I am using Slicer 5.0.2 on a Mac Studio with a M1 Max chip (10 cores, 64 GB memory) in order to segment the volumes of archaeological finds (in that case a Bronze Age sword hilt). I am working with a 5.84 GB nrrd file with the following dimensions:
Using the segment editor, I created 6 segments for the different components of the hilt and the background using Grow from seeds. The process was quite long, with a long update time for each modification, but that worked eventually. The segment of the blade shows extrusions and holes I would like to smooth. After removing the most obvious mistakes using 3D scissors, I tried to use a median filter with a 1 mm kernel size (I cannot increase it). Slicer then freeze with an endless spinning wheel. The activity monitor shows Sliceer is using around 20 GB of memory, which is fine, but almost all CPU power. I let it run for a couple of days without any change. I also tried the same operation with a smaller volume susing the “Crop Voume” module with a 2.00 spacing scale factor and to apply the smoothing on a small area using the smoothing brush, the result is the same. I always run the smoothing operations with the 3D view deactivated.
The smoothing works fine if I export the segments as stl files and open them on Meshlab, but I’d like to process everything in Slicer. Any idea how I can make it work?