## 3 Results
### Assessment of Intensity Variability and Segmentation Performance
#### 3.2.2 Comparison Amongst Brain Extraction Methods
\begin{table}
\begin{tabular}{c c c c c c c c c} \hline \hline  & \multicolumn{6}{c}{**Cerebral Spinal Fluid**} \\ \hline  & \multicolumn{3}{c}{**SPM-BFC**} & \multicolumn{6}{c}{**N4 ITK**} \\ \hline  & \multicolumn{3}{c}{**BET2**} & \multicolumn{3}{c}{**SWS**} & \multicolumn{1}{c}{**HD-BET**} & \multicolumn{1}{c}{**SynthStrip**} & \multicolumn{1}{c}{**BET2**} & \multicolumn{1}{c}{**SWS**} & \multicolumn{1}{c}{**HD-BET**} & \multicolumn{1}{c}{**SynthStrip**} \\ \hline Manual & \(p=0.250\) & \(p=0.132\) & \(p=1.000\) & \(p<0.001\)* & \(p=0.701\) & \(p=0.453\) & \(p=1.000\) & \(p<0.001\)* \\  & \(r=0.338\) & \(r=0.374\) & \(r=0.122\) & \(r=0.848\) & \(r=0.273\) & \(r=0.302\) & \(r=0.115\) & \(r=0.762\) \\ BET2 & - & \(p=1.000\) & \(p=0.023\)* & \(p=0.007\)* & - & \(p=1.000\) & \(p=1.000\) & \(p=0.012\)* \\  & & \(r=0.036\) & \(r=0.460\) & \(r=0.510\) & & \(r=0.029\) & \(r=0.388\) & \(r=0.489\) \\ SWS & - & - & \(p=0.010\)* & \(p=0.017\)* & - & - & \(p=0.057\) & \(p=0.023\)* \\  & & & \(r=0.496\) & \(r=0.474\) & - & - & \(r=0.417\) & \(r=0.460\) \\ HD-BET & - & - & - & \(p<0.001\)* & - & - & - & \(p<0.001\)* \\  & & & & \(r=0.970\) & - & - & - & \(r=0.877\) \\ \hline \multicolumn{6}{c}{**Deep Nuclear Grey Matter**} \\ \hline  & \multicolumn{3}{c}{**SPM-BFC**} & \multicolumn{6}{c}{**N4 ITK**} \\ \hline  & \multicolumn{3}{c}{**BET2**} & \multicolumn{1}{c}{**SWS**} & \multicolumn{1}{c}{**HD-BET**} & \multicolumn{1}{c}{**SynthStrip**} & \multicolumn{1}{c}{**BET2**} & \multicolumn{1}{c}{**SWS**} & \multicolumn{1}{c}{**HD-BET**} & \multicolumn{1}{c}{**SynthStrip**} \\ \hline Manual & \(p=0.100\) & \(p=0.066\) & \(p=1.000\)\(r\) & \(p=0.150\) & \(p=0.100\) & \(p=0.506\) & \(p=1.000\)\(r\) & \(p=0.171\) \\  & \(r=0.158\) & \(r=0.410\) & \(=0.137\) & \(r=0.366\) & \(r=0.388\) & \(r=0.295\) & \(p=0.122\) & \(r=0.359\) \\ BET2 & - & \(p=0.002\)* & \(p=1.000\) & \(p=1.000\) & & \(p<0.001\)* & \(p=0.777\) & \(p=1.000\) \\  & & \(r=0.568\) & \(r=0.022\) & \(r=0.208\) & - & \(r=0.683\) & \(r=0.266\) & \(r=0.029\) \\ SWS & - & - & \(p=0.003\)* & \(p<0.001\)* & - & - & \(p=0.057\) & \(p<0.001\)* \\  & & & \(r=0.546\) & \(r=0.776\) & - & - & \(r=0.417\) & \(r=0.654\) \\ HD-BET & - & - & - & \(p=1.000\) & - & - & - & \(p=1.000\) \\  & & & & \(r=0.230\) & - & - & - & \(r=0.237\) \\ \hline  & \multicolumn{6}{c}{**Amygdala**} & \multicolumn{6}{c}{**N4 ITK**} \\ \hline  & \multicolumn{3}{c}{**SPM-BFC**} & \multicolumn{6}{c}{**N4 ITK**} \\ \hline  & \multicolumn{3}{c}{**BET2**} & \multicolumn{1}{c}{**SWS**} & \multicolumn{1}{c}{**HD-BET**} & \multicolumn{1}{c}{**SynthStrip**} & \multicolumn{1}{c}{**BET2**} & \multicolumn{1}{c}{**SWS**} & \multicolumn{1}{c}{**HD-BET**} & \multicolumn{1}{c}{**SynthStrip**} \\ \hline Manual & - & - & - & - & \(p=1.000\) & \(p=1.000\) & \(p=1.000\) & \(p=1.000\) \\  & & - & - & \(r=0.036\) & \(r=0.108\) & \(r=0.144\) & \(r=0.108\) \\ BET2 & - & - & - & - & - & \(p=1.000\) & \(p=1.000\) \\ SWS & - & - & - & - & - & \(r=0.036\) & \(r=0.216\) \\ HD-BET & - & - & - & - & - & - & \(p=0.952\) \\ \hline  & \multicolumn{6}{c}{**Cerebellum**} & \multicolumn{6}{c}{**N4 ITK**} \\ \hline  & \multicolumn{3}{c}{**SPM-BFC**} & \multicolumn{6}{c}{**N4 ITK**} \\ \hline  & \multicolumn{3}{c}{**BET2**} & \multicolumn{1}{c}{**SWS**} & \multicolumn{1}{c}{**HD-BET**} & \multicolumn{1}{c}{**SynthStrip**} & \multicolumn{1}{c}{**BET2**} & \multicolumn{1}{c}{**SWS**} & \multicolumn{1}{c}{**HD-BET**} & \multicolumn{1}{c}{**SynthStrip**} \\ \hline Manual & \(p=1.000\) & \(p<0.001\)* & \(p=0.861\) & \(p=0.565\) & \(p=1.000\) & \(p<0.001\)* & \(p=1.000\) & \(p=1.000\) \\  & \(r=0.108\) & \(r=0.891\) & \(r=0.259\) & \(r=0.287\) & \(r=0.223\) & \(r=0.805\) & \(rComparing the five BE methods regarding the RSVs obtained, statistically significant differences were observed between them when using SPM-BFC (Table 5): CGM--differences between Manual, BET2, and SWS methods with SynthStrip, and Manual and SWS compared with HD-BET; WM--differences between SWS, HD-BET, and SynthStrip methods with BET2; CSF--differences between Manual, BET2, SWS, and HD-BET methods with SynthStrip, and BET2 and SWS methods compared with HD-BET; DNGM--differences between BET2, HD-BET, and SynthStrip methods with SWS; SB--differences between Manual, BET2, HD-BET, and SynthStrip methods with SWS; BS--differences between HD-BET and SynthStrip methods with SWS, and Manual and BET2 methods compared with HD-BET.