I would like to use Totalsegmentator to automatically segment the aorta from a CT scan of a baby. However, the results look very bricky. How can I improve the quality and reduce the pixelsize?
Slicer version: 5.8.0
The segmentation results will be resampled into the source volume’s resolution. If the source volume resolution is anisotropic (e.g., large spacing between coronal slices, as in the screenshot), you can use Crop volume module to resample the source volume to be isotropic before running segmentation.
Also make sure you disable fast mode in TotalSegmentator (that makes the resolution 2x coarser along each axis).
You can tune segmentation surface smoothing settings in the submenu of the “Show 3D” button.
Finally, if you really want to have high-quality rendering then don’t show the segmentation in 3D, just use the segmentation for colorizing volume rendering, by using Colorize volume module in the Sandbox extension. This is how you get renderings like this:
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