Medical Imaging from Medical Scanner to 3D Model

5.2.1 Introduction

A strong software interface is needed to accept input from every type or brand of scanner, to facilitate the selection of an anatomic structure visible in the medical images and to link this

Advanced Manufacturing Technology for Medical Applications Edited by I. Gibson © 2006 John Wiley & Sons, Ltd.

information to rapid prototyping machines for actual model production. Surgery simulation on a virtual computer model requires specific functions in the software to simulate surgical actions and to calculate certain parameters such as volume distance and bone density. Besides pure simulation of surgery actions, links to other software packages (CAD, FEA, CFD, etc.) can facilitate or even be necessary to complete the surgery simulation.

Materialise NV (Leuven, Belgium) provides high-quality solutions supporting clinicians in diagnosis and decision-making. In the digital age, computers and information technology have become a critical factor in reducing costs and improving efficiency in medical environments. Materialise is the worldwide leader in rapid prototyping modelling technology and provides surgeons with the most detailed and precise virtual 3D models available. Clinicians around the world use rapid prototyping models created by Materialise software to assist them in the most complex surgical cases.

Materialised interactive medical image control system (Mimics) is an interactive tool for the visualization and segmentation of CT images as well as MRI images and 3D rendering of objects. Therefore, in the medical field, Mimics can be used for diagnostic, operation planning or rehearsal purposes. A very flexible interface to rapid prototyping systems is included for building distinctive segmentation objects.

The software enables the surgeon or the radiologist to control and correct the segmentation of CT and MRI scans. For instance, image artefacts coming from metal implants can easily be removed. The object(s) to be visualized and/or produced can be defined exactly by medical staff.

Additional modules provide the interface towards rapid prototyping using STL or direct layer formats with support. Alternatively, an interface to CAD (design of custom-made prostheses and new product lines based on image data) or to finite element meshes is available. Basic functionality of Mimics

Mimics displays the image data in several ways, each providing unique information. Mimics divides the screen into three or four views: the original axial view of the image, and resliced data making up the coronal and sagittal views and 3D view (Figure 5.1). Several visualization functions are included such as contrast enhancement, panning, zooming and rotating of calculated 3D images. Colour scales are used to enhance small differences in the soft tissue or the bone. The alignment or scout image can be displayed. The original data can be resliced online or a resliced project can be exported. Online reslicing allows the display of cross-sectional and parallel images that are orthogonal and along a user-drawn curve in the axial view. The export resliced project tool offers an interface that allows the export of resliced Mimics projects along a user-drawn line. This line can be drawn in any view and in any direction.

Mimics enables different types of measurement to be performed. Point-to-point measurements are possible on both the 2D slices and the 3D reconstructions. A profile line displays an intensity profile of the grey values along a user-defined line. Accurate measurements are possible on the basis of the grey values using three methods: the threshold method, the four-point method and the four-interval method. These methods are ideal for technical CT users. Density

Rapid Prototyping Medical

measurements can be performed in ellipses or rectangles: area, mean, grey value and standard deviation are displayed.

Segmentation masks are used to highlight regions of interest. Mimics enables you to define and process images with several different segmentation masks. To create and modify these masks, the following functions are used:

  • Thresholding is the first action performed to create a segmentation mask. You can select a region of interest by defining a range of grey values. The boundaries of that range are the lower and upper threshold value. All pixels with a grey value in that range will be highlighted in a mask.
  • Region growing will eliminate noise and separate structures that are not connected.
  • Editing (draw, erase, local threshold): manual editing functions make it possible to draw, erase or restore parts of images with a local threshold value. Editing is typically used for eliminating artifacts and separating structures.
  • Dynamic region growing segments an object on the basis of the connectivity of grey values in a certain grey value range. It allows for easy segmentation of tendons and nerves in CT images, as well as providing an overall useful tool for working with MRI images.
  • Morphology operations act on the 'form' of a segmentation mask. All these functions remove or add pixels from the source mask and copy the results to a target mask. This tool is extremely effective when working with MRI images.
Figure 5.2 Examples of 3D objects in Mimics
  • Boolean operations enable different combinations of two segmentation masks (subtraction, union and intersection) to be made. These operations are very useful for reducing the work needed to separate joints.
  • Cavity fill fills the internal gaps of a selected mask and copies the result to a new mask. The filling process can be applied in 2D.
  • Cavity fill from polylines creates a segmentation mask, starting from a polyline set. This tool is very useful for filling internal cavities in preparation of files for FEA.

