Image to Finite Element Mesh: An End to End Workflow - 3D Slicer

NA-MICNational Alliance for Medical Image Computinghttp://na-mic.orgImage to Finite Element Mesh:An End to End WorkflowNicole Grosland, Ph.D.Vince Magnotta, Ph.D.The University of IowaSteve Pieper, Ph.D., IsomicsCurtis Lisle, Ph.D., KnowledgeVisnicole-grosland@uiowa.eduNA-MIC Tutorial Contest: Summer 2010

Learning ObjectiveAfter following this tutorial,you will be able to useSlicer3 to execute a fullworkflow from a sourceimage all the way throughthe creation andevaluation of an objectʼs3D volumetric finiteelement (FE) meshNational Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Pre-requisites• This tutorial assumes the user is familiar with loadingimage datasets and creating basic label maps in Slicer.Please consult the following prerequisite material if youwant to brush up on these skills first:–Data Loading & Visualization tutorial• Sonia Pujol, Ph.D., Harvard/SPL• http://www.slicer.org/slicerWiki/images/c/c9/3DDataLoadingAndVisualization_Slicer3.6_SoniaPujol.pdf–User documentation for the Slicer3 Editor module• Steve Pieper, Ph.D, Harvard/SPL, Isomics• http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Pre-requisites• The user may use hand segmentation or anysegmentation algorithm to create surfaces for meshing.One of the simplest algorithms to use is Slicer3’s FastMarching Segmentation module:• Fast Marching Segmentation documentation–Adriy Fedorov, Ph.D., Harvard/SPL–http://www.slicer.org/slicerWiki/index.php/Modules:FastMarchingSegmentation-Documentation-3.6National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Material• This tutorial requires the installation of theSlicer3.6 release and the tutorial dataset.They are available at the followinglocations:• Slicer3.6 downloadpage –http://www.slicer.org/pages/Downloads/• Tutorial dataset:–http://www.slicer.org/slicerWiki/index.php/File:IAFEMeshData-TutorialContestSummer2010.zipDisclaimer: It is the responsibility of the user of Slicer to comply with both the termsof the license and with the applicable laws, regulations, andrules.National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Material• A Users Guide is available for the IA-FEMesh module,which covers the step by step process of meshcreation.• For additional assistance, consult the Users Guideavailable here–https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf6National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Material• Interactive screencasts showing the following operationsare available from the NA-MIC wiki website:• Creating and importing a Slicer model–http://wiki.na-mic.org/Wiki/index.php/File:Meshing-1-labelmapmodel-import.mov• Simple Editing of Building Blocks around a surface–http://wiki.na-mic.org/Wiki/index.php/File:Meshing-2-buildingblocks.mov• Creating a mesh from a surface and building blocks–http://wiki.na-mic.org/Wiki/index.php/File:Meshing-3-meshcreation.mov• Evaluating and Improving Mesh Quality–http://wiki.na-mic.org/Wiki/index.php/File:Meshing-4-mesh-qualitytab.movNational Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Platform• The IA-FEMesh Slicer3 Module wasdeveloped using both Linux (32 and 64 bit)and Mac (OS X 10.4 -10.6)• The module has been tested on both Linux64-bit and Mac (OS X10.6)National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

OverviewIn this tutorial, we will…• Create a label map and a corresponding surface modelof a structure of interest from a source image• Import the surface model into the IA-FEMesh module• Interactively create a volumetric hexahedral mesh ofthe object of interest• Examine and improve the quality of the mesh• Export the mesh for continued processing in acommercial finite element solver (e.g. Abaqus)• Review the steps to create an object mesh fromimagery sourceNational Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Loading Image Data1. Select the Slicer3Volume Module2. Select the “VolumeFile” button to choosea file from thefilesystem. Manyimage formats aresupported.3. Hit “Apply” to read theimage into the currentsessionNational Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Creating a Labelmap• A label map is a special type of volume whereeach voxel contains a code indicating theobject to which the voxel belongs• Label maps are loaded and saved like images,but handled differently by Slicer because oftheir purposes as indicators• At right, we see a label map indicating thepresence of the finger bone superimposed overcorresponding background voxels from a CTimage of the finger11National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Creating a Labelmap• In Slicer3, a region of interest can be selected byhand or with an algorithm. The Slicer3 Editor moduleand the Fast Marching Segmentation module are twoof the easiest ways to create label maps• The Editor provides a palette of tools to interactivelyselect regions of an image:–Level Tracing automatically selectsnearby voxels similar to the selected point–The paintbrush is a way to clean up oradd missing voxels after Level Tracing12National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Creating a Label map• Select the Level Tracing tool, move it around on theimage, and click repeatedly to select the desired region• Repeat thevoxel selectionoperations foreach slicecontaining theobject to besegmented13National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

