradient echo (MP2RAGE) sequence offers superior gray (GM) and white matter (WM) contrast. This study aimed to quantitatively assess the agreement of whole brain tissue and deep GM (DGM) volumes obtained from MP2RAGE compared to the widely used MP-RAGE sequence. Methods Twenty-nine healthy participants were included in this study. All subjects underwent a 3T MRI scan acquiring high-resolution 3D MP-RAGE and MP2RAGE images. Twelve participants were re-scanned after one year. The whole brain, as well as DGM segmentation, was performed using CAT12, volBrain, and FSL-FAST automatic segmentation tools based on the acquired images. Finally, contrast-to-noise ratio between WM and GM (CNRWG), the agreement between the obtained tissue volumes, as well as scan-rescan variability of both sequences were explored. Results Significantly higher CNRWG was detected in MP2RAGE vs. MP-RAGE (Mean ± SD = 0.97 ± 0.04 vs. 0.8 ± 0.1 respectively; p<0.0001). Significantly higher total brain GM, and lower cerebrospinal fluid volumes were obtained from MP2RAGE vs. MP-RAGE based on all segmentation methods (p<0.05 in all cases). Whole-brain voxel-wise comparisons revealed higher GM tissue probability in the thalamus, putamen, caudate, lingual gyrus, and precentral gyrus based on MP2RAGE compared with MP-RAGE. Moreover, significantly higher WMprobability was observed in the cerebellum, corpus callosum, and frontal-and-temporal regions in MP2RAGE vs. MP-RAGE. Finally, MP2RAGE showed a higher mean percentage of change in total brain GM compared to MP-RAGE. On the other hand, MP-RAGE demonstrated a higher overtime percentage of change inWMand DGM volumes compared to MP2RAGE. Conclusions Due to its higher CNR, MP2RAGE resulted in reproducible brain tissue segmentation, and thus is a recommended method for volumetric imaging biomarkers for the monitoring of neurological diseases.

Original languageEnglish
Article numbere0254597
JournalPLoS ONE
Issue number8 August
StatePublished - Aug 2021


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