This post is mostly a note to myself so that I remember how to do this next time I upgrade or reinstall my system. But, perhaps it will be of use to others.

The program Bundler is one of a suite of programs that are very useful for photogrammetry on the desktop computer or laptop. Being a devoted Linux user, it's important to me to be able to run my software where and how I want it. Unfortunately, Bundler does not play well in 64-bit Linux (I am running Ubuntu 12.04-64 right now, in support of processing large data sets), generating segmentation faults upon attempts to execute. This is a fairly well-known problem (I found three or four pages mentioning this), but it can be tough to track down the solution. Fortunately, I found it here. What follows is essentially a short list of what I did to fix the error (with a general description of how I set up my system).

• Set up BundlerTools (a package including Bundler and other programs necessary for photogrammetry), using scripts at the BundlerTools website. I installed it into my home folder ("home/username/BundlerTools").
• Per the directions here, I installed ia32-libs and liblapack3gf:i386. The first one was already installed, just as a note. Code was:
• sudo apt-get install ia32-libs
• sudo apt-get install liblapack3gf:i386
• Then, following these directions, I copied libANN_char.so (found in BundlerTools/lib) to my /usr/lib folder, and made the file executable. Commands were:
• sudo cp /home/username/BundlerTools/bin/libANN_char.so /usr/lib/
• sudo chmod 755 /usr/lib/libANN_char.so
• And that did the trick!

The latest release of OpenOffice.org (version 3.2) just came out. I've been using release candidate 4 for the last week or so, and love it. For those of you who aren't familiar with the package, it's an open source office suite, with full-fledged word processing, spreadsheet, presentation, and database software (my experience is primarily with the first three). Plus, it's free! For the last four years, OpenOffice.org has been my primary office suite - my dissertation was written on it, all of my slides (and many poster presentations) are composed in it, and the great bulk of my data collection happens with this software. In that time, I've seen the software evolve from a decent package to a great package!

Improvements in this release include a faster start-up time, better copy-and-paste functionality in Calc (the spreadsheet), and much more. I've also noticed some bug fixes for the track changes and comments feature when working with Microsoft Word documents (something I do quite frequently, particularly for collaborations). All of these are mostly minor steps beyond the previous release, but it's still well worth the download time for the upgrade.

October 19 - October 23 is designated Open Access Week, in order to raise awareness of open access publication and scholarship. So, I'll be blogging a little bit more about open access during the next few days.

For my first post, I wanted to clarify a common confusion that I hear from many colleagues: open source vs. open access. Although the terms are related in some ways (indeed, they derive from a very similar philosophy), they refer to two discrete concepts.

Open Access: Focuses on the unrestricted sharing of research results, typically through open access journals (PLoS ONE, Palaeontologia Electronica, etc.).

Open Source: Computer software, typically (but not always) freely distributed, in which the source code is freely available. There are a host of other stipulations in some definitions, which are largely an elaboration upon this point.

Thus, PLoS ONE is open access; 3D Slicer is open source.

A few months ago, I decided that I needed a computer to take into the field. My primary laptop, a two-year old Dell Latitude DE1505 (which I love!) is steadily losing battery charge capacity. . .I'm lucky to get more than an hour out of it when unplugged. Because my primary field camp is relatively remote and without electricity, I needed something with a little more juice to it. Buying a new battery seemed a little expensive, especially for a laptop of that age (and I wouldn't gain that much in battery life anyhow). So, I started looking around for options.

I very quickly found the Asus Eee PC line as an interesting option. They're tiny, energy efficient, cheap, and run Linux easily. Who could ask for a better combination? So, I plunked down about 300ドル for the Asus Eee PC 901. . .I am writing the bulk of this blog post from my tent in a remote corner of Utah, if that is an indication of a worthwhile purchase! In this post, I'll discuss my experience using this little machine under paleontological conditions.

First, the physical characteristics of the Eee PC 901. It's really a netbook, which means small, small, small, measuring 8.8 inches in maximum width! This is great when you want something that's easily transportable, but the tiny keys on the keyboard take some getting used to. Additionally, many keys such as PageUp and PageDown are accessible only through a key combination (for instance, “Function” plus the “Up” arrow for PageUp) rather than as their own keys. After a little bit of practice, I got the hang of it. The track pad is small but adequate – for serious use, I'd probably plug in a regular mouse and keyboard, but it's more than enough for field use.