More about Segmentation• Clearing unwanted voxels can accomplished bypainting with the clear label color (label=0)• Step-by-step instructions for using the Slicer3Editor are available on the Slicer wiki site:–http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6• A screencast is available which demonstrateslabel maps and shows how models are created:–http://wiki.na-mic.org/Wiki/index.php/File:Meshing-1-labelmap-model-import.movNational Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Smoothing the Label• After editing is complete, smooth the labelmap to reduce jagged edges on the voxelcontour. Use the Label Map Smoothingmodule• A smooth labelboundary generatesthe best quality finalmesh15National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Create a Boundary Surface• Once label mapediting is complete, aboundary detectionalgorithm is run towrap a contouraround the label map• Select theModelMaker moduleto create the surface16National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Smooth Even More?• The Surface Toolboxcan smooth thepolygonal surface ofthe model further ifneeded• Remember, a smoothboundary makes forhigher quality boundaryelements in the volumemesh17National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Loading a Surface• The IA-FEMesh specific part of the workflowcan begin with a surface loaded from anexternal file OR• a Slicer3 Model is imported from the currentSlicer3 sessionSTL, VTK, or VTP fileCurrent Slicer3 Session (MRML Scene)Import Model18National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Importing a Surface Model• Any Model object in the current Slicer MRML scenecan be imported into the meshing module to start ameshing workflow• Select the ImportModel selectionfrom the Surfacetab in IA-FEMeshNational Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Creating a Building Block• The surface is surrounded by Building Blocksto represent the shape to the meshingalgorithm• Building blocks are made through aninteractive widget editing process• Please refer to the screencast as an exampleof the steps:–http://wiki.na-mic.org/Wiki/index.php/File:Meshing-2-buildingblocks.movNational Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Creating a Building Block1. Select the Block(s) Tab2. Select Create from the drop down menu3. Check Create Block from Surface Bounds4. Click Apply2.1.4.Sample Generated Building Block3.National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Manipulating the Building Block1. Select the Blocks tab2. Select Build/Edit from the drop down menu3. Select the from the building blocks toolbara) Allows manipulation of vertices, edges, and faces of building blocksb) Red spheres will appear at the vertices. The size of these spherescan be scaled1.3a.2.3b.National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Creating a Mesh• The surface imported into IA-FEMesh alongwith the building block surrounding thesurface are used to create the mesh• Mesh elements are created by projecting thebounding box mesh seeds through thevolume• Please refer to the screencast as an exampleof the process:–http://wiki.na-mic.org/Wiki/index.php/File:Meshing-3-meshcreation.movNational Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Assigning Mesh Seeds1. Select the Mesh tab2. Select Assign/Edit Mesh Seeds from the drop down menu1.2.National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Assigning Mesh Seeds (2)3. Select the button to visualize the distribution ofmesh seeds4. To change this assignment, select either Element Length orNumber of Divisions from the drop down menu.5. Click on a block with the left mouse button6. Enter the values of your choice7. Select Apply8. Select Cancel to exit the mesh seeds operation3.5.6.4.7. 8.National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Creating a Mesh1. Select the Mesh tab2. Select Create from the drop downmenu3. Select Volumetric Mesh4. Select Building Block in the followingdrop down menu5. Provide starting node/elementnumbers and a descriptive label tobe associated with the mesh definition6. Selection Elliptical in the Interpolationdrop down menu7. Uncheck Perform Smooth for theinitial attempt8. Select Apply to generate the mesh7.2.3.4.5.6.1.National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Check Mesh Quality• Once mesh creation is complete, advanceto the Quality tab on the interface to reviewthe quality according to several metrics• The process is demonstrated in thefollowing screencast–http://wiki.na-mic.org/Wiki/index.php/File:Meshing-4-mesh-quality-tab.movNational Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Checking Mesh Quality1. Select the Quality tab2. Select Evaluate/Display Mesh Quality from the drop down menu1.2.National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Checking Mesh Quality (2)3. Select your Metric of Choice from the Metric drop down menu4. Click the button5. Close summary report window after viewing6. Click Cancel to exit the mesh quality check module3.4.National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Check Interior Elements• Use the Cut Plane button to examineinterior elements by dragging the planeinteractivelyNational Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Improving Mesh Quality1. Select the Quality tab2. Select Mesh Improvement from the drop down menu3. Check to ensure that the surface, block, and mesh of interestpopulate the Mesh Component frame4. Select an interpolation method from the Interpolation dropdown menu5. Enter the desired number of smoothing iterations for theexternal nodes1.6. Click Apply2.3.6.4.5.National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Improving Mesh Quality (2)7. Adjust the smoothing parameters by toggling between theEvaluate/Display Mesh Quality and Mesh Improvementoperations until the desired mesh is achievedNational Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

