I am just wondering what to use. Ground truth?. If so, which tool can I use to obtain ground truth of 3D image with different sizes of vessels(including small ones)?. Phantom?,synthetic images?.
Sometime you can use the same validation methods that are available for 2D with 3D image segmentations such as inter and intra clusters validation methods which measure over and under segmentation issues. There are many literature which deals with the validation methods of 3D image segmentation. I came across a tool named Valmet see the following Web site http://www.swmath.org/software/1281 for more details and check the attached file. This tool has many validation methods for 3D image segmentation.
Valmet: A new validation tool for assessing and improving 3D object segmentation Extracting 3D structures from volumetric images.