After isolation of the region of interest, a 3D can be calculated. Therefore, parameters for resolution and filtering can be set. Information about height, width, volume, surface, etc., is available for every 3D model. Mimics can display the 3D model in any of the windows with visualization functions that include real-time rotation, pan, zoom and transparency. The ability to apply advanced rendering with OpenGL hardware acceleration offers high-quality rendering including Gouraud shading for optimal display of the 3D objects (Figure 5.2). Additional modules in Mimics

Mimics consists of different modules. Figure 5.3 shows the links between the main program and its modules. The different modules link Mimics to various application fields: rapid prototyping (RP), finite element analysis (FEA) and computer-aided design (CAD).

Import module

Mimics imports 2D stacked uncompressed images such as CT, MRI or microscopy data in a wide variety of formats, as well as offering a user-defined import tool. The import software provides direct access to images written on proprietary optical disks and tapes, converts them into the Materialise image format and preserves all necessary information for further processing.

Figure 5.3 Modular structure of Minics: links to different applications

A wizard helps to guide you through the import process. It allows for the merging of multiple image sequences into one project, to convert different image sets at once or to select specific images prior to creating the project.

RP slice module

The RP slice module interfaces from Mimics to any kind of rapid prototyping system via sliced formats and performs support generation.

When creating sliced files, a bilinear and interplane interpolation algorithm is used to enhance the resolution of the RP model. RP slice achieves optimal accuracy in a very short time by the direct conversion of the images to several sliced machine file formats: SLI and SLC for 3D Systems and CLI for Eos. High-order interpolation algorithms result in excellent surface reproduction from scan to model.

RP slice supports colour stereolithography: tumours, teeth and teeth roots and nerve channels can be highlighted in the RP model, giving an extra dimension. Patient information can be displayed by punched or coloured label.

One of the major difficulties in stereolithography and most other layer manufacturing techniques is the need for support structures. Both the generation (automatic or manual) and the removal (cleaning work) of these support structures are complex problems.

The basic function of the support structure is to support the part during the building process. The whole part is connected to a platform, and 'islands' that are isolated at a certain moment during the process need to be attached to the rest of the part. Another function of the supports is to reduce curling effects. Stereolithography resins have a tendency to deform during the building process because of internal stresses generated by the shrinkage. By building a strong support structure under a part, this deformation can be minimized.

When stereolithography is used starting from a CAD representation, the support structures can be designed in the CAD system, which is a large operation. In some instances, however, it is not possible to generate a support starting from an STL description. This is the case in medical applications where the layer information of the CT scanner is interfaced directly to the layer information of the stereolithography machine. This means that there is no surface information available and the standard techniques for automatic support generation cannot be used. In addition, the manual generation of the supports is impossible because the information is not present in a CAD system.

The RP slice module calculates automatically the support structures for the sliced file formats (SLI, SLC and CLI) needed in the production of the rapid prototyping model, starting from contour files.

Case study ofRP models: distraction osteogenisis and mandibular reconstruction in a patient with Goldenhar syndrome


Hemifacial microsomia is a syndrome in which an underdevelopment exists of one side of the face compared with the other side. In some children only an ear deformity is evident, while in others the ear is normal and only the jaw is affected. In more severe cases, all the structures of the first and second branchial arches can be involved. The ear, skin and underlying facial tissues such as muscles, nerves and bony structures are deficient or underdeveloped. When the eye and the spine are involved, the term Goldenhar syndrome is used. Hemifacial microsomia is the second most frequent facial anomaly, after lip and palate clefts. Studies indicated that the incidence in birth is estimated between 1 in 3500 and 1 in 5642 live births.

