isosurface - hangs or crashes

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?

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

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