Seeding basics for new user

Support
1

When painting in Segment Editor for “Grow from Seeds”, I understand you paint inside with one layer and circle around with another layer in order to segment out a structure. Without any added specification, how does the program recognize a difference between the two? Also, how to remove a areas that are “over painted”? Sometimes the seeding doesn’t render accurately or with appropriate coverage despite good contrast, and get very ragged organs (eg, liver). How to improve?

2

The algorithm grows each seed simultaneously. Growing is faster in uniform areas, so boundaries between segments usually end up where there is a big step in image intensity

If wrong segment is grown anywhere then just paint some more seeds there, with the correct segment. Since this usually happens in low-contrast regions, typically you need to paint with two colors, at both sides of hardly-visible boundaries.

For liver segmentation, I would recommend the fully automatic AI-based segmentation tool provided by NVidia AIAA extension.

3

Thanks Andras. I now better understand how the two colors are used to enhance contrast differential.

The extension requires 4.11.0 but unfortunately it won’t install properly on my PC.

4

Slicer-4.11 requires a PC not older than about 6-8 years. If your computer is a more recent one and Slicer does not run on it then let us know.

5

My “PC” is about 5-6 yrs old, but I installed a new motherboard and memory 6 mos ago. The error messages are of the form "The procedure entry point … could not be located in the dynamic link library… "

6

A post was split to a new topic: Liver visualization in 3D

7

What operating system do you use?
Can you post the full error message?

8

Hi @jax200 this is a known issue with today’s Slicer Preview build (Slicer 4.11.0-2020-09-28) which you can follow updates for this issue at Slicer 4.11.0-2020-09-28 does not start successfully · Issue #5208 · Slicer/Slicer · GitHub.

Instead you can download the previous Slicer Preview build for Windows at the following link:
http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.11.0-2020-09-25-win-amd64.exe&checksum=5e26ad3bfdc54f3c95221a583acc655e

9

Windows 10 x64

error

10

Thanks Andras - this extension worked quite well for me and look forward to experimenting with it further.