# Brain Extraction Methods in Neonatal Brain MRI and Their Effects on Intracranial Volumes
## 3 Results
### Comparison of Manual vs. Automated Brain Extraction Methods
#### 3.3.2 Intracranial Volume Estimation  
Table 8 shows the ICV of the 22 premature babies scanned at TEA, estimated with the manual and automated methods. The Bland-Altman plots illustrate the agreement between the ICVs extracted from the MRI using automated segmentation methods against the reference (Figure 3). Ideally, the BE methods being compared would yield identical results, resulting in null ICV differences, but such a perfect agreement is unlikely to occur. Instead, we would expect to observe a random distribution of ICV differences clustered around zero, indicating an unbiased pattern of disagreement [71; 72; 73]. By examining the spread of differences both above and below zero, we can determine the extent to which the \begin{table}
\begin{tabular}{l c c c c c c c c c c c c} \hline \hline  & \multicolumn{3}{c}{**HD-BET vs.**} & \multicolumn{3}{c}{**HD-BET vs.**} & \multicolumn{3}{c}{**HD-BET vs.**} & \multicolumn{3}{c}{**SWS vs. BET2**} & \multicolumn{3}{c}{**SWS vs.**} & \multicolumn{3}{c}{**SynthStrip vs.**} \\  & \multicolumn{3}{c}{**BET2**} & \multicolumn{3}{c}{**SWS**} & \multicolumn{3}{c}{**SynthStrip**} & \multicolumn{3}{c}{**SWS vs. BET2**} & \multicolumn{3}{c}{**SynthStrip**} & \multicolumn{3}{c}{**BET2**} \\ \hline  & 1\(\,\)Z\(\,\)I & **adj. \(p\)** & 1\(\,\)Z\(\,\)I & **adj. \(p\)** & 1\(\,\)Z\(\,\)I & **adj. \(p\)** & 1\(\,\)Z\(\,\)I & **adj. \(p\)** & 1\(\,\)Z\(\,\)I & **adj. \(p\)** & 1\(\,\)Z\(\,\)I & **adj. \(p\)** & 1\(\,\)Z\(\,\)I & **adj. \(p\)** \\ \hline
**Bottom mask** (slices 1 to 11) & 7.123 & 0.000 & 5.488 & 0.000 & 2.335 & 0.117 & 1.635 & 0.612 & 3.153 & 0.010 & 4.788 & 0.000 \\
**Middle mask** (slices 12 to 22) & 5.021 & 0.000 & 1.868 & 0.370 & 2.919 & 0.021 & 6.890 & 0.000 & 4.788 & 0.000 & 2.102 & 0.213 \\
**Top mask** (slices 23 to 33) & 5.839 & 0.000 & 0.117 & 1.000 & 1.985 & 0.283 & 5.722 & 0.000 & 1.868 & 0.370 & 3.854 & 0.001 \\ \hline \hline \end{tabular}
\end{table} 
Table 7: Pairwise comparisons of DC for each brain mask subset and method. For each comparison, we have reported the absolute value of the Z-statistics (1\(\,\)Z\(\,\)I) and the Bonferroni-adjusted \(p\)-value (adj. \(p\)). \begin{table}
\begin{tabular}{l c c c c c c c c c c c c} \hline \hline  & \multicolumn{3}{c}{**HD-BET vs.**} & \multicolumn{3}{c}{**HD-BET vs.**} & \multicolumn{3}{c}{**SWS vs. BET2**} & \multicolumn{3}{c}{**SWS vs.**} & \multicolumn{3}{c}{**SynthStrip vs.**} \\  & \multicolumn{3}{c}{**BET2**} & \multicolumn{3}{c}{**SWS**} & \multicolumn{3}{c}{**SynthStrip**} & \multicolumn{3}{c}{**SWS vs. BET2**} & \multicolumn{3}{c}{**SynthStrip**} & \multicolumn{3}{c}{**BET2**} \\ \hline  & 1\(\,\)Z\(\,\)I & **adj. \(p\)** & 1\(\,\)Z\(\,\)I & **adj. \(p\)** & 1\(\,\)Z\(\,\)I & **adj. \(p\)** & 1\(\,\)Z\(\,\)I & **adj. \(p\)** & 1\(\,\)Z\(\,\)I & **adj. \(p\)** & 1\(\,\)Z\(\,\)I & **adj. \(p\)** \\ \hline
**Volume-based metrics** & VS & 1.182 & 0.014 & 1.455 & 0.001 & 1.000 & 0.061 & 2.636 & 0.000 & 0.455 & 1.000 & 2.182 & 0.000 \\  & HD & 2.568 & 0.000 & 1.727 & 0.000 & 0.614 & 0.690 & 0.841 & 0.184 & 1.114 & 0.025 & 1.955 & 0.000 \\
**Surface-distance-based metrics** & HD5 & 2.318 & 0.000 & 0.545 & 0.967 & 0.682 & 0.479 & 1.773 & 0.000 & 0.136 & 1.000 & 1.636 & 0.000 \\  & MSD & 2.545 & 0.000 & 0.591 & 0.774 & 1.045 & 0.043 & 1.955 & 0.000 & 0.455 & 1.000 & 1.500 & 0.001 \\  & MDSD & 2.159 & 0.000 & 0.068 & 1.000 & 0.409 & 1.000 & 2.091 & 0.000 & 0.341 & 1.000 & 1.750 & 0.000 \\  & STSD & 2.364 & 0.000 & 1.318 & 0.004 & 0.500 & 1.000 & 1.045 & 0.043 & 0.818 & 0.213 & 1.864 & 0.000 \\ \hline \hline \end{tabular}
\end{table} 
Table 6: _Cont._  
Figure 2: TEA brain T2w MRI of a preterm neonate (born at 29 weeks GA) in three different axial slices (**a**) (from bottom to top: slice numbers 9, 17, and 26) and corresponding overlapping brain masks (in yellow) from each BE method: (**b**) Manual, (**c**) BET2, (**d**) SWS, (**e**) HD-BET, and (**f**) SynthStrip. disagreement between the methods is acceptable when replacing manual for automated BE methods.