Paul, ITK-Snap is a nice tool, but I am surprised you couldn't do what you wanted to do in 3D Slicer as it is quite feature rich. As a comprehensive program, Slicer does have a longer (but not necessarily any steeper) curve than ITK-Snap. Our goal in SlicerMorph is to ease that curve. Here are couple documentation on segmentation in Slicer, if you would like to give another try:
*Endocast segmentation tutorial *written by a student on forum: https://slicermorph.github.io/Endocast_creation.html. It explains two different approach to manually segment endocrania, and then compares their output to Segment Endocranium modules one (this is a few years old, so menus look a little different than current version, but the functionality is identical). *And our segmentation tutorials*: https://github.com/SlicerMorph/Tutorials/tree/main/Segmentation The nice thing about ITK-Snap it uses the same open-source libraries as Slicer (namely ITK) so whatever you do in it, you can bring it Slicer (or vice versa). On Thursday, February 23, 2023 at 12:38:59 PM UTC-8 Paul Penkalski wrote: > 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/f42a6320-1101-4888-8927-0fa679b206cen%40googlegroups.com.
