simtk.org

Posted: **Tue Mar 05, 2013 11:41 am**

Hi,
I'm trying to model joint movements for the bones in a bird skull. I decided to start with maxilla and mandible.
I scanned the skull with CT, and segmented them out with Amira. Now, I have the .surf and .k file for the bones, which means I have the bones meshed and have all the coordinates for each nodes.

I looked through "Preparing Your Data" part on the support page, but I didn't find anything that talks about how to start from what I have right now. I'm wondering if someone could give me some idea about what to do next based on what I have.
Thanks so much!!

David

Posted: **Wed Mar 06, 2013 3:56 am**

Hi,
if i understand you correctly you want to convert your scanned data into an OpenSim model.
OpenSim uses the .vtp file format for the visualisation of bodies. I have never done this before but there should be a way to convert your .k and .surf data into the .vtp format. For .vtp editing i used Paraview and as far as i can see it supports .k-files. In ParaView you can use "File->Save Data" (and use the ASCII-format) to save it as a .vtp, but maybe Amira supports .vtp itself too.

If you have generated the .vtp-files you can use them as a DisplayGeometry for your OpenSim bodies, for example for the ground body:

Code: Select all

<Body name="ground">
	<mass>0</mass>
	<mass_center> 0 0 0</mass_center>
	<inertia_xx>0</inertia_xx>
	<inertia_yy>0</inertia_yy>
	<inertia_zz>0</inertia_zz>
	<inertia_xy>0</inertia_xy>
	<inertia_xz>0</inertia_xz>
	<inertia_yz>0</inertia_yz>
	<Joint />
	<VisibleObject>
		<GeometrySet>
			<objects>
				<DisplayGeometry>
					<geometry_file>myGeometry.vtp</geometry_file>
					<color> 1 1 1</color>
					<texture_file />
					<transform> -0 0 -0 0 0 0</transform>
					<scale_factors> 1 1 1</scale_factors>
					<display_preference>4</display_preference>
					<opacity>1</opacity>
				</DisplayGeometry>
			</objects>
			<groups />
		</GeometrySet>
		<scale_factors> 1 1 1</scale_factors>
		<transform> -0 0 -0 0 0 0</transform>
		<show_axes>false</show_axes>
		<display_preference>4</display_preference>
	</VisibleObject>
	<WrapObjectSet>
		<objects />
		<groups />
	</WrapObjectSet>
</Body>

The .vtp-file needs to be in a "Geometry" folder in the same directory as your .osim file.

So again, i have never done this before and i am no developer so maybe OpenSim supports more file formats than i know, but .vtp files should work in any case.

simtk.org

How to start to model joints movement for meshed bones.

How to start to model joints movement for meshed bones.

Re: How to start to model joints movement for meshed bones.