Tutorials

Table of Contents
CHAPTER 1: IMPORT .................................................................................. 5
CHAPTER 2: MIMI ...................................................................................... 11
CHAPTER 3: SIMON .................................................................................. 25
CHAPTER 4: HIP ........................................................................................ 39
CHAPTER 5: OBTURATOR ....................................................................... 47
CHAPTER 6: MANUAL IMPORT ............................................................... 59
CHAPTER 7: SIMULATION TUTORIAL .................................................... 66
CHAPTER 8: FEA TUTORIAL .................................................................... 81
CHAPTER 9: CFD TUTORIAL ................................................................... 99
CHAPTER 10: NON-MANIFOLD ASSEMBLY TUTORIAL ..................... 113

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If you have chosen to install the demo files during the Mimics installation
procedure, only two of the files used in this tutorial will be put in the
MedData folder.
The others can be found on the CD or can be downloaded from our website
(http://www.materialise.com/software/download_ENG.html). You will need
to register first or, if you are already registered, sign in using your e-mail
address. On the first page choose Mimics and follow the link to Tutorial
Datasets.
The extra tutorial files are a self-extracting zip-file. To unpack the file,
double click on it and choose your MedData folder as destination folder.
The following tutorials are available:

Chapter 1: Import Tutorial that shows how you can import

images in Mimics

Chapter 2: Mimi Tutorial that shows how to do a basic

segmentation and 3D calculation.

Chapter 3: Simon Tutorial that shows some advanced

segmentation functions to remove artifacts.

Chapter 4: Hip Tutorial that shows how to use the

MedCAD module.

Chapter 5: Obturator Tutorial that shows how to make a mold of

a cavity by segmenting the Soft tissue
around the cavity.

Chapter 6: Manual Import Tutorial that shows how to use the manual
import function.

Chapter 7: FEA Tutorial Tutorial that shows how to use the FEA
module.

Chapter 8: Simulation Tutorial Tutorial that shows how to use the

Simulation module.

Chapter 9: CFD Tutorial Tutorial that shows how to use the FEA
module for linking to CFD.

Chapter 10: Non-manifold Tutorial that shows how to combine two

Assemblies meshes.

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Note: In Mimics you have the possibility to use both Hounsfield and Grey
Values. This is very important when setting a threshold and when you use
the Profile Line function. To switch between these two possibilities, go to
Options > Preferences, General tab and select the Pixel unit you want to
use. Most tutorials need one or more modules of Mimics (STL+, RP Slice,
MedCAD, Simulation or FEA). If you wish to try that section of the tutorial
and you dont have the required module(s) installed, an evaluation period of
that module can be obtained on request.

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Chapter 1: Import
The goal in the first part of this chapter is to teach you how to import images
and convert them into a Mimics project. The second part will illustrate how
to organize the images in the project you made.
In this tutorial we will discuss three topics:
How to do an Automatic Import
How to organize images
How to do a Semi-Automatic Import

Note: To import images from a tape you need to use the Dump Tape

function
Note: There are 3 ways to import images, depending on their format:
automatic import, when the format of the files is known to Mimics
semi-automatic, e.g. Bitmap or Tiff images
manual import (Case 6), when the file type is unknown and you
need to specify some parameters manually

1. Automatic import
To start the Import wizard, first select File and then choose Import Images.
An Import Project Wizard will be displayed where you can select where the
images to be imported can be found (STEP 1).
In the import wizard, browse to the MedData folder and select the folder
called Import1. A list of files will be displayed in the Filename column and
all the files will be automatically selected. Click the Next button.
If the format of the images is known to Mimics (see the general help files for
a list of known formats), you can select the images and press the Next

button. If you click on the import information button , an import

message will be displayed containing the correct path and format of the
images.
Note: In this case the file type is recognized, but in some cases the
message log tells you that one or more images are of an unknown file type.
If this happens, you have to perform a manual import (see Case 6).

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Note: If you want to keep all the files, press the Next button, otherwise first
change the selection of images to fit your needs. This selection can be done
in two different ways: either you can click on the first file and then on the
last one you want to include while keeping down the Shift button (this way
you will include all files in the interval) or you can select the files one by one
while keeping down the Ctrl button.
After clicking on the Next button you will reach the second step of the
Import Project Wizard, in which you need to select the studies to be
converted. The study you have just imported is already selected by default.
In this window some information about the project can be found, such as
the number of images, pixel size, patient name, orientation parameters, etc.

