# Brain Extraction Methods in Neonatal Brain MRI and Their Effects on Intracranial Volumes
## 3 Results
### Comparison of Manual vs. Automated Brain Extraction Methods
#### 3.3.1 Segmentation Metrics
\begin{table}
\begin{tabular}{c c c c c c c c c c c c c} \hline \hline  & & \multicolumn{2}{c}{**HD-BET vs.**} & \multicolumn{2}{c}{**HD-BET vs. SWS**} & \multicolumn{2}{c}{**HD-BET vs.**} & \multicolumn{2}{c}{**SWS vs. BET2**} & \multicolumn{2}{c}{**SWS vs.**} & \multicolumn{2}{c}{**SynthStrip vs.**} \\  & & \multicolumn{2}{c}{**BET2**} & \multicolumn{2}{c}{**HD-BET vs. SWS**} & \multicolumn{2}{c}{**SynthStrip**} & \multicolumn{2}{c}{**SyntheticStrip**} & \multicolumn{2}{c}{**BET2**} \\ \hline  & & **IZ**1 & **adj. \(p\)** & **IZ**1 & **adj. \(p\)** & **IZ**1 & **adj. \(p\)** & **IZ**1 & **adj. \(p\)** & **IZ**1 & **adj. \(p\)** & **IZ**1 & **adj. \(p\)** \\ \hline \multirow{8}{*}{**Voxel-overlap-based metrics**} & DC & 2.545 & 0.000 & 0.273 & 1.000 & 1.364 & 0.003 & 2.273 & 0.000 & 1.091 & 0.030 & 1.182 & 0.014 \\  & JC & 2.545 & 0.000 & 0.273 & 1.000 & 1.364 & 0.003 & 2.273 & 0.000 & 1.091 & 0.030 & 1.182 & 0.014 \\  & Pr & 1.500 & 0.001 & 1.227 & 0.010 & 0.0273 & 1.000 & 2.727 & 0.000 & 0.955 & 0.085 & 1.773 & 0.000 \\  & Se & 1.227 & 0.010 & 2.000 & 0.000 & 2.045 & 0.000 & 0.773 & 0.283 & 0.045 & 1.000 & 0.818 & 0.213 \\  & Sp & 1.455 & 0.001 & 1.318 & 0.004 & 0.318 & 1.000 & 2.773 & 0.000 & 1.000 & 0.061 & 1.773 & 0.000 \\  & FRR & 1.455 & 0.001 & 1.318 & 0.004 & 0.318 & 1.000 & 2.773 & 0.000 & 1.000 & 0.061 & 1.773 & 0.000 \\  & FNR & 1.227 & 0.010 & 2.000 & 0.000 & 2.045 & 0.000 & 0.773 & 0.283 & 0.045 & 1.000 & 0.818 & 0.213 \\ \hline \hline \end{tabular}
\end{table} 
Table 6: Pairwise comparisons of segmentation metrics of the automated BE methods. For each comparison, we have reported the absolute value of the Z-statistics (\(\mid\!Z\!\mid\!\)) and the Bonferroni-adjusted \(p\)-value (adj. \(p\)). \begin{table}
\begin{tabular}{c c c} \hline \hline \multicolumn{2}{c}{**Median [IQR] of**} & \multicolumn{2}{c}{**Median [IQR] of Surface-Distance-Based Metrics (In mm)**} \\  & **Volume-Based Metrics** & & **HD95** & **MSD** & **MDSD** \\ \hline
**BET2** & 7.185 & 32.357 [31.318; 33.586] & 3.600 [3.600; 4.438] & 1.382 [1.282; 1.582] & 0.884 [0.625; 0.975] & 1.940 [1.748; 2.166] \\  & \(-\)2.033 & 27.339 [11.027; 33.370] & 3.600 [3.125; 3.600] & 0.651 [0.571; 0.794] & 0.000 [0.000; 0.000] & 1.471 [1.106; 1.837] \\
**HD-BET** & 2.609 [13.300; 4.007] & 7.200 [6.063; 8.975] & 3.156 [2.500; 3.600] & 0.996 [0.463; 0.653] & 0.000 [0.000; 0.000] & 1.008 [0.863; 1.142] \\
**SynthStrip** & 0.083 & 7.500 [7.218; 9.674] & 3.600 [3.125; 3.600] & 0.720 [0.654; 0.941] & 0.000 [0.000; 0.000] & 1.127 [1.032; 1.281] \\ \hline \hline \end{tabular}
\end{table} 
Table 4: Volume-based metrics and surface-distance-based metrics statistics (median and interquartile range (IQR)) of four automated BE methods (BET2, SWS, HD-BET, and SynthStrip). \begin{table}
\begin{tabular}{c c c} \hline \hline \multicolumn{2}{c}{**Median [IQR] of Dice Coefficient**} \\ \hline  & \multicolumn{2}{c}{**Bottom Mask**} & \multicolumn{2}{c}{**Middle Mask**} & \multicolumn{2}{c}{**Top Mask**} \\  & **(Slices 1 to 11)** & **(Slices 12 to 22)** & **(Slices 23 to 33)** \\ \hline
**BET2** & 0.874 [0.857; 0.883] & 0.961 [0.959; 0.963] & 0.915 [0.904; 0.921] \\
**SWS** & 0.897 [0.877; 0.905] & 0.983 [0.980; 0.985] & 0.960 [0.947; 0.961] \\
**HD-BET** & 0.944 [0.935; 0.947] & 0.979 [0.976; 0.980] & 0.962 [0.949; 0.961] \\
**SynthStrip** & 0.926 [0.913; 0.930] & 0.968 [0.966; 0.970] & 0.948 [0.937; 0.952] \\ \hline \hline \end{tabular}
\end{table} 
Table 5: Dice coefficient statistics (median and interquartile range (IQR)) of automated BE methods (BET2, SWS, HD-BET, and SynthStrip) for each brain mask subset (bottom, middle, and top slices).