Hi! I am currently trying to segment some fossil material on a new desktop PC with the following specs: Lenovo ThinkStation Windows 11 Pro, Intel Xeon Silver 4208, 128 GB DDR4 (2400 MHz) RAM, Nvidia RTX A5000 24 GB, and a 512 GB NVMe SSD. The material in question is a stack of TIFF images obtaine…

There are many ways to improve the performance. But first you have to understand the memory usage during segmentation. If your volume is 11GB in size, during the segmentation (depending on the effect), Slicer may use 6-10 times more (so 60-100GB) transiently. That’s already at the limit of available…

Thank you very much for the prompt response! I will soon put into practice what you told me to adapt to the situation and be able to deal with the issue.

Thank you @muratmaga this is an excellent summary. I’m wondering how to make this easier for new users. I’ve submitted a pull request with a small change to ImageStacks extension to disable compression by default. What is your experience with Surface Nets? I’ve only tried it a couple of times and …

[image] lassoan: What is your experience with Surface Nets? I’ve only tried it a couple of times and it worked very nicely for me (with surface net smoothing). Should it be the default? Anything larger than toy data, I enable the surfacenets. I did not notice much of a difference in the model…

[image] muratmaga: [image] lassoan: What is your experience with Surface Nets? I’ve only tried it a couple of times and it worked very nicely for me (with surface net smoothing). Should it be the default? Anything larger than toy data, I enable the surfacenets. I did not notice much of a …

[image] lassoan: tasks that people thought would require a high-end workstation could be done on any laptop. I wish to add a little note on this particular topic. Working with segmentations on any modern laptop is fine and will be smooth, even without prior cropping. In my context, I use Sli…

[image] lassoan: What do you think about making surfacenets the default (maybe after releasing Slicer-5.8)? Yes, I think this is a good idea.

[image] lassoan: The popup could have buttons like “Ignore” (do nothing), “Reduce resolution” (change segmentation geometry), “More information” (open documentation page where the problem and solutions are explained in detail). This might work. [image] lassoan: People may not realize tha…

[image] muratmaga: if compression needs to be continued to be enabled by default Disabling compression by default for scalar volumes should be no problem. You only get about 50% compression anyway, which rarely matters. For labelmap volumes and segmentations the compression can be easily 100…

[image] lassoan: The main issue is reading images from standard zip files. As far as I remember, unless the zip files are saved in multiple streams, parallel unzip implementations are not much faster and you dont have random access (need to uncompress everything up to the byte you want to access…

Bad performance when segmenting 11GB micro-CT

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pieper (Steve Pieper (Isomics, Inc.)) September 14, 2024, 5:30pm 8

Yes, I think this is a good idea.

Changing the default algorithm for model creation in segment editor

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Bad performance when segmenting 11GB micro-CT

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