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Now you can click the Convert button and you will see a progress bar.
During the conversion process, the project will be opened automatically
displaying the Change Orientation window since one or more of the
orientation strings were missing in the original images.

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Now you need to set the Orientation Parameters that are missing and
change the ones that are incorrect. Actually if you look at the axial image
you see the orientation strings L and R, which stand for Left and Right
respectively together with A and P which stand for Anterior and Posterior. In
the coronal and sagittal image two Xs are displayed instead of the above
mentioned orientation strings. Move the mouse cursor to the top X in the
sagittal or coronal image. The cursor shape changes to a hand and if you
right-click, a menu appears with all possible orientation strings. Select
Top. Note that all the other orientation strings are completed
automatically.
If the orientation of the images is right you can click OK and your Mimics
project will be opened. Now you can process your images using the tools
explained in the tutorials dealing with Case 2 and Case 3 (Threshold,
Region Growing, Edit, etc..)

2. Organizing images
Once you have opened your project, you can decide to exclude some
images if they are not good or if you dont need all of them. For example,
we can decide to delete the images of the project Simon.mcs that dont
include parts of mandible or that dont contain any information.
To access the Organize Images window, go to File and then choose
Organize Images.

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First of all you can get a better look at the images changing the preview
size to Medium or Large by selecting the respective size from the Preview
size dropdown box.
If you look at the images you will notice that the ones that correspond to
table positions 49.5 and 48.5 do not contain any information about
mandible. So you can click on these two images to unselect them, the
green mark will disappear and the image will be unchecked in the list on the
left.
On closer inspection you can also notice that the image at table position
1.5 is the last one that contains information about the mandible. Right-click
on the image at position 1.5 and choose Unselect after this. All the
consecutive images will be unselected also.
Press OK and scroll through the axial images to check if the correct ones
are visible in the project, you should not see the ones you unselected.
You can now save your Mimics project with the name Organizing
Images.mcs going to File and then Save As. After you have done this you
can make a segmentation following the next tutorial (Case 2)

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3. Semi-automatic import
Now we will try to import the Bitmap images you can find in your MedData
directory in the "Import2" subdirectory. Again select File > Import Images
and browse to the C:\MedData\Import2\ directory. If you press the Next
button, a new window will be displayed.

The only information you need to provide/change is the slice distance and
the pixel size. This information should be collected by someone who is
familiar with the machine used to make the CT-Scan. It is very important to
insert the exact values since the dimensions of the volumes and the 3D
depend on them.
When the correct information is filled out, you can press OK to continue
with the second step of the Import Project Wizard. Now the import
continues in a similar way to the automatic import. You will need to select
the study you wish to convert and your Mimics project will be created after
clicking on the Open button. Now you should be able to set the orientation
parameters as described in the previous paragraph and calculate a good
3D.

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Chapter 2: Mimi
In the second case of this tutorial we will show you some basic features of
Mimics. The topics that will be discussed are:
Opening the Project
Windowing
Thresholding
Region Growing
Creating a 3D representation
Displaying a 3D representation
STL+ Procedures
Generating a STL file
RP Slice procedures
Generating a contour file
Generating supports
View of the end result

1. Opening the project

From the File menu, select Open (Ctrl+O). The Open dialog box shows all
projects in the working directory. Double click on the mimi.mcs file (Mimics
project file).
All images are loaded and displayed in three views. The view on the right
shows the images as they are exported by the scanner (xy-view or axial
view). The upper left corner is a reslice of these images in the xz-direction
(xz-view or coronal view) and the bottom left is a reslice in the yz-direction
(yz-view or sagittal view). The different colors of the intersecting lines refer
to the colors of the contour lines of each view so every line refers to the
slice in the corresponding view. You can easily navigate through the images
by clicking on any point of the CT images in any view: the intersecting lines
will move crossing each other in the point you clicked and all the views will
be updated showing the corresponding slices.

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If you need to change the orientation of a view, go to File > Change

Orientation. This will open a window in which you can change the
orientation parameters simply by clicking on it with the right mouse button
(see tutorial Case 1).

Every indicator can be turned off by selecting View > Indicators in the
Menu Toolbar.
In the right border of the window you will see a slider that allows you to
scroll through the images from the active view.

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In our current project (Mimi), all images are correct. If, however, you have
an image set from which you want to remove some images, go to File >
Organize Images. There you can add or remove images (see tutorial Case
1).

