Segmenting the Canine Skull

Despite not actually heard back from anyone official on the project idea, I decided to do some segmenting.  Yes, this is what I do for fun on a Saturday night.

The bane of my segmenting existence - ethmoid type bones, and turbinates

I am not looking forward to the canine nasal cavity.  There are a lot of delicate structures in there, that are very, very hard to segment out in Amira.

Canine skull, from an awesome person on deviant art

I have started on other, potentially easily to identify bones on the skull.  However, I've already run into issues there.  The scan I am using, while beautiful, doesn't have the clearest suture lines.  I'm switching back and forth between the three views (sagittal, coronal, and axial) and often viewing the scan side by side with the projected 3D model.  This allows me to see my changes in real time, so I can compare with reference texts and photos.

Amira 3D point cloud

Trying to identify the jugal bone

And the bones of the canine skull are different than those of a human.  So, while the experience I gained segmenting out many, many skulls at my previous job is helpful here, I am struggling somewhat with where suture lines are supposed to be.  I would love to get my hands on an actual skull.  Which is an idea to run by my vet expert....

EDIT: 4 hours later, I'm starting to feel some concern.  I chose what I thought would be 'easy' bones to start off with, but... it has been around 3-4 hours of work and I'm just now finishing them up.  And I'm fairly certain that the lacrimal bone is in there somewhere.  I'm hoping that I just misjudged what would be less difficult, and not that the rest of the skull will be even more complex.  I definitely need a physical canine skull.  Photo references are all well and good, but an actual skull would be much more useful.

Zygomatic bones in red.  (It would be helpful if all of my references agreed on the bone names.) 

 

Graduation?

One of the things that I regret the most about my time at UIC: BVIS - not finishing.  I went through the (awesome) program, but I never technically finished.  I left for the great California wilds with the research project undone, and it has truthfully been a source of shame for me.

One of those times when you speak up proudly, but mumble the last bit: "Yes, I went to UIC, *but... mumblemumbleresearchprojectunfinshedmumble*."

So!  I am going to finish.  And to aid in that very doable endeavor, I'm going to blog about it as well.  I know it's going to make for scintillating reading.

To start off, I emailed John, the director of the program at UIC now, to find out if I could still graduate at all.  I figured the worst he could say was 'no.'  But, I recieved both a positive answer and the timeline I needed to work in.  That resolved, I decided to scrap my old research on the "Virtual Heart."

I didn't finish the first time, and I had the feeling that if I tried to continue down that road... it was unlikely to happen this time either.  I need a project that I can really get behind.  One that I am likely to enjoy working on most of the time, to get me through that whole 'have to write a ginormous paper' part.

Not to mention, I would truly have to do the literature over again, as most of the articles I had read at the time are already obsolete.  There have been great strides in the virtual world - personally, I've already learned so much about it!  So, not such a great 'research project' now.

One of the things that John asked me was what would I be researching.  This, surprisingly enough, took me aback.  What would I be researching?  Well.... hmph.  What would I be researching?  What would be novel about my project?  What qualified my idea as research potential?

I had this vague idea that I wanted to do something with canines.  And I wanted to concentrate on the skull.  At least most likely.  I had this nebulous concept of 2D to 3D to real time... but then, what would I be researching?  I needed a second opinion.  And I needed to find out what the situation in the veterinarian world actually was.

This was starting to sound like the beginning of a literature review...

I started to research, and it looked very likely that a new type of education was very much needed in the vet world.  But I really wanted to hear from someone close to a 'source.'  So, I was able to get in touch with a Dr. Spriet, from UC Davis, after a bit of perseverance.  I learned that just because people can get very busy, that doesn't mean they are personally ignoring you.  Don't get discouraged.  We had a great talk about the clinical relevance of different projects, the state of veterinary education now, etc.  And I have a much firmer idea of what type of project I want to do now.

So, now I 'just' need to get cracking on a better proposal and then start my literature review.  Have I mentioned that I dislike writing papers? 

The short proposal of a proposal:

Veterinarian programs have been seeing a significant decrease in the number of hours devoted to animal cadaver dissections, turning instead to DICOM slices, and potentially incorporating pro-sections.  This further complicates the learning of complex areas of anatomy, such as the cranial nerves.  Understanding the cranial nerves and their location is especially important when diagnosing node disease in canines, and has been identified as a key difficult study point.  Currently the anatomy of the cranial nerves in canines is taught using a combination of CT and MR slices with basic annotations, power points, journal papers, and anatomy text books.  Cranial nerves are difficult to identify on CT due to contrast resolution, but the bone window for the skull foramina can be located.  Comparing that with the MR slices allows cranial nerves to be located in the most basic sense of the word.  And with actual dissection of the animals becoming much more rare due to time and money constraints, students find the spatial awareness of where cranial nerves are to be hard to understand.

I propose to use a combination of high resolution CT scans and MRI data to build an interactive 3D model of the bones of a canine skull and it's cranial nerves.  The individual bones would be identifiable, as well as the major landmarks and foramina.  The cranial nerves would be added in using Maya, and also be interactive and identifiable.  The structures can be labeled and annotated to increase student knowledge.  Pertinent labels will be identified using the expert help of Dr. Spriet, from UC Davis.  A slider with the CT and/or MRI slice data (superimposed over the 3D model for comparison) will be included to facilitate learning the spacial cues in both 3D and 2D.

