Information for Workshop Participants

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ct-scan data	participants	Travel	Housing

Daily Schedule

During the workshop we will be giving lecture/demos covering background information and key steps in building and analyzing finite element models of biological structures. Most evenings are unscheduled but you can get access to the computer lab. Here is the 2008 Workshop schedule (11kb PDF ) and the reading list (14kb PDF ) for lunchtime discussions. Keep in mind that the timing of the lectures is tentative; how quickly we move through the material will depend on the needs of the group. All on-campus training and lunch will be in the Engineering Lab (B2 on the campus map (514kb PDF ). Your Residence Hall Card covers breakfast at the 'Blue Wall' on the first floor of the Lincoln Campus Center (C3 on the campus map).

The workshop begins with dinner at the Monkey Bar (69kb PDF ) in downtown Amherst at 7:00pm on Saturday May 31st. I will swing by the dorm at 6:15 to take people there, but if the weather's nice it's also a pleasant 20 minute walk from the dorm to the restaurant.

Your registration fee covers breakfast and lunch each day (June 1 - 7)and dinner on Wednesday and both Saturdays. The dorm suites have kitchens and there is a grocery store close by if you'd like to get snacks, etc. Also note that we've planned a mid-week canoe trip to get a look at lovely Western Massachusetts and get out from behind the computers for an afternoon. Don't forget to bring sunscreen and a hat!

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CT-Scan Data

Depending on the quality of your CT scans and the complexity of your modeling project you should be able to build and analyze at least one model during the workshop. Although our models of bat skulls are quite labor intensive, we’ve found that some bones are surprisingly easy to model. Just in case June is your lucky month, consider bringing 2 or 3 sets of CT-scans to work on. Note that these scans should already be reconstructed as image stacks (sequentially numbered slice images of your object of interest).

There are a number of things to consider when choosing slice stacks for this workshop.

1) Choose scans that have the best contrast between bone and surrounding tissues.
 
2) If you plan to model muscle forces, choose scans that include all of the muscle insertion sites. This will significantly simplify the task of defining the direction of muscle force vectors.

3) Know the absolute value of at least one linear measurement of the specimen, because scale information is often lost in the process of going from object, through at least 4 software packages, to finite element model. An actual physical measurement is the easiest way to recover from this if (when) it happens. If your object is dry bone or something similar, actually having the specimen in hand isn’t a bad idea, but this really only helps if your specimen is only bone or horn; wet specimens won’t be helpful without dissection.
                                                                                                                      
4) Each image stack should consist of multiple image files (typically 200-1500 images) and the file names should be ordered sequentially.  If you are mainly interested in gross morphology, then JPEG is an acceptable format for your slice images. Be aware though that JPEG is a lossy compression algorithm (it reduces file size but results in some loss of data) so if you are interested in fine detail a lossless format such as TIFF or BMP is more appropriate. The data sources that can be imported as image stacks to VGStudio MAX (the initial package we will be using) are: RAW data, TIFF, JPEG, JPEG2000, BMP, PPM, HDF, DICOM, BIR, Toshiba and Shimadzu images. Volume imports are also possible, but that is outside the scope of the workshop and we can’t promise to make that work for you, so it would be best to save your CT volume as an image stack.

To ensure that your CT files are trouble-free, we'd like to take a look at them before the workshop. When your images are ready, please put them in a folder and zip the entire folder to compress it and make it into a single file (this is necessary because our incoming FTP server cannot allow the creation of directories for security reasons). Then upload the folder to our ftp server using an FTP client (Core FTP Lite is a freebie that works well). Log on to 'marlin.bio.umass.edu' using 'anonymous' as the username and your email address as the password. Then drag/drop your compressed file into the "incoming" folder. For security purposes, you can't see the content of 'incoming' but your files should transfer if you follow these steps. Email us when you have uploaded your file(s). We'll take a look to be sure there aren't any obvious problems. This will also insure that you will have a backup in case of disk errors or lost luggage or whatever.

If you have any problems or questions about any of this, contact Sean Werle by email or phone: 413-348-0032.

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Participants

Regina Campbell-Malone - My research has focused on the biomechanics of ship strike in the North Atlantic right whale. My work has contributed to a finite element model of mandibular fracture as an injury that is seen in whales struck and killed by ships, but I did not create the numerical model. I would like to learn more about how it was created.  Several novel findings from my thesis regarding the odd structure of the right whale mandible have me focused on the feeding apparatus of baleen whales in an effort to determine how it is loaded during feeding in skim feeders vs. gulp feeders. With little insight into the muscle insertions at this point I cannot create a model with any accuracy (these whales are huge and cannot be scanned whole using medical imaging systems). BUT! two necropsies from now I hope to have all the data that I need to reconstruct the mysticete feeding apparatus /in silico/ and make valuable comparisons connecting form and function.

Mason Dean - My dissertation research focuses on form and function relationships in vertebrate musculoskeletal systems.  I'm particularly interested in elasmobranch fishes (sharks, rays and relatives), which demonstrate extremely high levels of performance with cartilaginous skeletons; the unique form of cartilage calcification that characterizes this group surely plays an important role in managing loads that would otherwise be extremely damaging to a material that cannot heal.  In the FEA workshop, I will either focus on loading regimes at the more "micro" level of the individual subunits that comprise the calcified tissue or more "macro" shape considerations of whole jaws in species that eat hard food.  Either investigation will give me a better insight into the role calcification plays in reinforcing and distributing stresses in the elasmobranch skeleton.