2. Windowing
First of all, we have to adjust the contrast of the images displayed in the
different views. Contrast enhancement is a very good tool for selecting
parts with different intensities, e.g. bone vs. brain tumor. This action can be
performed at any time.
You can change the contrast in the corresponding tab of the Project
management. The contrast tab shows the histogram of the project with a
line representing the window. The gray values or Hounsfield units below
the start point of the line will be displayed in black. All gray values above
the end point of the line will be displayed in white. The gray values in
between the window will be mapped on a shade of gray.
You can change the window size by clicking your left mouse on one of the
points and dragging it to its new location. To move the window select the
line and drag it to its new position.
You can also choose one of the predefined windows by selecting the
appropriate scale from the menu on the bottom of the tab.
The following steps will describe the necessary actions to achieve a nice
segmentation mask. A segmentation mask is a collection of pixels of
interest that constitute an object you wish to work on. One can create
several - dependent or independent - masks, each displayed with their own
identifying color. Usually several masks will be needed to obtain a final
segmentation object that contains the information that is needed.

3. Thresholding
Thresholding means that the segmentation object (visualized by a colored
mask) will contain only those pixels of the image with a value higher than or
equal to the threshold value. Sometimes an upper and lower threshold is
needed; the segmentation mask contains all pixels between these two
values.
For example:

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A low threshold value makes it possible to select the Soft tissue of the
scanned patient. With a high threshold, only the very dense parts remain
selected. Using both an upper and a lower threshold is needed when the
nerve channel needs to be selected. Defining a good threshold value also
depends on the purpose of the model. If you just want a nice looking model,
a lower threshold value is recommended since it will result in a model with
fewer holes. On the other hand, when the model serves for modeling
prostheses a higher threshold value is preferred.

Click the Threshold button .

To change the threshold value, press the left mouse button on a slider in
the Threshold Toolbar and move the slider by moving the mouse (while still
holding the left mouse button).
Some tips for selecting an adequate threshold value:
Look at different images. You can change images of any view by:
using the arrow keys, the page up and page down keys
using the slider on the right in the window border
moving the slice indicators

Click the Profile button .

In the axial view draw a line over the bone as shown below. To draw this
line, click the left mouse button in the soft tissue to indicate the starting
point, move the mouse over the bone click. Along this line an intensity
profile is generated. The straight horizontal lines represent your current
threshold value. Click on Start Thresholding and drag the lower straight-
line up/down to set a good threshold. If you want a good visualization
model, select a threshold slightly above the intensity plateau of the soft
tissue. If your model will serve for modeling prostheses, place the line
between the soft tissue plateau and the top value of the bone. If a proper
threshold is set, click on End Thresholding to save the current value.

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Zoom in on a part youre interested in. First, from the pull-down menu next

to the zoom button, select Box. Click the Zoom-button : the mouse is
displayed as a loupe. Click the left mouse button on the image and drag for
creating a zoom rectangle, release for zooming. To return to the whole

image, click the Unzoom-button .

A good threshold value for Mimi is about 270 (Hounsfield scale). The
threshold value is displayed in the Min. box of the Threshold toolbar. To end
thresholding, click the Apply button.
After the thresholding operation a green mask will be created. In a project
you can have different masks but you can use the segmentation tools only
on the active mask. To choose the active mask, select it in the mask tab in
the project management. In case the project management isnt active,

select the project management button in the main toolbar.

You can also hide any mask by clicking on the glasses of the corresponding
color.

4. Region growing
The region growing tool makes it possible to split the segmentation created
by thresholding into several objects and to remove floating pixels.

Click the Region growing button or press Ctrl + R. The mouse is now
cross-shaped and the Region Growing window is on the screen.

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Select the Source (= Green) and Target mask (= New Mask). Click the left
mouse button on one point in the green area of the object of interest (which
is a part of the current segmentation object, i.e. part of the skull). The
program starts to calculate the new segmentation, all points in the current
segmentation object that are connected to the marked point will be used to
form a new mask. The new segmentation is colored yellow.
Click the Close button to close the Region growing window.
To make this new mask active, select "Yellow" in the Visualization toolbar.
Clicking on the green glasses will hide the green mask. Clicking the button
again will make the green mask visible.
Check the mask on different images.
When we check the images, we see that everything looks fine. Its time to
build a 3D representation.
Note: Thresholding needs to be done before region growing, since all
previous work is lost after changing the threshold value.