Case report

An eight year old boy was presented at the Department of Cranio and Maxillofacial Surgery of the University Hospital Maastricht. The child showed a severe underdevelopment of the left side of his face. The left zygomatic arch, the left ear and the left hemimandible were deficient. A broad maxillary cleft with dental agenesis was observed. The child was known to have a

Figure 5.4 Osteotomy planning on an RP model

scoliosis and finally a tetralogy of Fallot. Because of the variety of symptoms, the anomaly could be diagnosed as Goldenhar syndrome.

Distraction osteogenisis

The complexity of this case made it necessary to study the surgical options for the necessary corrections. A stereolithographic medical model of the affected skull was made. The objective of the first intervention was to correct the position of the left orbito-maxillary-complex (OMC) by distraction osteogenesis and thus narrow the cleft. Using an RP model, precise planning of the osteotomy at a Lefort III level of the left OMC was possible (Figure 5.4). The vector of movement of this bony complex was established precisely by a rehearsal operation on the RP model. A Riediger mid-face distractor, a device that allows distraction osteogenesis over a maximum distance of 20 mm, would be used. This distractor had been specially developed for indications of mid-facial advancements at a Lefort III level. The intervention was carried out according to the planning. The distraction vector was guided intraorally by an orthodontic appliance. The distance of distraction turned out to be 12.5 mm. The postoperative result showed a more favourable position of the OMC. A dramatic narrowing of the cleft was observed.

Mandibular reconstruction

The next phase of the treatment consisted of hemimandibular reconstruction. A new RP model was built for study of the design for the reconstruction of this mandibular deficiency (Figure 5.5). The model could also be used for a wax-up of the missing left mandible. The final design

Figure 5.5 Reconstruction of the mandible

showed a titanium tray for carrying slurry of tricalcium phosphate (TCP) granulates (Curasan) and bone chips mixed with PRP. The intervention was combined with removal of the Riediger mid-face distractor. A short intervention was made to fix the custom-made titanium hemi-mandible reconstruction with titanium screws. The tray was filled up with the TCP/bone mixture as planned.


Complex cases such as patients with Goldenhar syndrome are much better understood using an RP model. Both the preoperative planning and the vector planning for the distraction osteogenesis have been made easier. The mandibular reconstruction would never have been possible without the RP model. In both interventions there was a considerable reduction in operation time.

Dr Jan Karel Th. Haex, Dr Jules M. N. Poukens and Prof. D. Riediger -University Hospital Maastricht, The Netherlands.

Published in Phidias Newsletter, Volume 7, December 2001.

STL+ module

The Mimics STL+ module interfaces from Mimics to any kind of rapid prototyping (RP) system via triangulated files. These files are created with a bilinear and interplane interpolation algorithm to enhance the resolution of the RP model.

Standard 3D file formats such as STL or VRML (as input to virtual reality) are available. The STL format can be used by any rapid prototyping system. Powerful adaptive filtering offers a significant reduction in file size. It is possible to export from a mask, a 3D object or a 3dd file. The available export formats are ASCII STL, binary STL, DXF, VRML 2.0 and point cloud.

Several calculation parameters can be specified. STL+ makes it possible to reduce the number of triangles of the exported files, to interpolate the images and to smoothing the 3D files.

There are two methods available for reducing the number of triangles: matrix reduction and triangle reduction. Matrix reduction allows the grouping of voxels to calculate the triangles. Triangle reduction makes it possible to reduce the number of triangles in the mesh. This makes it easier to manipulate the file.

There are also two methods available for interpolating the images and generating the 3D mesh: grey value interpolation and contour interpolation. Contour interpolation is a 2D interpolation in the plane of the images that is smoothly expanded in the third dimension. Grey value interpolation is a real 3D interpolation.

