This week I’m going to show you how I carried out my assessment in the Virtual Anatomies module, in a similar way to James Makes a Monkey Skull with a similar over exaggerating title but less complaining about the software.
This time my task was to reconstruct the missing right canine of a chimpanzee skull that had been scanned in an MRI machine and make it look acceptable to be 3D-printed. Sadly, the 3D printing part is very unlikely to happen.
The first thing to do is open the DICOM stack, or series of images which are taken in an MRI scanner or a CT machine. Then open up some orthoslices to get an idea of what the scan looks like.
Once I was orientated I had to choose a brightness threshold by selecting the whole image so that I have to do less work later on separating parts out – if the image is too bright, all of the parts merge into one from the software’s point of view.
My threshold was from -670 to 3250 grey value units. Any lower than -670 and too much thin trabecular bone is lost. The really high value is necessary to make sure all of the tooth enamel (really hard, therefore bright) is included.
Unfortunately, this doesn’t get rid of the mat the skull was resting on, nor the skull cap or chin of the skulls in front of and behind this one in the scanner (top left panel in the image above). I deleted all these by adding them to the ‘material’ Exterior.
Next, I separated the mandible where my threshold value hadn’t separated it fully from the skull (the top and bottom teeth were too close together and the brightness had leaked from one to the other). I could then select the mandible in all slices just by clicking on one slice…
… and give it its own identity.
I could now save the mandible as a separate file and delete it from this file by adding it to Exterior, leaving just the cranium. This makes it easier to segment the upper left canine (you can see this best in the second image below).
Segmenting the canine
This part involves manual selection of the canine in each slice of the image – no short cuts here. I started in the XY plane to get a nice round shape to the external part of the tooth.
The top left panel shows the tip of the canine taking shape in 3D (blue).
I continued in the YZ plane to get the internal architecture right. The gap in the middle is the pulp cavity of the tooth where the nerves and blood vessels lie.
To finish off the segmentation of the tooth root I returned to the XY plane to get the tubular shape right.
Once the canine was fully segmented I deleted the cranium leaving just the canine, and saved it as a separate file.
For it to be useful in filling the gap on the chimp’s right-hand side, I needed to flip or reflect the finished canine in the X axis.
Then I adjusted the bounding box down to a reasonable size to make it easier to manipulate for the next stage.
Merging the canine with the skull.
First, I needed to have the canine and skull open together in the same window.
Then slide, rotate and resize until the canine fits well in the socket at a similar angle to the one on the chimp’s left.
And merge the canine with the cranium.
You might be able to see in the pictures above that more of the canine is exposed on the chimp’s right, so the time has come to attempt to cover this up by creating more bone in the upper jaw, or maxilla.
There are a couple of ways I could have done this. One option is going through layer by layer, selecting a region of Exterior and adding it to cranium, but I chose the harder option of selecting the corresponding area on the left side of the face, segmenting it out and flipping it in the same way as the canine. This is harder because it also involves going through layer by layer afterwards and smoothing bits that don’t look quite right.
So, segment out some maxilla:
Flip in X and adjust the bounding box:
Open the merged canine and cranium along with the mandible and position the maxillary bone appropriately:
And merge the maxilla segment with the cranium. I also changed the colour of the mandible to make it more obviously a separate segment.
And that’s how I made a chimp face, free of all complaints about Avizo software because it worked like a charm.
Until next week,
Also, a happy birthday to Dr Phil Cox, and big thank you to Jason and Miguel for hosting such a wonderful party last night. I hope Miguel enjoys his time at home.
Avizo: Konrad-Zuse-Zentrum. 20/03/2012. Avizo Standard Edition (7.0.1) [computer programme]. Berlin: Konrad-Zuse Zentrum.