Apologies auto formatting add a . to the link address and made it unrenderable. Here is the correct link to the endocast segmentation tutorial: https://slicermorph.github.io/Endocast_creation.html
On Friday, February 24, 2023 at 7:51:59 AM UTC-8 Murat Maga wrote: > 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/morphmet2/0a067ec7-d690-4196-8228-4a3f42b386a0n%40googlegroups.com.
