## 3 Methodology
### Data Acquisition  
Two different publicly available datasets had been used in this work. Thirty patients had come from a novel public dataset from the University Medical Center of Ljubljana (UMLC) [25]. Another 15 patients had come from the MSSEG 2016 challenge training dataset [26], as the testing dataset had not been available. Although the combined dataset had a variety of different scanners, there were only 5 patients for each of the MSSEG 2016 scanners, and the overall sample size had only been 45 patients (Table 1).  
For the UMLC patients, there were three available contrasts: 2D T1, 2D T2, and 3D FLAIR. The lesions in each of these sequences are depicted differently, as shown by Figure 1. FLAIR and T2 MRIs portray lesions as hyperintensities (brighter spots) while T1 MRIs portray them as hypointensities (darker spots). The T1 sequences had been obtained with turbo inversion recovery magnitude, a repetition time (TR) of 2000 ms, an echo time (TE) of 20 ms, an inversion time (TI) of 800 ms, a flip angle (FA) of 120\({}^{\circ}\), and a voxel size of 0.42 \(\times\) 0.42 \(\times\) 3.30 mm\({}^{3}\). Each T2 sequence had been obtained with turbo spin echo, a TR of 6000 ms, a TE of 120 ms, an FA of 120\({}^{\circ}\), and a voxel size of 0.57 \(\times\) 0.57 \(\times\) 3.00-3.30 mm\({}^{3}\). Each FLAIR sequence had been obtained with a TR of 5000 ms, a TE of 392 ms, a TI of 1800 ms, an FA of 120\({}^{\circ}\), and a voxel size of 0.47 \(\times\) 0.47 \(\times\) 0.80 mm\({}^{3}\). Each image came in 192 \(\times\) 512 \(\times\) 512 volumes, with the exception of patient 11 whose image came in a volume with dimensions 176 \(\times\) 512 \(\times\) 512.  
\begin{table}
\begin{tabular}{c c c} \hline \hline
**Dataset** & **Scanners** & **Patients** \\ \hline UMCL [25] & Siemens Magnetom Trio 3T & 30 \\ \hline \multirow{4}{*}{MSEG 2016} & Siemens Verio 3T & 5 \\  & Siemens Aera 1.5T & 5 \\ \cline{1-1}  & Philips Ingenia 3T & 5 \\ \hline \hline \end{tabular}
\end{table}
Table 1: Dataset Description.  
For the MSSEG 2016 dataset, three scanners were used to obtain a sagittal 3D FLAIR image, sagittal 3D T1 image, and an axial 2D T2 image. The acquisition details for this dataset are shown in Table 2.  
The ground truth for the UMCL dataset had been created by consensus among three different raters (Figure 2), and the ground truth for the MSSEG 2016 dataset had been created using segmentations from seven different raters. Since the presence of more expert raters creates higher intervariability, the creators of the MSSEG 2016 dataset had used the Logarithmic Pool Based STAPLE algorithm to provide a consensus ground truth [26].  
\begin{table}
\begin{tabular}{c c c c} \hline \hline
**Scanners** & **Sequence** & **Volume Dimension** & **Voxel Resolution (mm\({}^{3}\))** \\ \hline \multirow{3}{*}{Siemens Verio 3T} & FLAIR & 144 \(\times\) 512 \(\times\) 512 & 0.5 \(\times\) 0.5 \(\times\) 1.1 \\  & T1 & 176 \(\times\) 256 \(\times\) 256 & 1 \(\times\) 1 \(\times\) 1 \\  & T2 & 44 \(\times\) 240 \(\times\) 320 & 0.69 \(\times\) 0.69 \(\times\) 3 \\ \hline \multirow{3}{*}{Siemens Aera 1.5T} & FLAIR & 128 \(\times\) 256 \(\times\) 224 & 1.03 \(\times\) 1.03 \(\times\) 1.25 \\  & T1 & 176 \(\times\) 256 \(\times\) 256 & 1.08 \(\times\) 1.08 \(\times\) 0.9 \\  & T2 & 25 \(\times\) 320 \(\times\) 320 & 0.72 \(\times\) 0.72 \(\times\) 4 Gap: 1.2 \\ \hline \multirow{3}{*}{Philips Ingenia 3T} & FLAIR & 261 \(\times\) 336 \(\times\) 336 & 0.74 \(\times\) 0.74 \(\times\) 0.7 \\  & T1 & 200 \(\times\) 336 \(\times\) 336 & 0.74 \(\times\) 0.74 \(\times\) 0.85 \\ \cline{1-1}  & T2 & 46 \(\times\) 512 \(\times\) 512 & 0.45 \(\times\) 0.45 \(\times\) 3 \\ \hline \hline \end{tabular}
\end{table}
Table 2: MSSEG 2016 MRI Acquisition Description.  
Figure 1: Shown are images of the same patient’s brain in the UMCL dataset [25]: (**a**) FLAIR MRI, (**b**) T2-Weighted MRI, (**c**) T1-Weighted MRI, and (**d**) consensus segmentation.