Cranial nerves have not been well identified for veterinary students, especially not in an interactive 3D environment.  Combining the DICOM data with the 3D models is a very interesting area of study, and not well researched at this point.  Pairing the two would be a great step forward in the 3D anatomy world as a whole.  While a few people have been able to achieve the combination of a volume rendering of a CT dataset and a 3D surface model, I have not seen slice data combined with a 3D surface model.  However, this is the more likely way a vet will be viewing the data in the practice.  So, combining these learning tools would be of a great benefit to veterinary students.  The process of this development would be CT/MR segmentation (Amira) to 3D (Maya/3D Coat) to Realtime Interactive app (Unity3D).

Obviously, I still have areas to research for my literature review.  I need to better understand canine cranial nerve anatomy, document 3D as a learning tool, and start to research how to begin to combine DICOM with 3D surface models.

Dr. Spriet was also interested in comparing equine cranial nerves with canine, but I was worried that taking it to that level may be overreaching on this project.  I think I could do the segmentation, but I have the feeling that researching and coding the combination of CT and surface models will be an interesting undertaking.  I may be completely wrong, but that would be my initial assessment.

Types of Hand Rigs

So, it seems that I am destined to be rigging hands for years to come.  It's been quite a while since first rigged my hand for the spider crawl, which actually turned out pretty fun.

That was one of the first tests I did using that IK/FK rig for the hand.  A simple walk cycle - I can see now how certain fingers slide inappropriately and there could be a lot of refinement.  And I beg your indulgence in this video - a short clip of the hand from the animatic I made for a school project, back in the day.  But a good example of the animation I was doing then.

I'm not even going to go into what I would change - but I would love to revisit this animation.  And I may do so eventually.  It was a fun concept.

However, this is one example of what kind of animations can be produced with a semi-decent IK rig.  A more generalized type of motion, very fluid, not very precise, but more 'movie-like.'

I consider this to be a 4 (on a scale of 1 to 5) for complexity.  I didn't include a way to manipulate individual carpal bones, like you can do with this type of rig.

Hand rig with carpal bone manipulation

Most rigs don't need carpal bone changes, as they actually change very, very little.  I also realized that most rigs aren't using actual bones either, but pretty much all of mine do.  A 'hazard' of being a medical illustrator.

I have done some animations that actually show the changes in carpal bones during tensing and relaxing of specific motions.  However, those were all FK only rigs, as I needed to very specifically place and animate all of the bones (based upon fluoroscopic videos and segmented bones from CT scans from the tensed and relaxed positions).  This was another early rig, and I can think of better ways to do it now, but it served it's purpose at the time.

I just finished another rig, one for an arm, including the hand.  We are testing out a new, innovative type of motion capture (that I can't actually say much about now...) and we needed a basic rig for said testing.

So, I have a FK rig for the shoulder, elbow, wrist, and fingers here.  I used to bind anatomical bones to rigs using the rigid bind method, as they are rigid bodies, but that actually really limits you on later editing.  So, I now bind using the smooth bind, but I limit the influences to 1 and bind to selected joints only.  This helps me during the process of editing the rig as necessary (and makes for very pretty colors).

The hand itself is a fairly simple rig as well.  The thumb has a metacarpal joint, but the fingers do not.  The finger metacarpals are pretty stationary (with some exceptions, but not an appreciable amount for this type of rig).  The fingers and thumb can bend at every joint, and the wrist also has basic movement as well.



I'm not entirely happy with the way the wrist moves, as there is sliding motions involved in true wrist movement, and my rig just has the rotation involved now.  I'm thinking there might be some MEL scripting that I can incorporate to automatically slide the joint as it rotates, but I haven't worked it out yet.  I'm letting it percolate in the back of my head right now.

As you can see here, the joints were improperly rotated at first.  This caused the fingers to deviate improperly when formed into a basic fist (as well as other movements).

I generally use the finger curl/fist movement to initially test a rig as it shows big problems right away without a lot of testing needed.

I popped back into the component editing and straightened out my joints further.

And now you can see that the fist is correct.  This is the extent of this rig, as it is only being used to test another system.









I've certainly learned a great deal since that initial hand animation.  I use hand rigs quite often at Stanford, mostly just to position different types of anatomy, especially the bony structures.  I don't use the IK-FK method often, as I usually need to position bones quick and dirty like.

My next greatest challenge (probably a 12 on the scale) is to make a rig that can handle all of the soft tissue elements (muscles, ligaments, arteries, and nerves) as well as the bones.  That's... going to take some thinking.

Rodin Gallery

So, I think I spent more time trying to figure out an image gallery for this blogger blog than I did at the museum.  Not literally, but it sure feels that way.  And we'll see how this works.  Please, let me know how this style of image gallery works for you, and if you prefer this gallery style. Or if you would rather the larger, expandable version of the images, I would love to know that too.

I had a great time at museum, and these are a few of the follow-up images I tried to take of the Rodin hands.  

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And for your viewing pleasure, a few of the other images from the day.