5. Creating a 3D representation
In the mask tab you see all created masks listed with their respective
threshold. The names of these masks are Green and Yellow. Selecting one
mask will make it active.
Now, you still know that the Yellow mask contains the skull, but after a
month, when you reload a project, it might be difficult to know in which
mask your end result was stored. Therefore, it may be interesting to rename
the mask (in Project Management, Masks tab). Click on the name Yellow so
that it becomes editable; replace Yellow with a more telling name like skull.

Click on the Calculate 3D button .

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The "Calculate 3D Models" Dialog box is displayed. Here you can select
from which masks you want to calculate the 3D model. To select multiple
masks hold the Ctrl key while selecting the other masks. In this case select
skull and press the Calculate button to generate a 3D object.
You can set the visualization quality of your model. This is only the
visualization on the screen; this parameter doesnt need to have any impact
on the model that you will actually build on an RP machine!!! Of course, the
lower the quality, the less time the program needs to calculate the 3D
image and the less memory is needed to load the 3D image afterwards.

6. Displaying a 3D representation
In the vertical 3D toolbar on the right, you can set the visibility of the
different calculated 3Ds. This can also be done in the Project
Management's 3D Objects Tab, by clicking on the glasses.
Once the 3D image is loaded, different operations are available:

rotate the model with the button on the right of the 3D window
or moving the mouse pressing the right button
select different standard views, like Top, Front, Bottom, by clicking

on the button on the right of the window

zoom with the buttons or Pan with the

change the color of your model and background by clicking the right
mouse button and selecting the option Color
The model can also be displayed transparent. To do so, push the Toggle

Transparency button . You can switch between different degrees of

transparency (high-medium-low-opaque) by clicking the square button

in the transparency column of the 3D objects tab.

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To change the background color, go to View > 3D Background Color and

select the color you prefer.

7. STL+ procedures
The intermediate file between Mimics and STL+ can be one of the following:
.3dd file
Masks
3D Objects
You can create a skull.3dd file by clicking the Export 3dd button in the
Project Managements Masks Tab or with the option Export > 3dd in the
main toolbar. After clicking the Save button the .3dd files will be placed in
the MedData folder.
This step is not always necessary. Calculation of the machine files can be
done directly on the masks or on 3D objects. Click on the STL+ button in
the Masks Tab of the project Management. Press the STL+ button and a
window will pop up on the screen with 3 different tabs for each option.
Choose the Masks tab, select the mask called skull and click the Add
button. Choosing the 3D tab would have enabled you to select a 3D object.
Please note that multiple 3Ds or masks can be selected and added to the
list but it is not possible to add both masks and 3Ds.
If you're interested in creating files for Rapid Prototyping or exporting an
STL or VRML file, please continue this tutorial.
After selecting the mask or the .3dd file and pressing the Add button, the
file appears in the output area. If you wish, you can rename the output file
to skull (in the same way as you would in Windows Explorer).
Select the output format. Depending on the type of output file format, there
are different possible formats, like STL or VRML.

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7.1 Generating a STL file

Click the Next button: the Conversion to STL Dialog box is displayed.
You can use the parameters as they are displayed in the screenshot.
Further details about these parameters can be found in the manual. By
clicking on the help button you will immediately be taken to the respective
chapter.
To generate an STL file, fill in the appropriate values like in the dialog box
and click the Finish button. The calculation starts and an STL file is
generated.

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8. RP Slice procedures
8.1 RP Slice procedures
Within the RP slice dialog you are able to generate a contour file from a
mask or a 3dd and you can also generate a support file from a contour file.

8.2 Generating a contour file

Go to Project Management, Masks tab and choose from the action list
the RP Slice button . Choose the mask called skull from the list in the
Masks tab of the RP Slice window that just opened and press the Add
button, the mask will appear in the area below. Select the SLI Output
format.
Click the Next button, the Conversion to RP format Dialog Box is displayed.
You can use the following parameters in the RP Slice Parameter dialog
box.

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Click the Next button to proceed; the Calculation Parameters dialog box is
displayed. Fill in the values as displayed below.

Further details about these parameters can be found in the RP slice part of
the manual.
Click the Finish button; the calculation starts and an SLI file is generated.
For calculating the support structures, please continue this tutorial.

8.3 Generating supports

For building the object with Stereolithography, a support is generated
directly from the slice file with RP Slice module . Go to the RP Slice
window, Contour files tab and select .SLI file option in the Input format field.
Select the file you created in the previous section and press the Add
button.

