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19 projects in result set.
Are subject-specific musculoskeletal models robust to parameter identification?
- This study analyzed the sensitivity of the predictions of an MRI-based musculoskeletal model (i.e., joint angles, joint moments, muscle and joint contact forces) during walking to the unavoidable uncertainties in parameter identification, i.e., body landmark positions, maximum muscle tension and musculotendon geometry. To this aim, we created an MRI-based musculoskeletal model of the lower limbs, defined as a 7-segment, 10-degree-of-freedom articulated linkage, actuated by 84 musculotendon units. We then performed a Monte-Carlo probabilistic analysis perturbing model parameters according to their uncertainty, and solving a typical inverse dynamics and static optimization problem using 500 models that included the different sets of perturbed variable values. Model creation and gait simulations were performed by using freely available software that we developed to standardize the process of model creation, integrate with OpenSim and create probabilistic simulations of movement. | |
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Activity Percentile: 92.37 Registered: 2014-11-10 15:19 |
Musculoskeletal Model of the Lumbar Spine
- The work here features a number of different OpenSim models of the lumbar spine developed to study lumbar kinematics and dynamics.
Briefly, the models consist of the following bodies:
# rigid pelvis and sacrum
# five lumbar vertebrae (separated by joints with three rotational degrees of freedom)
# torso (thoracic spine + ribcage)
The motion of the individual joints are defined using constraint functions specifying the motion of the lumbar vertebra as functions of the net lumbar motion (flexion-extension, lateral bending and axial rotation). Future models will incorporate joints with stiffness properties to more accurately mimic the action of the intervertebral joints.
The most complex of these models also feature the 238 muscle fascicles associated with the 8 main muscle groups of the lumbar spine necessary to study the contribution of the lumbar spinal musculature to spinal motion. Simpler models incorporating two and seven of the main muscle groups of the lumbar spine are provided as well for completeness.
Read more about the model in the paper, freely downloadable at http://link.springer.com/article/10.1007%2Fs10237-011-0290-6.
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September 2011 Addendum
Click on the "Downloads" link to the left for downloads related to more recent work.
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September 2012 Addendum
The Constrained Lumbar Spine Model does not require any of the files uploaded after the creation of the Constrained Lumbar Spine Model project. The .vtp files (and descriptions) are included here for the benefit of those of you who wish to create your own model that has origins shifted to the center of the bones since this typically saves a number of transformations. Many apologies for any confusion(!).
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March 2014 Addendum
(1)
This model was build with OpenSim 2+. Version 3+ will not allow you to use periods (.) in your variable names. Unfortunately, a bunch of the variables used (muscles mainly) have periods in the names so it will throw an error if you try and run it in OpenSim version 3+. To fix this, either use version 2+, OR, rename the variables appropriately.
(2)
We have all graduated and are no longer actively working on this project (we haven't been working on it since the end of 2011 actually). At this point, you probably know more than us about OpenSim so we apologize in advance if our support is subpar.
(3)
The complex mode is not meant to be run straight out of the box. It has almost 250 muscles after all and unless you have a super computer, running CMC, or FD on it is going to bring up the rainbow ball of death on your computer.
Rather, it's meant to be a reference for those of you who intend to build up your own model. My advice would be to start with the simple 4 fascicle model, get it to work, then incrementally build up from there using the parameters provided in our model as a starting point. Copy-Paste is your friend here. :)
(4)
If this is your very first OpenSim project, I strongly _strongly_ *strongly* suggest that you go through the examples provided with the OpenSim version you just downloaded and understand how they work. This will save you months of pain down the road. | |
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Activity Percentile: 87.02 Registered: 2010-11-04 02:25 |
CoBi Core Models, Data, Training Materials
- This project contains a variety of materials from Computational Biomodeling (CoBi) Core of the Cleveland Clinic, relevant to physics-based simulation of the biomechanical system. These may include various published/unpublished models, data, and training material generated through various small projects. | |
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Registered: 2010-10-07 13:09 |
Data and Media Management for Biomechanics (DMMB)
- (written for biomechanics researchers interested in managing and distributing big data/ media)
This project will serve as a tool to help researchers categorize, organize, prioritize, and distribute big data collected specifically in biomechanical applications. Additionally, this project will serve as a project map a guide for how to streamline and distribute biomechanics-related media (photographs, videos, interactive modules, etc.). | |
Registered: 2014-02-04 18:53 |
Modeling the Intervertebral Discs as a Stiffness Matrix: a SpineBushing element
- This project features a "SpineBushing" element that can be used to model the intervertebral disc as a 6x6 stiffness matrix. This permits the study of the disc's force-motion relationship for the case where the coordinates are coupled to each other.