A smoothing algorithm can be applied to make rough surfaces smoother.

MedCAD module

The MedCAD module provides a direct interface to CAD systems via surfaces, curves and objects exported as IGES files.

Based on the segmentation mask, MedCAD automatically generates the contours (polylines) of the mask. These polylines are used to fit b-spline curves, b-spline surfaces and objects (circle, sphere, cylinder, plane, etc.). The objects can also be created interactively. All these entities can be exported as Iges files, and are directly usable for the design of custom-made prostheses in any CAD system.

To verify the CAD implant design, Mimics imports the design as an STL file. MedCAD enables the user to visualize and manipulate the implants within the medical images in 2D cross-sections as well as in 3D.

FEA module

The Mimics FEA module makes it possible to link from scanned images to finite element analysis and computational fluid dynamics by exporting the files in the appropriate file format. 3D objects can be calculated on the basis of the scanned images and these surface meshes can be prepared for finite element analysis purposes. The remesher in the FEA module ensures that the most optimal input for that FEA package is eventually obtained. Materials can be assigned to volumetric meshes, based on the Hounsfield units in the scanned images.

The Mimics remesher significantly improves the quality and speed of FE analyses on STL models. It allows the easy transformation of irregularly shaped triangles into more or less equilateral triangles and increases the reliability and accuracy of FEA results on STL models. Most FE packages do not allow the manipulation or optimization of the mesh generated when a part is imported. This might reduce the accuracy of the results. With the remesher it is possible to optimize the file and deliver good meshes that will run in the FEA software (Figures 5.6 and 5.7).

After loading a volume mesh, the FEA calculates an appropriate Hounsfield value for each element of the mesh on the basis of the scanned images. Several Hounsfield unit ranges, each representing a material, can then be specified. A density, an elastic modulus and a Poisson's

Figure 5.6 3D view of the vessel before remeshing

Figure 5.7 3D view of the vessel after remeshing

Figure 5.9 Material distribution histogram

Figure 5.8 Material distribution representation

Figure 5.9 Material distribution histogram ratio can also be assigned for those materials. The volumetric mesh with the assigned materials can then be exported to a Patran neutral, Ansys or Abaqus file (Figures 5.8 and 5.9).

Simulation module

The Mimics simulation module is an open platform for surgical simulations that makes it possible to perform a detailed analysis of data using the anthropomorphic analysis templates, plan osteotomies and distraction surgeries, or simulate and explain a surgical procedure for implant design.

To perform an anthropomorphic analysis - standard template or user defined - indicate the appropriate points (landmarks). Planes and measurements are automatically created once the points they depend upon are created. New landmarks can be created, copied, edited or deleted. Each landmark can have some default properties that can be set when creating the landmark or by editing an existing landmark. Both distances and angles can be measured. For distance, either the distance between two points or the distance between a point and a plane can be measured. As for an angle, this can be measured using three points or using two lines.

The Mimics simulation module offers a powerful 3D package for all kinds of surgery simulation application. Various tools and STL operations for simulating osteotomy and distraction surgeries are available: cut and split operations, merging of objects, mirroring of parts, distractor placement and repositioning of objects with or without a distractor. The following examples demonstrate the use of the simulation module.

Example 1: cranial implant

Cut, mirror and repositioning operations make it possible to define the required shape of a cranial implant by mirroring one side of the patient's skull (Figures 5.10 to 5.12).

Example 2: osteotomy planning

Simulation of a complex maxillary osteotomy followed by repositioning of the newly formed parts (Figures 5.13 to 5.18).

Rapid Prototyping Implants
Figure 5.12 Hole with mirrored part from the intact side
Rapid Prototyping Implants
Figure 5.15 Split operation
Figure 5.16 Second cutting path
Figure 5.17 Second split operation
Figure 5.18 Repositioning

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