CT-Scanning the Archbishop
November 18, 2009
Last week, for the first time ever, I spent the entire working week on palaeo. I took a week away from my job, and spent it staying in London, working on the Archbishop at the Natural History Museum. (For those of you who have not been paying attention, the Archbishop is the informal name of the specimen NHM R5937, a brachiosaurid sauropod from the same Tendaguru area that produced Giraffatitan brancai, and which has been generally assumed to represent that species.)
Brachiosauridae incertae sedis NHM R5937, "The Archbishop", Cervical U in right lateral view. Photo copyright the NHM since it's their specimen.
My main goal was to take final publication-quality photographs that I can use in the description (which I have committed to try really, really hard to get submitted by the end of 2009). There’s quite a bit of material (more than for Xenoposeidon, anyway!) — six cervicals in various states of preservation/preparation, cervical ribs, two complete dorsals, two more dorsal centra and a dorsal spine, some scap scraps, a partial ?pubis, a long-bone fragment and “Lump Z“, whatever that is. What you see above is my best lateral-view photograph of what I’ve designated “Cervical U”. One of these days, I’m going to do a post on how to photograph large fossils — something it’s taken me five years to get the hang of — but for today, I want to tell you about an exciting adventure with Cervical U. [Update: I wrote the How To post a few months later.]
Because my other big goal on this trip was to get it CT-scanned. Thanks to the generosity of John Hutchinson of the Royal Veterinary College, and to the help of the NHM people in arranging a loan, everything was set up for my host Vince Bickers and me to ferry the specimen up to the RVC, scan it and return it.
But first it had to be packed:
The Archbishop, Cervical U, packed and ready for transportation. Behind, Lorna Steel and Sandra Chapman of the NHM, who did the work.
Lorna and Sandra spent a long time looking for a crate big enough to pack the bone in, but came up empty — there was one that was long enough but not wide enough, one that was tall enough but not long enough, and so on. In the end we sat the bone, on its very solid plaster base, on a plastic pallet, and wrapped it in pillows, bubble-wrap and that blue stuff whose name I don’t know.
As it happened, the scan had to be delayed for a day due to lack of personnel at RVC, but Vince and I took the vertebra up on the Thursday anyway; he had to return to work on the Friday, but I took public transport to RVC for the big day. Before we went into the scanning room, John showed me his freezer room:
Just a couple of the freezers at RVC
I found it amusing that they have enough Segments Of Awesome that they have to label the various elephant-part freezers differently. And further down the aisle:
John Hutchinson proudly shows off his dead baby rhino.
Then it was off to the scanning facility, where we found that we had to unpack the vertebra: it was small enough to go through the machine, but there was no way the pallet was going through. Once we’d unpacked it and removed it, it fit pretty nicely:
The Archbishop's Cervical U all lined up and ready to go through the scanner, courtesy of John and radiographer Victoria Watts.
Because the scanner spits out X-rays in all directions, it’s controlled from a separate room, behind lead-impregnated glass:
Inside the control room
We ran three scans before we got the settings right — we needed more voltage to get through the bone and matrix than we’d first realised, and a filter was causing unhelpful moire patterns. The third scan was definitely the best, and the one I expect to be working with.
[Boring technical side-note: I plan to use 3D Slicer for visualisation thanks to Andy Farke’s series of tutorials. But, frustratingly, I wasn’t able to load the DICOM files from the scan into that program: it crashes when trying to load them (segmentation fault) even though it works fine on the ankylosaur skull that Andy walked us through in the tutorials. I fixed this by gluing the 300-odd files together into a single stack file that 3D Slicer was able to read. For the benefit of anyone else who needs to do this, the command (on a Ubuntu Linux box) was: medcon -f *.dcm -c dicom -stack3d -n -qc]
Here is an example slice, showing part of the condyle in posterior view:
CT slice through the condyle of The Archbishop's Cervical U, in posterior view. Dorsal is to the left.
The grey blobs at the bottom of the image are the plaster jacket that supports the vertebra; the white is bone, and the light grey inside it is matrix that fills the pneumatic spaces. I’m showing the condyle here because its cavities are clearly visible: further back in the vertebra, they are harder to pick out, perhaps in part because of the iron bars scattering the X-rays. It’s notable that this vertebra is less pneumatic than would be expected for a brachiosaurid — by eye, it looks like like the condyle is only 20-30% air, and this slice is not unrepresentative. Most neosauropods would be at least twice this pneumatic, so we may have an Archbishop autapomorphy here.
I’ve not yet persuaded 3D Slicer to build a 3D model for me, but I’m pleased to say that before I left RVC, John mocked up a quick-and-dirty render of the bone using only density threshholding, and I can at least show you that.
The Archbishop, Cervical U, CT scan 3d model in left ventrolateral view
Here we see the bone from the left side, previously obscured by solid plaster. From a single static image, it’s not easy to make out details, but we can at least see that there is a solid ventral floor to the centrum … and that those two crossed iron bars obscure much that we would like to see. You will get more of an idea from the rotating video that this is screencapped from.
