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: > Thanks so far for the suggestions everyone. > > I tried using the SlicerMorph extension of 3D Slicer v. 5.3.0, but every > time I run it the program crashes. The DICOM file is about 2 GB, and I'm on > a powerful workstation that I regularly use for CT data segmention in > VGStudio Max. Has anyone else had this problem or know a workaround? I'm > trying to generate a cranial endocast of a gray seal skull, to give you an > idea of size. The cranium is about 16 cm long and 10 cm wide at its max, > and the scan resolution is about 0.11 mm. > > I looked into the Arothron package but notice it only runs on meshes, is > that correct? Because the seal skull is so thin at places, the meshes are > rather hole-y. That's why I figured there might be a benefit of working in > the CT data, but maybe I'm wrong. > > I'm open to more suggestions and thanks again for any feedback! > > Christy > > On Thursday, February 23, 2023 at 2:12:05 PM UTC+1 Thomas O'Mahoney wrote: > >> Dear Christy, >> 2 freeware options: >> You can do this in 3Dslicer using the extension Slicermorph's 'segment >> endocranium' function (Slicer can obviously segment the original stacks >> from a wide variety of sanners as well): >> https://github.com/SlicerMorph/SlicerMorph#module-descriptions >> If you already have 3d models from segmentation, you can use the >> Endomaker function in the R package Arothron. This is particularly useful >> if you have lots of models and want to easily fully automate this via >> scripting. https://doi.org/10.1002/ajpa.24043 >> Both Murat Maga (PI on Slicermorph) and Antonio Profico (who wrote >> Endomaker) are members of this list. >> Regards, >> Tom >> >> >> >> On Thu, 23 Feb 2023 at 11:43, Christy Hipsley <[email protected]> >> wrote: >> >>> Hi all, >>> >>> I'm looking for programs to generate cranial endocasts from CT data of >>> mammal skulls. While I can do this manually, I prefer something >>> (semi-)automated to minimise potential user-bias. >>> >>> Thanks for any advice, >>> Christy >>> >>> *Dr Christy Anna Hipsley | **Associate Professor* >>> Department of Biology, University of Copenhagen >>> >>> >>> -- >>> 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/morphmet2/671faccd-f795-4791-bab6-cc510fa9d438n%40googlegroups.com >>> >>> <https://groups.google.com/d/msgid/morphmet2/671faccd-f795-4791-bab6-cc510fa9d438n%40googlegroups.com?utm_medium=email&utm_source=footer> >>> . >>> >> -- 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/morphmet2/7b5b9d4f-962b-425d-98f7-7b4060a4515cn%40googlegroups.com.
