Agreement and Reliability between Clinically Available Software Programs in Measuring Volumes and Normative Percentiles of Segmented Brain Regions

OBJECTIVE: To investigate the agreement and reliability of estimating the volumes and normative percentiles (N%) of segmented brain regions among NeuroQuant (NQ), DeepBrain (DB), and FreeSurfer (FS) software programs, focusing on the comparison between NQ and DB. MATERIALS AND METHODS: Three-dimensional T1-weighted images of 145 participants (48 healthy participants, 50 patients with mild cognitive impairment, and 47 patients with Alzheimer’s disease) from a single medical center (SMC) dataset and 130 participants from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset were included in this retrospective study. All images were analyzed with DB, NQ, and FS software to obtain volume estimates and N% of various segmented brain regions. We used Bland–Altman analysis, repeated measures ANOVA, reproducibility coefficient, effect size, and intraclass correlation coefficient (ICC) to evaluate inter-method agreement and reliability. RESULTS: Among the three software programs, the Bland–Altman plot showed a substantial bias, the ICC showed a broad range of reliability (0.004–0.97), and repeated-measures ANOVA revealed significant mean volume differences in all brain regions. Similarly, the volume differences of the three software programs had large effect sizes in most regions (0.73–5.51). The effect size was largest in the pallidum in both datasets and smallest in the thalamus and cerebral white matter in the SMC and ADNI datasets, respectively. N% of NQ and DB showed an unacceptably broad Bland–Altman limit of agreement in all brain regions and a very wide range of ICC values (-0.142–0.844) in most brain regions. CONCLUSION: NQ and DB showed significant differences in the measured volume and N%, with limited agreement and reliability for most brain regions. Therefore, users should be aware of the lack of interchangeability between these software programs when they are applied in clinical practice.