After Mesh Generation• After mesh generation is complete, the usercan add material properties and loadingconditions to prepare for external finite elementsolver execution• The following slides cover these options. Foradditional detail, refer to the IA-FEMesh UsersGuide–https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdfNational Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Assigning Material Properties1. Select the Materials tab2. Select the User-Defined option from the main menu3. To add additional element sets, press• A number of options are available for selecting element setsNational Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Material Properties (2)Element Set Definition Examples• Cortical Bone Set Definition1. Select the surface element button: .2. Hold Ctrl button while using the left mouse button to drag a rubberband box around theelements of interest• Selected elements will be green3. To accept the chosen elements, click the right mouse button while hovering over the mesh• Accepted elements will turn red4. Opacity can be modified to better visualize the data5. Once the selection is finalized, enter a Set Label (e.g. cortical bone)6. Click to accept the selection• Cancellous Bone Definition1. Repeat the steps above except hit the button prior to accepting the element selection andassigning a new Set Label.2. Reduce the opacity to see the element set you have defined3. Click the button to close the Define Element Set window 1. 2.National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Assigning Material Properties• Material Property Assignments1. Select an element set using the “Element Set” drop downmenu2. Enter the desired Modulus3. Enter the desired Poisson’s Ratio4. Click Apply5. Repeat this procedure for each material assignment6. Click Cancel to exit the operation1.2.3.4. 6.National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Assigning Material Properties• Visualizing the Material Property Assignments1. Select the Materials tab2. Select Display Material Properties from the drop down menu3. Select the desired element set from the Element Set drop downmenu4. Use the button to display a cutting plane which may bemanipulated to view internal element definitions2.3.4.National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Load and Boundary Conditions1. Select the Load/BC tab2. Select the STEP – Load/BC Assignments from the drop down menu3. Select4. Select from the Node Set toolbar• This enables the nodes associated with a face of a buildingblock to be readily chosen4.1.2.National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Load and Boundary Conditions (2)5. Hold the Ctrl button and use the left mouse button to choose a nodeassociated with the building block face of interest• Nodes associated with selected face will be highlighted in green6. To accept the chosen nodes, click the right mouse button whilehovering over the mesh• All nodes associated with the chosen face will turn red• Opacity can be changed using the slider bar7. Once the selection is finalized, enter a Set Label8. Click9. Click6.7.8. 9.National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Load and Boundary Conditions (3 )10.Provide a descriptive heading in the Step Subheadingtextbox11.Select desired Load/Displacement type in the drop downmenu12.Select the appropriate Node Set13.Assign x, y, and z directions11.12.13.National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Load and Boundary Conditions (4)14. Select Apply to update the Load/BC assignments15. Visual confirmation will be provided on the mesh in theView Panel15.National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

1. Select the *STEP Definitionsbutton• Please refer to theABAQUS manualregarding theseparameters2. Use the NSET and ELSETdrop down menus to selectthe sets of interest3. Click Apply in each submenuto commit your selectionIA-FEMesh Tutorial - MIMX LaboratoryNational Alliance for Medical Image Computing--

• Save the FE Mesh1. Select Save from the Mesh Tab• This can be performed at any step through themesh development process• Export the FE Mesh in ABAQUS file format1. Select Export ABAQUS file from the Mesh Tab• This can be performed at any step through themesh development processIA-FEMesh Tutorial - MIMX LaboratoryNational Alliance for Medical Image Computing--

Review of Workflow Steps• Input an image• Create, smooth, (andoptionally dilate) the labelmap• Use ModelMaker to create apolygonal surface model• Use Surface Tools to furthersmooth model polys usingLaplacian smoothing• Import the model into IA-FEMesh using Surface/ImportModel from the MRML scene• Create Building Blockssurrounding the surface• Assign mesh seeds andCreate the Mesh• View the mesh quality• Improve the mesh qualitythrough smoothing• Add Material Properties• Add Initial BoundaryConditions• Export to FE Solver(Abaqus)National Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Conclusion• It is now possible to perform end to endprocessing from source imagery all the waythrough Finite Element mesh generation, meshanalysis, and mesh optimization using Slicer3• Volumetric meshes for objects can be createdthrough a simple, intuitive process• Any Slicer3 model can be imported to start themesh generation processNational Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR

Acknowledgments• National Alliance for Medical Image ComputingNIH U54EB005149National Institute of Biomedical Imaging and BioengineeringR21EB001501 and R01EB005973Musculoskeletal Imaging Modeling and EXperimentation (MIMX)LaboratoryThe University of IowaNational Alliance for Medical Image Computinghttp://na-mic.org © 2010, ARR