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When one contour file is selected, the Next button in the RP slice
Mask/3dd/contour file selection window opens the window displayed
below.

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Note: It is also possible to generate slice files for Stratasys machines.

Instructions on how to use these files in Quickslice are also provided (read
the STL+ Reference Guide).
The program defaults to full height, so that the whole model is supported.
This isnt always necessary. Check the slices from bottom to top and search
for new islands. To prevent that these islands start floating during the
building process, they certainly need support. In the case of "Mimi", a
support till layer height 50.00 is sufficient (depending on the resin used).
Press the Finish button to start the support generation; an SLI file is
created.
You now have a model and support file, good luck with the building of the
model !!

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9. View of end result

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Chapter 3: Simon
The Simon case is an example of a dental segmentation. The mandible of
the patient was partially edentulous and needed a prosthesis. First, a scan
prosthesis was made that resembled the new teeth to be implanted. The
patient had this prosthesis at the correct position in his mouth during the CT
scan. Because scan prostheses are made out of barium sulfate, an opaque
material, they are clearly visible in a CT image. The result is that you see
both the bone and the prosthesis in one image, well positioned against
each other. Such a procedure with a scan prosthesis gives better esthetic
results and the surgeon is able to make a better planning.
The images in the Simon project are CT scans of the jaw together with the
scan prostheses. It will be your job to do the segmentation of the mandible
and the prosthesis.
The topics that will be discussed are:
Opening the Project
Preparation of the data
o Windowing
o Thresholding
o Region growing
o Editing
o Artifacts
o Multiple particles
o Scan prosthesis
Boolean Operations
View of the end result

1. Opening the project

In the File menu, select Open (Ctrl+O). Double click the Simon.mcs file.

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2. Preparation of the data

2.1 Windowing
For correct windowing see the windowing procedures in "Mimi" (Case 2).

2.2 Thresholding
Go to an axial image where the mandible (without the teeth) is visible (for
example, at position -30.50). Press the Profile line button and draw a line
over the bone. The figure below shows a profile line and the corresponding
profile dialog box. Press Start thresholding and drag the threshold line to
a value of about 538 (Hounsfield scale). End the thresholding and save
your settings. Close the dialog box.

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Profile line over the bone (upper image) and the corresponding profile
dialog box

2.3 Region growing

Press the Region Growing button and click on the bone of the skull to
start the region growing. The skull is now added to a new mask. Click on

the Project Management icon . In the Masks tab, double click the name
of the mask and change it to skull. Make the previous mask invisible
(make sure the skull mask is active before making the first mask invisible).

2.4 Editing - Thresholding

2.4.1 Separating maxilla and mandible
To separate the mandible from the maxilla, we have to disconnect them
manually. Therefore we erase a layer from the active mask somewhere
between the mandible and the maxilla. Then we perform a region growing
on the mandible. The result is that both mandible and maxilla will be in a
different mask and thus separated.
Look at the sagittal image and place the horizontal indicator between the
maxilla and the mandible. Note that it will not be possible to separate them
correctly in every image, so we have to find the best possible position.

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In the corresponding axial image all pixels have to be removed from the
active mask. The position of the axial image corresponding to the position
of the horizontal indicator in the figure above, is -4.50. Go to this image and

press the Edit masks button . Select the Erase mode, choose a big
square as type of cursor and remove all pixels from the active mask. Make
sure you dont forget any! Go to a lower image in the data set and do a
region growing of the mandible (do not activate the Leave Original Mask
option). Now you have two masks, one for the mandible and another for the
maxilla.
Note: In the region growing toolbar, if you activate the Leave Original Mask
option, the pixels selected with region growing will be put into a new mask,
but they will also remain in the original mask. If the result of the region
growing is not satisfying, you still have the complete original mask and you
can start over. If this option is not activated, the pixels selected during
region growing are removed from the original mask. In this case you cant
do the region growing again from the same original mask.
Change in the Project Management the name of the two masks to
mandible and maxilla respectively. In figure below, these two masks are
shown and the red line in between indicates the layer that was removed
from the active mask.
But be careful! Because it was not possible to perform the separation 100%
correct, we will still have to edit the images and make sure that all the pixels
that belong to the mandible are really in the mandible mask.

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Scroll through the coronal images and check if every pixel that belongs to
the mandible is in the proper mask. Do you notice at position 64.50 that
some pixels (at the left side in the image) from the maxilla are wrongly put
in the mask of the mandible?

