[Yash]

Thanks a lot for that link.
Yes, we’ve been trying to dedicate some resources to replicating this work, and I’ll keep you guys in the loop!

best,
—
Yash

[Yash]

I had tried this yesterday, by exporting my 3D Slicer Segmented DICOM files as HDR Files, and gathering the same through an ImageContainer, like so:

	<ImageContainer name="image" template="ImageUC" filename="C:\path\to\image.hdr"/>
	<MeshGenerationFromImage template="Vec3d" name="meshGen" printLog="true" drawTetras="true" 
	image="@image.image" transform="@image.transform"
	cellSize="0.5" facetAngle="30" facetSize="1" cellRatio="3" facetApproximation="1" ordering="0"
	label="1 2 3" labelCellSize="0.2 0.5 0.1" labelCellData="100 200 300"/>

but got a CImg IOException, saying it had failed to recognize the file. Is there a page that demonstrates the process of going from a DICOM to a format easily accepted by SOFA (that would be really helpful)?

[Yash]

Hi Rosalie,
I tried segmenting a section of my DICOMS into a VTK, that I tried to tetrahedralize using the sample script you had suggested in the previous forum post, like so:

<?xml version="1.0"?>
<Node name="root" gravity="0 0 0" dt="1"  >

	<RequiredPlugin pluginName="CGALPlugin"/>
	<RequiredPlugin pluginName="image"/>
	<BackgroundSetting color="0 0.16862745098 0.21176470588"/>
	<VisualStyle displayFlags="showVisual" />
	<OglGrid/>
	<OglSceneFrame/>
	<OglLineAxis/>

	<!-- <ImageViewer template="ImageUC" src="@image"/> -->
	<MeshGenerationFromImage filename = "path/to/image.vtk"
							 name = "meshGen" template = "Vec3d"
							 facetAngle = "30" facetSize = "30"
						     facetApproximation = "1"
							 cellRatio = "2" cellSize = "20.0 "
							 odt = "true" odt_max_it = "2"
							 perturb = "true" perturb_max_time = "20.0" />
	<Mesh name="volume" points="@meshGen.outputPoints" 	tetras="@meshGen.outputTetras"/> 
	<VTKExporter name="export_vol_mesh" exportAtBegin="1" exportAtEnd="0" triangles="true" tetras="true" filename="output_ken_bone.vtu" />

</Node>

I got the following error on running the above:
_readImageHeaderAndGetError: does not find image format for 'path/to/image.vtk'
Looking a bit more into the error, I see that the error is thrown in ImageIO.h in CGAL. Going through this file, I wasn’t sure if the VTK format was even accepted as a valid 3D Image format by it.
Am I missing something here. Can you give me any tips about how to go on investigating?
Thanks! 🙂

[Yash]

Thanks a lot Rosalie. I have actually been using your previous post to aid in my Mesh Generation from a 3D Image.
I agree, going through a surface mesh would lower the quality of the generated volume mesh.
I’ll try to work on this and get a preliminary output. 🙂

Thanks again!

[Yash]

Hi Alex!
Thanks a lot for that. Yes, I was trying to use MeshGenerationFromPolyhedron, but just following the basic syntax for my STL wasn’t working very well. The resulting model wasn’t showing up in Paraview, and resulted in the aforementioned error in SOFA.
I think I’ll try to go the 3D-Image route, which seems more direct. Would you say this is usually the route you guys take to go from a CT-Scan to a SOFA Simulation?

Thanks again!

[Author]

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