The screen is also small, but very legible. I find that when I'm typing in a word processor, particularly when reclining in my tent, it's helpful to zoom in a bit to get a good look at the text. Not unexpected for a netbook, again. The screen brightness is pretty good, although as with nearly any laptop it is tough to read in direct or bright indirect sun.

Now on to the nuts and bolts. Because I bought a Linux model, it came with a 20 gigabyte solid state drive (essentially, a USB stick for a hard drive). The solid state drive allows the computer to eke out every bit of battery life, because it doesn't have to keep a hard disk spun up all of the time. That said, 20 gigs isn't that much space these days, so I bought an 8 gig SD card for extra file capacity. The Eee PC has an SD card slot on the side, which is a major bonus!

The default operating system for the Eee PC is either Windows Vista (blech) or a custom build of Linux based on the Mandriva distribution. Open source paleontologist that I am, I went with the latter option. The factory Linux OS is adequate and intuitive, but I was frustrated by the difficulty in installing custom software or even updated packages of some key systems. I want OpenOffice.org 3.1, not 2.7! So, I installed a distribution called “Easy Peasy.” Despite (or perhaps because of) its cheesy name, “Easy Peasy” runs pretty much flawlessly on my machine. The desktop environment differs from Ubuntu in having nice large buttons on the desktop rather than a drop-down menu—a simplification, but a good one for something with a screen of this size. It's easy to install or upgrade applications (same method as with Ubuntu), and the default applications are comprehensive and up to date.

When within wi-fi range, the wireless card in my EeePC works flawlessly. In fact, I usually get better signal pick-up and connection reliability than the Windows or Mac users working alongside me (this is a hallmark of most Linux laptops I've worked with). Unfortunately, it does not seem to be particularly easy to turn off the wi-fi card with the default settings in Easy Peasy. So, I installed eee-control, a little utility that I highly, highly recommend for anyone using an EeePC. This fixed the problem quite elegantly! Unfortunately, I didn't find this piece of software until after I got back from the field.

I haven't completely run my battery down out in the field, but the battery life estimator indicates around 4.5 to 5 hours on a full charge. I suspect I could get longer life by turning off wi-fi (and I'll have to see how eee-control helps out in this regard), but this is still pretty darned good! I purchased a power inverter in order to charge the netbook as needed from our field truck's cigarette lighter. This setup has been working well.

In the field, I've been using my EeePC to keep track of the specimen field catalog as well as working on various writing projects (including this blog post) after hours in my tent. All told, the machine is more than adequate for these tasks. I'm not running my computer during the heat of the day, so I can't speak for its behavior at 100 degrees, and I am careful to store it away from any major sources of dust or grit. As mentioned above, it is tough to read anything on the screen under bright lighting conditions.

In the end, I would rate my Eee PC 901 a solid A-. The very portable size and long battery life for a good computing experience. The only things preventing me from issuing a completely glowing recommendation is the rather limited default Linux operating system (an easily rectified problem) and the initial problems with turning off the wi-fi card in Easy Peasy. I wouldn't recommend this as someone's primary computer (the tiny keyboard would probably give you hand cramps after awhile, and the processing speed and hard drive space are minimal for any real multimedia tasks or storage), but the affordable price makes the EeePC 901 a quite attractive option for a travel or field computer.

Wow! The past few days have been a real whirlwind. As mentioned in my last post, our long-awaited paper (well, long-awaited by my co-authors and me) on Triceratops horn use and paleopathology was unleashed by PLoS ONE on Tuesday evening. We've received some wonderful feedback through this blog and email, and are very ready to move on to the next research project.

Because this blog focuses partly on open access and open source software, I wanted to write briefly about how these issues factored into our research. This is one of the most "open" projects I've attempted to date, from start to finish. Here are the details:

• The data collection and statistical analysis were completed in OpenOffice.org Calc, with the calculations based on a spreadsheet file I found (and tested against known examples) from somewhere on the internet (but can't remember where, now!). R will also do the appropriate calculations, but I stuck with the spreadsheet because my data files were so small and straight-forward.
  
• The manuscript was written in OpenOffice.org Writer, but my co-authors and I batted it back and forth in Word format (because Darren and Ewan are using the latter program). We had no problems with this strategy, and the format conversions were a snap for the relatively simple documents we were using.
• The bibliography was compiled and formatted using Zotero. Zotero even has a readily available style file for PLoS, so this made my life very easy.
  
