Hi Christy, Another good option is ITK-SNAP: http://www.itksnap.org/
Although it isn't designed specifically to segment endocraniums, it has several automatic algorithms that I've used to segment fossil braincases automatically and it worked really well. You may have to clean up the segmentation a little at the end, but that's true for any program. Then you can save the segmentation as a 3D model or mesh. You might download it and do a quick test segmentation, and you'll see how straighforward it is. I had tried 3D Slicer prior to that and couldn't get it to do anything useful. Then someone recommended ITK-SNAP. Of course there are a few commercial apps too, but they aren't any easier to use, and not really any more powerful than ITK, and obviously more expensive. Downsampling the scan is a good idea. I often do that. You can also crop it, e.g. if it's a scan of the whole skull and you only need to segment the endocranium. I like IrfanView which can do batch crop and resize and has a DICOM plugin (and it's free, at least the older versions). 0.1 mm is pretty high resolution unless you're scanning mice! Cheers, Paul P. On 2/23/23, Murat Maga <[email protected]> wrote: > Without the data it is hard to tell, but often those crashes are memory > related. Memory usage during segmentation increases 8-10 folds based on the > segmentation effect being used. So if your dataset is 2GB, you need minimum > of 16-20GB of "available" RAM for Slicer to work properly. If you can share > your dataset, I can take a look. > > Also for endocast segmentation there is no need to work with full > resolution images. You can downsample your image (via the CropVolume) by 2, > and then try. That will reduce your data volume by 8 folds. Your > experiments will go faster too. > > The other important parameters is the size of the largest hole to plug, and > the smoothing. Default parameters we included worked fine for large apes, > but I am not sure for seal skulls. > > > > On Thursday, February 23, 2023 at 7:24:30 AM UTC-8 Christy Hipsley wrote: -- You received this message because you are subscribed to the Google Groups "Morphmet" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/morphmet2/CAJveYNT5LrdYjdMLhpoc_zvgj%2BCQw%3Dm4KzCbGsr3Ban6hb0Dqw%40mail.gmail.com.