Looking at this and comparing it with the right-lateral photo at the top of the post, it’s apparent that the density threshhold was set too high when making this model: all the bone along the lower right margin of the middle part of the centrum is good, but it’s been omitted from the model. In other words, the vertebra is more complete than this proof-of-concept model suggests. Hopefully I will shortly be able to show you a better model.
Sauropod Vertebra Picture of the Week 
November 18, 2009 at 2:46 am
Very cool! Interesting tip on gluing the DICOMs together. . .hadn’t thought of that before.
November 18, 2009 at 3:24 am
BTW, Mike – you probably want to refer to it as “Brachiosauridae incertae sedis”, rather than “indet.” Indeterminate implies that the material is not diagnostic, and cannot be assigned to any genus or species (even a potential new one). Based on your previous comments on this blog, I understand that you think it will be assignable to a species (perhaps one not yet named), the specimen is better currently filed under “incertae sedis” because it is unassigned within Brachiosauridae, but diagnostic.
November 18, 2009 at 5:03 am
It’s beautiful. Can’t wait to see more scans! I was almost dying of laughter at the “elephant foot freezer” lol. I’m guessing this is an anterior cervical, since that CT scanner looks a bit small for the posterior cervicals of something as big as the Archbishop…
If cervicals from Supersaurus ever get scanned (or Puertasaurus or Sauroposeidon), I’m guessing it will take one of the huge open-type MRI machines… the kind used to scan live, WHOLE elephants…
November 18, 2009 at 7:25 am
It was truly an hono[u]r to scan something so regally magnificent as The Archbishop. I hope to scan The Pope someday. And I am pleased that the glory of the Freezers of Awesomeness has been shared with the world.
November 18, 2009 at 9:46 am
wow. Fantastic… thanks for sharing.
Aside from the wonderful pneumatic structures etc, what information is won from the this scan? Does it help assess deformation processes / reconstruction?
November 18, 2009 at 10:17 am
Randy, thanks for the clarification on indeterminate/incertae sedis — I’ve fixed my caption accordingly.
Nima, believe it or not I have still yet to confidently determine the axial position of any of my cervicals (although I am clearer with the dorsals). Near the top of my list is getting them in order. I don’t think this is very anterior, though, as Cervical V is much smaller. Sauroposeidon has been CT-scanned — indeed those CT scans were the foundation of Matt’s career, as they set him off down the path of investigating pneumaticity. See his publications at http://sauroposeidon.net/cv.html
Davidmaas, I really can’t say yet what I am going to learn from the scans. So far I can barely pilot the visualisation program. It’s a bonus that I’ve so quickly been able to identify an oddity, the low level of pneumatisation.
November 18, 2009 at 11:05 am
The scan at least underscores some issues with rendering CT of matrix-filled bone (especially of the vertebrae) due to differential permineralization. Relative density of the material also underscores some of the necessary meticulous slice-by-slice modification of the scans in order to compose a model, and was necessary at least for the scan of the skull Sue, given the composition of the Hell Creek sediments (Brochu, 2003). Meticulous editing of the slices by appearance may be required for the bulk of the scan-to-model work, but as you noted, parts of the bone are almost undifferentiable from the matrix, and the result is the scan product above.
November 18, 2009 at 11:37 am
Low pneumaticity, interesting. I wonder how individually variable pneumaticity was, between different sauropods of the same species? Humans sometimes have weird developmental stuff happen with sinuses, I think; if we had 1000 Sauroposeidons or Brachiosauruses, I wonder what oddities would appear?
November 18, 2009 at 11:50 am
William, now you are asking one of the key questions: how does degree of pneumatisation vary between individuals? Here are three more: how does it vary along the neck, how does it vary long the length of an individual vertebra, and how does it vary through ontogeny? Then of course there is variation between taxa across the tree. So what we have here is a five-and-half-dimensional space that we want to fill with observations so that we can start to deduce conclusions. Trouble is, there are, so far, 22 published observations (neatly summarised by Wedel 2005:table 7.2), which is not really enough to let us map out 5.5-space! That’s one reason why, at the moment, each observation is valuable — it adds 4% to the total knowledge in the world.
(Matt, or anyone else: if I’ve missed any published ASP values subsequent to Wedel 2005, do say.)
November 18, 2009 at 2:22 pm
I hope when you describe it there’s an arch(i)episcopos in its name somewhere. :)
John Hutchinson: I hope to scan The Pope someday.
There’s a Pope too?
November 18, 2009 at 7:51 pm
I will here predict (without claim) that pneumatization in cervicals will be found to increase progressively toward the skull. The Archbishop, then, will turn out to be relatively proximal.
What are those iron bars for, anyway? Is such treatment common, or is this one particularly fragile / friable?
November 18, 2009 at 8:52 pm
I suspect, Nathan, that the bone is in several fragments and the iron bars and the plaster jacket on them is needed to keep it together in one piece.