• The figures were edited for contrast and brightness in GIMP (no other manipulation was performed on the images) and assembled in Inkscape.
• The journal, PLoS ONE, was selected because of its high profile, high impact, and open access. Thanks to the open access policy, our article is readable by anyone who wishes to see it. I hope that the broader exposure will facilitate debate and further research on the topic--only time will tell. If I have any future articles of potentially broad interest, PLoS ONE will definitely be on my list of candidate journals.
• The popularization of the article was initiated by PLoS ONE, with follow-ups by numerous journalists and bloggers. Thanks to the wonders of the internet, many of the articles are available for free. And, I am happy to say, most of them are pretty well-done.
  

I hear from a reliable source that your Digital Methods in Paleontology course has this blog listed as a recommended website for some supplemental readings. So, to all of you UT Austin students, welcome! I hope that the content here is at least somewhat useful. . .don't hesitate to post if you have any questions or comments. I (and my readers) are particularly eager to hear if you run across any other good software tools that aren't listed here, or if you have your own feedback on some of the software I've reviewed previously.

Your first reading assignment (if I'm reading the syllabus correctly) is found here. . .it gives some good background info on the blog. If you're completely bored, I would strongly recommend this post as a logical follow-up. Despite the name of this blog, I am not an open source zealot, and the referenced post gives some of the pros and cons of using open source software. Don't know what open source software is, exactly? This page is as good as any for a succinct introduction to the concept.

Good luck in the coming semester, and enjoy the class!

I've detailed, R, that wonderful piece of statistical software in a previous post, but an article in today's NY Times gives some nice additional background to the whole project. Check it out if you want to know "the rest of the story." There's also a delightfully snarky quote from a spokesperson for SAS, the chief commercial rival to R.

“I think it addresses a niche market for high-end data analysts that want free, readily available code," said Anne H. Milley, director of technology product marketing at SAS. She adds, “We have customers who build engines for aircraft. I am happy they are not using freeware when I get on a jet.”

Because everyone knows that commercial software is always reliable. Personally, I don't care what software an engineer uses to design a jet. Just as long as the software and the engineer both know what they're doing. The same goes for the software (a mix of commercial, open source, and free closed-source programs) I use in my own research--I'm not a complete open source zealot (all my FEA analyses are on commercial software, because I still haven't found an open source alternative that doesn't require a computer science degree), but if I can get the job done for free, the price is right!

Thanks to Denim and Tweed for pointing me towards this link.

Randy Irmis just passed on what looks like a very useful, feature-rich, open source GIS application - MapWindow GIS. Because the center of the application is an ActiveX control, this program will be most at home on Windows. I haven't yet had a chance to try it out yet, but would love to hear from anyone who has!

Every once in a great while, a program comes along that completely changes the way you do things. For me, this program was 3D Slicer. I remember the early stages of the "CT Revolution," when CT reconstruction required 10,000ドル worth of software and 4,000ドル worth of hardware. Heck, this attitude even persists today with some folks! When I started on my dissertation, which was going to require a lot of CT analysis, I knew I either had to get a whole lot of money fast, or else find a free alternative. 3D Slicer came along at just the right time.

3D Slicer is an open source, 3D reconstruction package that is intended to work with tomographic data of all types - particularly CT and MRI. It excels at making high-quality surface reconstructions (although a volume rendering module is nearing maturity, too), volumetric measurements, and all other sorts of things. Oh yeah, and it's FREE. Slicer became the workhorse for my dissertation (and many others at my graduate institution).

The documentation was pretty incomplete (and still is, in some areas) when I started with Slicer. So, I spent long hours of just trying to load data and get a simple model. Things are better now, but because Slicer is geared for the biomedical crowd, most of the tutorials for the program that are available on-line follow biomedical examples. So, I decided to put together a Slicer tutorial that would benefit paleontologists.

The present tutorial, issued in a series of posts, follows a paleo-oriented example for using Slicer version 3.2, the latest official release. Version 3.3 is available in alpha form, and no major changes in the interface are evident. So, you should be able to follow this regardless of your version. Note that the 2.X series has a pretty different interface, although many of the fundamentals are the same (even if you have to look under different menus or toolbar buttons).