Move both indicators until their point of intersection indicates the wrong
pixels (figure above). It concerns two layers of pixels, belonging to a tooth
of the maxilla. In the two corresponding axial images (position -6,50 and -
5,50), erase the tooth from the mask of the mandible. You cannot be
mistaken, because that tooth is also indicated with the point of intersection
of the indicators (figure below). If the two layers of pixels are shown in grey
values in the coronal image, you can be sure you erased the whole tooth
from the mandible mask. If not, move the indicators again in the coronal
image so their intersection points to the wrongly colored pixels. In the axial
image, remove the pixels that are indicated by the indicators from the active
mask.

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Note: you can still access the 1-click navigation function by pressing the
SHIFT button while you are editing. You can then click with your left mouse
button on the point you want to navigate to.

Axial images (position: left -5,50, right -6,50): the indicators point out the
tooth that does not belong to the mandible mask.
In the sagittal image at position 87.25 (or the coronal image at position
43.25) another collection of badly masked pixels is visible. But now its the
opposite situation! Three layers of pixels that belong to the mandible are not
in the mandible mask. Two layers belong to the maxilla mask and the other
layer is the one we erased in the beginning to make the disconnection.
Again, mark these pixels with the indicators as it is done in the figure below.
In the corresponding axial images (at positions -4.50 and -3.50 and -2.50)
the pixels (of a tooth) should be added to the mandible mask. We will make
use of a local threshold to do this. To make this threshold clear, a short
intermezzo is inserted below.

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Indicators point to pixels that should belong to the mandible mask (sagittal
view).
Local threshold: In the obturator case it is mentioned that there are three
modes to choose from in the Edit toolbar, i.e. draw, erase and threshold.
The threshold mode (Ctrl + T) is used to set a local threshold. This means
that if you apply a local threshold in a particular area of one image, this
threshold doesnt apply to the other images in the project. Remark that the
threshold weve set in the beginning of this case was global and it applied to
every image in the dataset.
When you activate this mode, the box with the two default threshold values
is shown on your screen. To set a different local threshold, press one of the
two arrow buttons and double click on a threshold value. After you changed
the value, press Enter. When you move the square over the image while
pressing the left mouse button, every pixel that comes to lie within the
square and has a threshold in the threshold range you just set, will be
added to the active mask. On the other hand, all the pixels that already
belonged to the active mask and that dont have a grey value within the
range will be removed from the mask.

The local threshold range

For the moment we dont have to change the threshold values, but it will be
used later on in this case to remove artifacts out of the image.

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Maybe you now wonder why we will add the pixels of the teeth that belong
to the mandible with this local threshold method and not with the draw
mode we will use in the obturator case. With the draw mode, cant you also
add pixels to a mask? Yes, thats true, but there is a difference! With the
draw mode you add every pixel you touch with your cursor. With the
threshold mode you do the same, but there is one more condition before
they are really added: their HU values must lie in the range shown in the
box (figure 3-7). In this case, its much safer to add pixels by taking into
account their grey values. Our segmentation will be more accurate.
Press Ctrl + T. The Edit toolbar shows up and the threshold mode is already
selected. Choose a circle as type of cursor and make it more or less the
same size as a tooth. Make sure that the mandible mask is the active mask.
Press the left mouse button and go over the tooth with your cursor. Make
sure you got the tooth completely. You can check this very easily by looking
at the sagittal or coronal image: if the wrongly masked layers (figure 3-6)
now have the color of the mandible mask its alright, otherwise youve
forgotten some pixels. Suppose you added too much pixels, just press E (or
select the Erase mode with your mouse) and erase them. If you repeat the
thresholding in the necessary axial images (see before to know their
positions) you should become a sagittal image like in the figure below. Now
we can say that the whole mandible is in the mandible mask.

Sagittal image after local thresholding

2.4.2 Artifacts
The images still dont look nice, because of all the artifacts. We are going to
get rid of them by again performing a local threshold, but not the default one
like we just used to add the pixels.

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To enter the Edit mode, press Ctrl + T. The threshold mode is already
selected. Click on the top arrow of the threshold range box (figure 3-7) and
double click the threshold 1 value. Change this value to 3000 (if you are
working in Hounsfield Units) and press Enter. Because the Hounsfield Units
of the artifacts are lower than the ones of the teeth. Go with your cursor
over the artifacts and notice that they disappear. Why do we use this high
local threshold? Because the HU values of the artifacts are lower than the
ones of the teeth. So by setting a very high threshold the artifacts will be
removed from the mask because their grey values are not in the range.
Moreover, if you accidentally go with your cursor over the teeth, their pixels
will remain in the mask, except for the edges (their HU are lower). If you
removed the edges from the mask, dont panic. Set the threshold range
back to the default one by clicking once on the lowest arrow and move your
cursor over the tooth again to restore the edges. So, this is the way you
should work. Scroll through the axial images and remove all the artifacts
from the mask of the mandible.

