Segmentation in Slicer extremely slow when using the Scissors tool in slice view

[Russell_Engelman]

@muratmaga

1. You did not set the correct spacing of your data. I highly doubt the image spacing of this scan is 1x1x1mm. While this will not affect things like segmentation, if you are planning to take measurement, or calculate volumes/areas, they will be wrong.

The purpose of this video was merely meant to replicate the issue in question. I have also done this before with the space thickness set to the actual values for the specimen and the loading time was unaffected.

@muratmaga

I noticed you are using Scissors tool like a drawing tool (since you set the expansion to 0mm, meaning you are only changing that slice). Is there are reason you are doing that?

I was using the Scissors tool because this is what I had been explicitly told was Slicer 3D’s equivalent to the Lasso tool in other CT software when asked on this forum previously. See attached link. The description I was given of the Draw tool implied it was not suitable for creating a complex segmentation or trimming the results of a thresholding because it was said it would overwrite if a new region was drawn.

Is there a Lasso tool in the Segment Editor module in Slicer?

You can set the slice thickness for Scissors tool (set thickness to 0 to limit it to the current slice). You can also use the Draw tool (if you draw another segment then it will be erased from the current segment). You can use masking settings to limit editing inside a selected segment (so that you only need to pay attention when you draw the contour inside the segment). You may save time by segmenting manually on every 5th slice and then fill between using the “Fill between slices” effect.

@jamesobutler

Would you be able to repeat the creation of this video again, but instead use latest Slicer stable 5.8.0?

I can do this. I had thought I was using Slicer 5.8.0 but I suppose if the filename said otherwise it must be the case. When I had checked the documentation it said 5.8.0, but I wonder if what happened is that I downloaded the newer version but forgot to uninstall the old one, so when I searched for the program documentation it brought the newer file up.