The guiding equation is,
F_2 = -K * Delta_Q
where F_2 is the generalized 6x1 force vector acting on the upper vertebra, K is a stiffness matrix, and Delta_Q is the generalized 6x1 displacement vector specifying the change in position from neutral between the points of attachment of the stiffness element.
By Newton's 3rd law,
F_1 = - F_2.
The SpineBushing features two *key* differences from the existing bushing element:
(1) we incorporated a full 6x6 stiffness matrix instead of the current three translational and three rotational stiffnesses.
(2) the **change** in relative motion is used and not the relative motion itself. In 1-D, you can think of this as having a spring with a resting length equal to the distance between the specified attachment points on the two bodies in the neutral posture. (The typical bushing element, on the other hand would be analogous to a spring with zero resting length.)
Further details are provided in the accompanying documents. | |
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Activity Percentile: 1.15 Registered: 2011-10-12 05:41 |
Matt DeMers' project
- This is just a place for me to track, manage, and backup data for my ongoing projects. | |
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Activity Percentile: 0.00 Registered: 2009-07-31 22:54 |
Evaluation of In Vivo Knee Load Predictions Using Instrumented Implants
- This project seeks to advance the field of musculoskeletal modeling by critically evaluating muscle and contact force estimates at the knee during gait using data collected from patients with force-measuring knee implants. | |
Activity Percentile: 0.00 Registered: 2010-11-18 17:17 |
Wearable Sensor Glove to prove positive effect in stroke patients for rehab
- This project is going to allow physical therapists to better understand the positive affects of their physical therapy by witnessing positive movements from patients. A negative effect of a stroke is not just the initial neuro-muscular lose but also the over-compensation of the less impaired limb to take over space needed for the severely impaired limb to re-establish its neuro-muscular pathway. Although a full recovery can not be expected the severely impaired limb still has hope to fill the role of the less dominant hand. Not as focused on as the dominant hand, the role of the less dominant hand is unarguably important and necessary that is why we have two hands after all these years of selection. This project is a work compilation of 4 undergraduate students headed by the computer science student, Luke Greenleaf, under the advisement of Dr. Foulds and the Biomedical Engineering Department at NJIT. This summer we will be creating a prototype that will allow us to begin proving that we can collect continuous data and recreate the meaning of that data in order to understand the movement initiated for both hands and understand a patients use of their severely impaired limb. | |
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Activity Percentile: 0.00 Registered: 2012-06-05 22:01 |
Comparison of Opensim Lower Limb Models in Producing In Vivo Hip Contact Forces
- The project compares the hip contact forces generated by two opensim models to ascertain the validity of each model. The analysis focuses on the scenario of edge loading to produce results of in vivo contact forces useful for simulation of hip implant wear. | |
Activity Percentile: 0.00 Registered: 2011-11-15 22:00 |
ME/BIOE 485 (Modeling and Simulation of Human Movement)
- This project is a central repository for reading materials, assignments, and student-written computer code related to ME/BIOE 485 (Modeling and Simulation of Human Movement). It includes model files and other related files needed to generate and analyze muscle-actuated simulations of human movement using OpenSim. | |
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Activity Percentile: 0.00 Registered: 2008-04-01 04:50 |
Simulation Labs utilizing OpenSim software
- Handouts, solutions, tips & tricks and other info pertinent to running OpenSim Simulation Labs. Originally from BJ Fregly at University of Florida | |
Activity Percentile: 0.00 Registered: 2011-01-26 18:31 |
Extracting conserved domains from cryo-EM maps.
- In our research, we are dealing with the problem of computationally identifying the domains of large macro-molecules (such as Chaperonin) that remain conserved upon conformation change, by comparing low-resolution volumetric electron microscopy (EM) maps. A simple instance of this problem can be shown to be NP-complete. As of now there is no computational tool to solve this problem efficiently or even approximately. We are developing the first method to do so.