The artifacts in the left image are removed with a local threshold. The right
image shows the result

2.4.3 Multiple particles

Lets calculate the 3D image of the mandible. Press the Calculate 3D
button and select the mandible mask to be calculated (choose low quality).
You get the message that the mask consists out of multiple parts. Answer
with Yes.

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Visualize the 3D by pressing the 3D button. Rotate the model and remark
that there are little particles floating around the mandible. That caused the
message you got about the multiple parts. The particles are due to the
editing youve done to remove the artifacts. To avoid this you have to do a
region growing before calculating the 3D. Press the 3D view button again to
get back the sagittal image. Press the Region growing button and click into
the mandible. Change the name of this new mask to Total mandible. Now
calculate and visualize the 3D model of the final mandible. You can delete
the first 3D (with the particles) listed in the 3D tab of the Project
Management.

2.4.4 Scan prosthesis

Can you distinguish between the natural teeth and the scan prostheses in
the 3D model of the mandible? Its quite simple; the natural teeth are
connected to the bone, while the scan prostheses are not. There are 3 teeth
of the scan prostheses at the patients left side and one at his right side. In
the figure below, the scan prosthesis (axial view) is marked with rectangles.

Axial image indicating the prosthesis in the boxes.

We would like to have the mandible without the prosthesis and the
prosthesis itself into two different masks. There are two ways to achieve
this. The first one is to proceed with the segmentation of the final mandible
and to remove the prosthesis from the active mask. The second option is to
perform a segmentation of the prosthesis. We opt for the latter. We will do a
region growing of the prosthesis twice, once at either side. But, we first
have to make sure that the prosthesis is completely disconnected from the
natural teeth. The intention is to remove (from the final mandible mask) the
pixels surrounding the prosthesis and the pixels connected to the
prosthesis. The goal is to get the prosthesis nicely isolated in every image.
Keep the following advice into account: remove enough pixels in the
surrounding of the prosthesis, because sometimes in 2D it looks like there
is no connection, but there is still one in 3D. So a 3D model can be very
tricky!

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Project Management Masks tab

Make the mask of the final mandible active and press the Duplicate
button in the Masks tab of the Project Management window. This way a
backup mask is created that we can use to do the segmentation of the
prosthesis, while the original Final mandible mask is left unchanged. The
original one will be used later on to perform Boolean operations. Proceed
with this backup mask (if you dont like the color, press the Color button in
the masks tab and choose the color you like). Scroll through the axial
images and remove (enough!) pixels surrounding the prosthesis from the
active mask. In the figure below it is shown for the axial image at position -
11,50.
If you think you disconnected the prosthesis completely, press the Region
Growing button. Make sure your target mask is a new mask (if not, select
new mask from the drop down list) and that you activate the Leave
Original Mask option. This last option is very important!

The prosthesis is disconnected in this layer

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Click on the left or the right prosthesis. If you disconnected the prosthesis
entirely, only the prosthesis should be shown in the color of the target
mask. If this is not the case, make the previous mask active again, delete
the last mask in the list (generated for the region growing) and remove
more surrounding pixels from the backup mask. Also in the layers where
you dont see the prosthesis it can be useful to remove some pixels
belonging to the teeth next to the prosthesis. repeat these actions for the
prosthesis at the other side. Give the masks of both prostheses proper
names.

2.5 Boolean Operations

Lets examine what weve obtained so far: the final mandible (with
prosthesis), the left prosthesis and the right prosthesis in three different
masks. Thats nice, but we said earlier that we would like to have the
mandible without prosthesis. We can achieve this with some Boolean
operations we can achieve this. Press the Boolean operations button

. Let's use the following calculation:

Mandible without prosthesis = total mandible left prosthesis right
prosthesis
Follow the steps below:
Mask A: final mandible
Operation: minus
Mask B: left prosthesis
Result: new mask (called mask C for reference)
After these options are set, press the Apply button.
Mask A: mask C (obtained in the first step)
Operation: minus
Mask B: right prosthesis
Result: new mask
After these options are set, press the Apply button.
Press the Close button. The last mask (the one that should be active now)
contains the pixels of the mandible without the prosthesis. Calculate and
view the 3D of this mask. Show also the left and right prosthesis. The other
3Ds can be set invisible. You should have a model that looks like this one.

