Sunday, March 1, 2009

3D Slicer: The Tutorial Part V






A New Dataset



Taking a New Path





Let's Make An Endocast!







Introducing the Paint Tool


Making Some Progress


Modeling Your Efforts

Finishing Up



Anonymous said...

Paleo-nerd turned computer nerd, lol! (I hope you know I'm kidding.)

Anywho, Andy. I'm going to do my trademark "Fossil Fact" sometime this week and I'd like to talk about Acrocanthosaurus atokensis. And, I was wondering if you can help me. Can you review it when I have it posted so I tell my readers correct information? You can reach me at

Anonymous said...

Andy - Interesting post, but what are the costs involved? I.E. How much does a scanner cost? What is the cost-per-scan? How much do the endocasts cost? Any chance smaller museums and universities with smaller programs will be doing this in the near future?

Andy said...

The software is free. . .as for scanning costs, most folks are able to work out free (or extremely cheap) scanning arrangements with local hospitals. In my experience, the radiology folks are usually thrilled to scan a few fossils! Medical CT scanners are perfectly adequate for most fossils. . .if you have a specimen that needs a little more juice, you might have to pay to send it to Austin or Penn State (I think costs are detailed on the web pages for their respective scanning facilities). As for printing out a 3D copy of the endocast, I'm not sure what this costs as I've never had to do it. All of my work is done virtually. . .So, these sorts of techniques could be worked from any institution, regardless of size.

For most paleontologists, the really big price tags come from software licensing costs for commercial software packages. So, Slicer presents a non-commercial alternative (and, it is probably all you need for most applications).

Nick said...

Fantastic tutorial, Andy. I've been waiting on this one for awhile.

Andy said...

Thanks! I hope it's worth the wait. . .let me know if you have any comments or suggested corrections.

Unknown said...

I have been using Slicer 3.x on Windows XP and am having stability problems, like SLicer shutting down when I try to use the editor to make models, etc. Anyone else have this experience, or are you all so open-sourcy that you don't even know anyone who uses windows? (I should switch to linux, yes?)

Andy said...

Hi John--

We use a Windows machine at my museum for some Slicer work, and had similar issues with random shutdowns while using some tools. In the end, I found I just had to try a few different builds (either a "nightly test build" or a "stable release") to find the build that worked best. I don't remember which one it was off-hand, but can get back to you on this tomorrow, when I'm in the office. If you haven't subscribed to the Slicer users mailing list, this might also be a good chance to join and voice your concerns there, too. They're really good about response and feedback for these sorts of issues!

If it's just the model building component that's a problem, you can try building the model the "old fashioned" way, through the appropriate module as outlined in my last post.

I have found that the Linux version is generally more stable, but I'm not such a Linux zealot as to suggest you drop everything and become a Linux user! It's a good option, but not the only option. Windows (and even the Mac OS) have their good points, too.

Chris said...

Hey John, great tutorials! Im working through them so we can implement this technology in the army lab I work in. You said that you expereinced a bug with the change island tool. Was it that you could not select the island to be changed? I'm having difficulty with changing the islands and am using v3.2. Thanks again for the tutorial.

Andy said...

As I recall, my problem was when I tried to have it change islands across multiple slices - I haven't tried some of the newer builds (3.3 or 3.4), so they may have fixed it in there. Sorry I can't be of more help!

(it's always worth signing on to the Slicer mailing list, too. . .they can often give some good pointers)

Unknown said...

Slicer 3.4 has many improvements in the editor module. The four island functions (identify, change, remove and save) are working. If you enable volume check points, you can undo.

stev4n said...