Emmanuel (Noli) Ergas - My research interests include tracking long-term functional changes in vertebrate evolution. My latest interests have focused on the synapsid lineage (sprawling to parasagittal gait, post-dentary bones to a 3-bone middle ear, temporal fenestration, etc). I hope to complement my knowledge of biomechanics and the finite element modeling software with the ability to transform CT scan data into realistic finite element meshes.

Celine Ide - The existence of naturally occurring narrow- and broad-headed individuals within the European eel (Anguilla anguilla) populations is since long known. Previous studies demonstrated sexual differences in growth, with females growing faster than males, but which is irrespective of the observed difference in head shape. The different head shapes have been related to different diets, where broad-headed eels would feed on bigger and harder preys. Although some research has been focusing on this dimorphism, very little is still known about how and when this dimorphism arises and what parts of the body plan are involved.  With the help of FEA we hope to find out if the skulls of the different morphs have a different behavior under load (for example: is the skull of broad-headed specimens stronger for eating bigger and harder preys).

Heleen Leysen - My research focuses on the musculoskeletal architecture of the head in Syngnathidae (pipefishes and seahorses). Syngnathids are characterized by an elongated snout with small terminal jaws. They are extremely fast suction feeders, with their feeding strike characterized by a rapid neurocranial elevation accompanied by an equally rapid retraction of the hyoid. This results in prey capture times of even less then 6 ms. However, the long, tubular snout with small diameter also has its disadvantages, for instance a limitation of the prey size and an increase in the moment of inertia of the head during dorsorotation. The overall goal of this research is to investigate to what degree the extreme morphological specialization of the feeding system in syngnathids has constrained its functional capacity. A finite element analysis on the skull could help to determine where the largest stress, as a result of the strong pressure during suction feeding, is situated. Since expansion of the buccal cavity generates a large negative pressure, this must imply large mechanical stress in the head of these species. Therefore, morphological specializations to resist the pressure are assumed to be present. As species with a larger snout length or smaller diameter should generate a larger pressure difference to create the same water flow, expectations are that these species will have more or different specializations to withstand the negative pressure. Comparison of the stress distribution in a long snouted seahorse (Hippocampus reidi) and a short snouted one (H. zosterae), will allow preliminary testing of this hypothesis.

Bryan Nowroozi - I have recently become interested in pursuing a side project on the repetitive loading of the knee joint in marsupials. Most marsupials have a knee joint that functions in a similar manner as the knee joint of other mammals, however, instead of a bony patella, they possess a fibrocartilaginous patelloid. While the patelloid is prevalent among marsupials, it is not exclusive to this group of mammals, as both lemurs and rabbits also possess not only a bony patella but also a suprapatelloid, just superior to its bony counterpart as the name suggests. I am currently preparing histological sections on the patella and suprapatelloid of the rabbit, and will be trying to model these structures at the Finite Element Analysis workshop. This study is in its infancy, and so the Finite Element model will serve to be our pilot study that we will hopefully be able to expand upon in the future.

Sharlene Santana - I am interested in using FEA to investigate how the skulls of mammals are mechanically optimized to their feeding behaviors. My focus is in Neotropical leaf-nosed bats, which exhibit a wide diversity of feeding habits, cranial morphology, and feeding behaviors. I will be taking the workshop to learn the process of building and analyzing FE models from CT scans, and will use these techniques in my future research.

Mike Quintanilla - I interested in using FEA to study the load bearing characteristics of cuticle in the legs of large insects. During the workshop I plan to build and analyze a model of a rhinoceros beetle (Dynastes neptunus).

 

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Travel to Amherst

Car: Amherst is located in western Massachusetts only a few miles off I- 91. Download driving directions in PDF format (238kb ). There is a free parking lot next to the dorm; you can get a parking pass when you check into the dorm.
Plane: The closest airport is Bradley International Airport (BDL) in Hartford, CT. You can rent a car at the airport. If you are interested in sharing a car rental let me know and I can put you in touch with other attendees who want to do the same. Follow the Bradley International Airport link to find a list of car rental agencies.  Alternatives to renting a car include making reservations with Valley Transporter for shuttle service (@$90) or visiting the Peter Pan bus line website to check on bus service between Bradley and Amherst near the time of your arrival.
Train: One northbound Amtrak train arrives in Amherst each day from Washington, DC via New York City. It is a 20-25 minute, slightly uphill walk from the train station to the UMass campus. You may want to call a taxi (Red Cab of Amherst, 413 253-3333). A number of trains stop in Springfield MA each day. If you can't make the Amherst train, consider taking a train to Springfield and taking the bus to Amherst.
Bus: Peter Pan Bus Lines connects Amherst to most major cities in the Northeast. Peter Pan busses often stop on Campus - ask your driver as you approach Amherst! Alternatively, it is a 20-25 minute, easy walk from the bus stop in downtown Amherst to the UMass campus. You may want to call a taxi (Red Cab of Amherst, 413 253-3333).

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Housing

Workshop registration includes suite-style housing in North Building C on the UMass Amherst Campus from Saturday, May 31st until the morning of Sunday, June 8th. The building is in the northeast corner of the campus, see C1 of this campus map (729kb PDF). You can check into your room at the front desk anytime on May 31st. If you are driving, ask the the front desk staff for a free permit to park in lot 44, just north of the building.