# Comparison of Manual versus Semi-Automatic Segmentations of the Stenotic Carotid Artery Bifurcation
## 2 Materials and Methods
### Segmentation and Preparation (VascuCap vs. Slicer)  
We used an image processing software (vascuCAP Build A.3 25 January 2021 12:22:43; Elucid Bioimaging, Wenham, Mass) [22] to outline segments of the luminal and outer wall surfaces of the common and internal carotid arteries. After automatic segmentations, manual refinement was applied to correct the boundaries at the reconstructed surface in the lumen by two medical experts in consensus reading ([PERSON], [PERSON]). The external carotid artery was excluded from the study after the bifurcation. The exclusion of the external carotid artery was realized by cutting it off, preferably with a surface perpendicular to the axis. After this semi-automatic segmentation and the vascular reconstruction had been performed, plaque geometry and tissue composition were automatically computed for the entire artery section. The segmented lumen data for each patient were extracted from the VascuCap software.  
Manual segmentations were performed in an open-source software (3D Slicer, version 4.10.2. Kitware Inc., New York, NY, USA) by non-medical experts ([PERSON], MBN) in consensus reading. Initial selection of voxels outlining the luminal segment were made by manually adjusting the lower and upper thresholds based on voxel density. Subsequently, each cross section was analyzed to include or exclude additional voxels by painting over or erasing, respectively. In order to check the viability of the manual segmentations, the three homogeneous groups were processed as follows.  
The first patient group set was segmented individually by the medical (ZM, ZC) and non-medical experts (BC, MBN) without any corroboration from the other party (denoted as \"Individual\" in Figure 1). The second set was segmented collectively and at the same time with strong corroboration with the other party (denoted as \"Collective\" in Figure 1). After the corroboration the following conclusions were reached: 1. bifurcation segmentation has to be performed with more than two window settings; only using the automatic window setting is not satisfactory; 2. calcification should be manually reduced to compensate for the overestimation of the CTA; 3. circular calcification can conceal the contrast medium, and this artefact may give a false impression of occlusion or lead to under-segmentation of the lumen. The third set was segmented again individually without transferring any information on thresholding criteria or problematic vessel regions, but the conclusions of the collaboration were built into the methodology. Between the sessions, at least 2-week delay periods were held.  
Initially, every image was segmented by both methods, then all the raw segmentations were loaded into 3 DSlicer and the surface meshes were smoothed equally with a factor of 0.2. This step was needed for the later centerline calculation and cross-sectional analysis. Centerline calculations were performed by utilizing the Vascular Modelling Toolkits (VMTK) [23] framework. The initial centerlines were resampled and smoothed in VMTK to enable the proper calculation of curve-fitted perpendicular coordinate systems along the centerline. Based on these geometrical properties, the cross-sections were extracted along the centerline. Since the cross-sections are not circular, the equivalent diameters were calculated from the cross-sectional area. Although the cross-sectional area as an evaluation parameter can be sufficient, we chose the diameter because of a further evaluation step described later. The steps of the calculations can be seen in Figure 2.  
Furthermore, the area between the curves is shaded according to whether the differences with respect to the segmentation performed in VascuCap are positive (dark red) or negative (navy blue). For the sake of convenience, shading is the same as in [24]. Thus, the phrases over-segmentation (light red shaded area) and under-segmentation (light blue shaded area) will be used if the diameter curve from Slicer has a positive or negative difference, respectively, compared to that from VascuCap.