isosurface - hangs or crashes

Support
1

Hi All,
I am looking to create an isosurface to help with the selection of fiducials. However, when I try to create a surface (segment editor>show 3D or grayscale model maker [no smoothing, and permutations of 0 to 0.5 decimation]) slicer just hangs (I left it for 67minutes in one instance) or crashes. The CT dataset is large (3GB), but I can load and create isosurfaces in Seg3D in about 90 secs (markup function in seg3d is pretty poor).

Using the latest version 4.10.1

Any suggestions?

2

Everything indicates that you run out of memory. You can do one or more of these:

  • crop (to the region of interest) and resample (to make the number of voxels about 300 along each axis) the volume before you do anything
  • increase the virtual memory size (computation time will still remain long)
  • smooth the segmentation (using Smoothing effect) before you click “Show 3D”
  • disable model smoothing (drop-down menu of Show 3D) - it may make generation faster by a factor of 10-50x.

But maybe the simplest is to just use volume rendering for surface extraction. Choose a preset and use the offset slider to choose isosurface value. You may need to crop&resample input volume to fit into GPU memory.

1 Like
3

many thanks Andras,
I would be surprised if it were a memory problem - I have 96GB ram (I use the same machine for computational modelling). Unless there is some setup in slicer I have missed which means it is not using the memory correctly? I will check out the volume rendering options, though I have struggled with the landmarking of surfaces with volume rendering in the past - landmarks tend to sink through the surface.
best and thanks