The screenshots used here were taken from the October 1, 2008 build of Slicer 3.2, running under Ubuntu Linux 8.04. But, all of the gizmos and gadgets should run just the same under Windows or the Mac OS.

Let's get started!

Starting Assumptions
This tutorial assumes that you (the reader) have some measure of computer competency - you know how to install programs, unzip files, and the like. It also assumes that your computer has enough processing power to handle the data sets. Memory, rather than processing power, is the important thing - you'll probably want at least a gig of RAM, and more is always better.

Getting Slicer
Visit the Slicer Download page, for a whole set of instructions and options. New users probably want to get a Stable Release, but those who want the latest bleeding-edge features should opt for a Nightly Build or Snapshot. Most operating systems are represented (Mac, Windows, Linux, and Solaris). As mentioned above, you'll want at least Slicer 3.2 for the purposes of this tutorial.

Getting an example data set
The dataset used in this tutorial is that for AMNH 5405, a Euoplocephalus skull. These data have been generously posted to the web by Larry Witmer, available here. To begin, download the data and unzip them in the directory of your choice. In my case, I put them on my Desktop in my home directory, and renamed the folder to AMNH5405.

Starting Slicer
Depending on how you installed Slicer, you may access it from the Windows menu, or the folder into which you installed it, or some other place. In my case, I have it installed into a folder called Slicer3.2, in my home folder. In order to start Slicer, I open the folder and double-click on the "Slicer3" icon. The program starts up with a friendly welcome screen, while various modules are loaded, and then you see the blank user interface - no data are loaded yet.

The screen shots accompanying the tutorial from here on out will appear just after the relevant steps.


You'll note that as you move your mouse around, various context helps come up to indicate what each icon does. Because this is a "bare bones" tutorial, we'll only be looking at the ones needed for the task at hand.
Loading Your Data
Let's dive right in! The first step is to load the CT data that we want to reconstruct. There are one or two ways of loading data, but let's go with the simplest. Under the "File" menu, choose "Add Volume." Now, a new window appears, with your directory structure on the left and a list of files on the right. In the left part, navigate to the directory that contains your data (AMNH5405, in this case). Click on it, and then you should see a whole list of DICOM files. Click on the one at the top of the list, and then hit the "Apply" button at the bottom of the window.
Wait patiently as the data are loaded - depending on the speed of your machine, this may take a little while. It took about 13 seconds on my relatively high-powered computer. Now, you should see your data!
Here ends the first part of the tutorial. The next post will continue with "Looking at the Data."

My university has done a wonderful thing, in accepting only PDF files for deposition of a thesis or dissertation with the graduate school. Gone are the days of printing 5 copies of a 300-page document on acid-free paper that costs 20 cents a page (and then finding out that one of the margins is 0.1" too wide, so please correct and resubmit before the deadline in three hours). The transition is a wonderful step forward, and also means that it is much easier to distribute the dissertation.

As a proponent of free and open source software (having made the big switch about a year ago), I wanted to do as much as I could within the realms of that universe. This posting summarizes the software I used, with the hope of inspiring others to follow a similar path (whether in whole or in part).

Data visualization: I processed all of my CT scan data in 3D Slicer. For segmenting structures, generating surfaces, and measuring volumes, look no further! [I still need to do a more complete post on this one.] Additional analysis was done in ImageJ.

Data analysis: Initial data entry in OpenOffice.org's Calc, with analysis primarily in R and an occasional venture to PAST.

Figures: Raster image editing was done in the GIMP, and line drawings or composite figures were assembled in Inkscape.

Word processing: All done in OpenOffice.org's Writer. The PDF output function was very nice for sending drafts to committee members and advisors, and the software's Microsoft Office compatibility is such that I could also send and receive marked-up documents (in .doc format) pretty easily. For the final document, I exported each chapter in PDF format.

Referencing: All of my references were sorted, organized, and rendered as bibliographies with Zotero. Along the way, I created custom styles for Journal of Vertebrate Paleontology and Zoological Journal of the Linnean Society. More on this process in another post.

Document assembly: To assemble all of my dissertation's chapters into a single PDF document, I used Ghostscript. The output was quite pleasing, and easily accomplished through the command line in a matter of seconds.

Presentations: For my oral dissertation defense, I created my presentation using OpenOffice.org's Impress.