3D Slicer Crashes When Working With Data With Large Number of Slices

Russell_Engelman
Thu, 16 Feb 2023 04:32:02 +0000
Support

I recently tried to download a dataset from MorphoSource (https://www.morphosource.org/concern/media/000084459?locale=en) to segment in 3D Slicer. The dataset is very large and I am trying to export a surface mesh of the data. However, when I try to threshold the image stack in Slicer the program invariably crashes. Specifically, I can threshold the model, but when I try to view the 3D volume or save it the program becomes unresponsive and crashes. My workflow is simply “load model → open segmentation module → threshhold → try to do something with threshholded image → crash”.

Notably, this dataset (~5 gB) is much smaller than others I have successfully loaded on this computer, and when I try to load the same data into Avizo/Amira the latter program will not load the image stack at all. It doesn’t even crash, the dataset or its loading screen just fails to appear.

The only thing I can think of is this image stack has more than 2000 slices. I remember reading that there is an issue in Avizo/Amira where if an image stack is more than 2000 images the program will fail to load it as it can only consider < 2000 slices at once (and I have had similar issues with scans over 2000 slices there). I was wondering if 3D Slicer has a similar issue?

Has anyone had this issue or know how to resolve it?

6 posts - 4 participants