Previous attempts have been for some simple instances of this problem, like identifying secondary structures in intermediate-resolution maps (helixhunter: http://ncmi.bcm.tmc.edu/software/AIRS/ssehunter/sse-help.htm) and docking a component of a bio-molecular assembly into latter's EM map. For intermediate resolution maps (<10A), one could use helixhunter to identify secondary structures and then use them to find conserved domains. But about 80% of the maps in EMDB database (http://www.ebi.ac.ac.uk/msd-srv/emsearch/) are of low resolution (>10A), where secondary structures "fuzz-out" beyond the recognition limits of helixhunter or even any manual technique. However, we believe that it should be still possible to extract motifs or domains which are bigger entities than secondary structures and could remain in the "detectable range" may be upto 20A resolution. | |
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Activity Percentile: 0.00 Registered: 2007-12-18 17:02 |
2007BioE15 Bruns
- Project for class. Hey! Guess what! It is required to put a longer \"detailed\" description into this area by the set up form! The retarded error message just says \"longer\", so who knows how long I have to keep spitting up this junk to keep the darn thing happy? | |
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Activity Percentile: 0.00 Registered: 2007-04-11 01:29 |
Creating a Tensegrity Robot
- This project is to study the applicability of utilizing this program to create a tensegrity robot and a virtual environment for the tensegrity robot. | |
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Activity Percentile: 0.00 Registered: 2010-08-11 01:17 |
Dynamical reweighting toolkit
- This project provides a set of tools for the computation of dynamical properties (such as time-correlation functions, transition matrices for Markov models, and rate constants) from simulation data collected at multiple temperatures, such as simulated or parallel tempering simulations. Tools and datasets used in the paper(s) are provided within this project. | |
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Activity Percentile: 0.00 Registered: 2008-08-26 10:08 |
S-HOW Motion
Movement Characterization based on wearable technology
- Wearable technology allows to capture data on the field, allowing new kinematics capture scenarios: interacting with the subject (for example by mobilization), running outside, going upstairs/downstairs, working at the desk, pitching on the field, walking along tens of meters.
This project will provide little by little new sets of motion data, initially mainly kinematics, which can be useful in research for several reasons:
1) explore kinematics of complex movements
2) explore new simulation opportunities
3) concentrate your time (not your attention of course) more on simulation and data interpretation rather than capturing kinematics
4) enhance your available data sets for running Opensim simulation
5) discuss and share ideas around new motions to be captured, new scenarios where you need simulation
Data will be mainly provided applying the measurement protocols called ISEO and OUTWALK published on Medical & Biological Engineering & Computing in 2008 and 2010.
[1]A. G. Cutti, A. Giovanardi, L. Rocchi, A. Davalli, and R. Sacchetti, “Ambulatory measurement of shoulder and elbow kinematics through inertial and magnetic sensors,” Med Biol Eng Comput, vol. 46, no. 2, pp. 169–178, Feb. 2008.
[2]A. Cutti, A. Ferrari, P. Garofalo, M. Raggi, A. Cappello, and A. Ferrari, “‘Outwalk’: a protocol for clinical gait analysis based on inertial and magnetic sensors,” Med Biol Eng Comput, Nov. 2009. | |
Activity Percentile: 0.00 Registered: 2013-10-01 07:48 |
The Osteoporotic Virtual Physiological Human
- Nearly four million osteoporotic bone fractures cost the European health system more than 30 billion Euro per year. This figure could double by 2050. After the first fracture, the chances of having another one increase by 86%. We need to prevent osteoporotic fractures. The first step is an accurate prediction of the patient-specific risk of fracture that considers not only the
skeletal determinants but also the neuromuscular condition. The aim of VPHOP is to develop a multiscale modelling technology based on conventional diagnostic imaging methods that makes it possible, in a clinical setting, to predict for each patient the strength of his/her bones, how this strength is likely to change over time, and the probability that the he/she will overload his/her bones during daily life. With these three predictions, the evaluation of the
absolute risk of bone fracture will be much more accurate than any prediction based on
external and indirect determinants, as it is current clinical practice. These predictions will be used to: i) improve the diagnostic accuracy of the current clinical standards; ii) to provide the basis for an evidence-based prognosis with respect to the natural evolution of the disease, to pharmacological treatments, and/or to preventive interventional treatments aimed to selectively strengthen particularly weak regions of the skeleton. For patients at high risk of fracture, and for which the pharmacological treatment appears insufficient, the VPHOP system will also assist the interventional radiologist in planning the augmentation procedure.
The various modelling technologies developed during the project will be validated not only in vitro, on animal models, or against retrospective clinical outcomes, but will also be assessed in term of clinical impact and safety on small cohorts of patients enrolled at four different clinical institutions, providing the factual basis for effective clinical and industrial exploitations. | |
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Registered: 2010-03-08 08:57 |
2007BioE215 Eser
- BioE215 Coursework Spring 2007 | |
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Activity Percentile: 0.00 Registered: 2007-04-07 02:13 |
Shoulder mechanics: Undergrad research in muscle mechanics of the shoulder
- This project is a combination of experimental and computational approaches to understanding shoulder mechanics. We are investigating the role of muscle architecture in joint mechanics. | |
Registered: 2010-03-26 19:28 |