Vertabrat says: [i]There’s a Pope too?[/i]
Lol at this rate with all the sauropods being dug up around the world in different places, I wouldn’t be surprised if there IS a ‘Pope’ soon. Or an Ayatollah, a Rabbi, a Metropolitan or a Dalai Lama…
The funny thing is, in a way the name “Archbishop” made sense when I looked at that famous pair of dorsals that have often been mislabeled as B. brancai in books. It looks very vaguely like an Archbishops mitre seen sideways (well at least a Catholic or Anglican one anyway).
That elephant foot freezer is still stuck in my mind LOL… I’m making that thing my new wallpaper.
November 18, 2009 at 9:13 pm
Nathan, Cervical U seems very solid, possibly because of things that were done to it be preparators rather then because of its intrinsic integrity, so my feeling is that the bars were not necessary — especially in light of how solid the plaster base is. But getting them out again would be a total sod, and I don’t imagine it ever happening. Cervical V was prepped out of its jacket much more recently — a year or two ago — and is VERY crumbly, so maybe U was the same before being consolidated.
November 18, 2009 at 10:35 pm
You can’t do a good nuclear magnetic resonance scan as long as those bars are in there, although it would be fun to watch somebody try it. Maybe they could be oxidized out, gradually, from the ends. (Keep dabbing in H2O2?)
Future fossils should be braced up with fiberglass.
November 19, 2009 at 3:38 am
I’m looking forward to seeing what you’re going to name your first dinosaur, Dr. Taylor.
With regards to that, I remember Scott Hartman bemoaning the existence of “Reallybigosaur” names such as Supersaurus and Ultrasauros when we were both working at the Wyoming Dinosaur Center, and John Hogbin the molding and casting guy there discussed alternatives with me. He came to the conclusion that we could really mess with people’s heads by simply naming a taxon something like “Bob”. Not “Bobsaurus”, not Bobraptor”, just “Bob”.
November 19, 2009 at 4:26 am
…Oh, silly me. This would be your second dinosaur, after the most excellent Xenoposeidon.
November 19, 2009 at 8:32 am
Indeed this will not be the first! In fact, it won’t be the second, either — with Matt and another co-author, I have another new-sauropod manuscript ready to resubmit after rejection and revisions, which I really ought to get done tonight (except that I am having too much fun with the Archbishop to get excited about doing that rather dull job). That one, too, has — if I say it myself — a name that you are going to like a lot more than a Reallybigosaur name.
November 19, 2009 at 6:19 pm
Mike – you’re such a tease! In any case – although the new name you are alluding to is awesome, it could have been even more awesome if you had gone with a different suffix. But then again, I’m biased.
November 19, 2009 at 9:07 pm
I’m with Jamie. Pick up a copy of “Name Your Child”. Practically all of those names are unused and eminently available. It’s your right as the person who did the work to make everybody else say the name you chose. With very short names they have no excuse to abbreviate; for Bob sue, you won’t see any B. s. (so to speak). It’s your job, though, to make Bob sue important enough that they are obliged to write about it, despite their embarrassment.
November 19, 2009 at 9:42 pm
I admit I have toyed with the idea of giving it the name Archbishop.
Not gonna, though.
November 23, 2009 at 3:07 am
LOL yes, that would be a bit odd… though things like Minmi and Drinker are even odder… And Jobaria and Erketu both basically mean “demon” in other languages… whatever name you pick, Mike, I’m sure it’ll be impressive.
BTW, here’s some good news! For those of you that want to see all versions of my Brachiosaur Parade (which of course includes the Archbishop), the full story with all the images is up now – here’s the link:
http://paleoking.blogspot.com/2009/11/brachiosaurs-parade-90-million-years-of.html
January 4, 2010 at 4:03 pm
[…] is sample size. I harped on this in 2005 (Wedel 2005), and Mike just brought it up again in a comment on a previous post. In fact, what he had to say is so relevant that I’m going to just cut and […]
September 20, 2010 at 8:35 am
[…] I went off to lunch with Kent and Martin. Despite the lighthearted attempts of session moderator John Hutchinson to build the session up as a two-way fight, it was all rather peaceful and enjoyable. After lunch […]
March 24, 2011 at 1:45 am
[…] in early Februrary, Darren and I got an email out of the blue from biomechanics wizard and all all-round good guy John Hutchinson, saying that he’d obtained the neck of a baby giraffe — two weeks old […]
December 12, 2011 at 11:05 pm
[…] Gasco for the first time. And it’s always good to spend time with people like biomechanics wizard John Hutchinson and occasional SV-POW! guest-blogger Heinrich Mallison. (Apologies to those I’ve not […]
March 6, 2012 at 11:32 am
[…] across to What’s In John’s Freezer?, the awesome new blog of biomechanics wizard and brachiosaur-cervical scan facilitator John […]
August 17, 2020 at 11:26 pm
[…] before Matt and others were CT-scanning sauropod vertebrae to understand their internal structure, Werner Janensch was doing it the old-fashioned way. […]