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3. View of end result

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Chapter 4: Hip
In the fourth tutorial we will discuss some of the possibilities of the MedCAD
module. To finish this tutorial you will have to have a license for the
MedCAD module.
The topics that will be discussed are:
Opening the Project
Preparation of the data
o Thresholding
o Region growing
Calculation of the Polylines
Patching of the contours
Creation of MedCAD objects
Visualization possibilities

1. Opening the project

The objective for this part is the creation of a file ready to use in all CAD-
systems supporting the IGES-interface. The part of the "Hip" well focus on
is the right femur of the patient (left in the images). In this IGES-file a basic
reference system calculated on the data as well as a partial modeling of the
outer contours using freeform surfaces will be present.
It is strongly advised to first follow the tutorial of Case 2 to obtain the
necessary skills for segmentation and image processing.
In the File menu, select Open (Ctrl+O). The Open dialog box shows all
projects in the working directory. Double click the hip.mcs file (Mimics
project file).

2. Preparation of the data

2.1 Thresholding
A good minimum threshold value for this case is 1235 (Grey Values) or 211
(Hounsfield values). Set this threshold in your base mask and apply it. The
procedure is explained in more detail in Case 2.

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2.2 Region growing

We want to make a model of the right femur (left in the image set).
Therefore use the following steps:
Click the Region Grow button or press Ctrl + R.
Set the Source to Green (if this is your base mask) and Target to
New Mask. Check the Multiple layer box.
Click the left mouse button on one point of the right femur (left on
the images). The right femur has now been grown into a new mask
(Normally if you have started fresh the femur will be in the yellow
mask now).
To calculate your 3D, go to Project Management, Masks tab, select the
yellow mask and press the Calculate 3D button. The yellow mask will be
automatically selected in the Calculate 3D window, but you need to set the
quality to high and press the Calculate button.
You can find more details about this in Case 2.

3. Calculation of the Polylines

Go to the Project Management.

Project Management - Masks tab

Select the yellow mask and click on the action button, select the Calc
Polyline option from the action list. The Create Polylines dialog box
appears with the Yellow mask already checked; click OK. The borders of
your yellow mask will be calculated and displayed as a polyline in both 2D
and 3D images.

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3D view of the polylines

You can also calculate polylines by clicking the button in the

segmentation toolbar.

4. Patching of contours
Since we are only interested in the outer contours, we need to select these
out and grow them to a new set of polylines.
Go to layer -523 and zoom in on the right femur in the 2D image (xy plane).

Click the Polyline Growing button in the MedCAD toolbar.

Set all parameters as displayed in the image below: i.e. the set to start
from, the set that will contain the grown polylines, ... In order to select a
polyline, you need to draw a rectangle over it or simply click on its contour.
Hold the left mouse button down, drag it and then release the left mouse
button.

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The growing of the polylines stopped at layer -513 because of a small

extension on the bone This needs to be removed in layers 513 and -511.
Next the polylines need to be updated and then we can proceed with the
polyline growing:
Click the Edit masks button and go to the erase mode or press Ctrl
+E
Make sure that the Yellow mask is Active

Erase the extension on the bone

Press the Ctrl + U key or the Update Polylines button in the Edit
toolbar
Repeat this for the following images.
Scroll back to image -513 and click the Polyline Growing button. Set
"selection 2" as the target polyline and use 96 % as matching parameter.
Select the polyline.
Scroll to image 485 (figure below).

Image 485 of the Hip

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At this slice you see a cavity in the contour. If you want to restore this with
editing, keep in mind that it will be the yellow contours that will be updated,
so we need to remove the pink polyline first.
Do a Polyline Growing from Selection 1 to a New Set ; be sure to turn Auto
Multi-Select off. You can delete this set by selecting it in the Project
management and then pressing the Delete button.
Lose the cavity by drawing in the mask and updating the polyline (Ctrl + U).
Similar editing and updating of the polylines needs to be done on slices: -
483 till -479, -475, -471 (on the femur head). Don't forget to update for
every image.
When all corrections have been made, the polyline growing can continue.
Go back to layer -485 and perform the Polyline Growing (from Set 1 to
Selection 2, matching parameter 95 %, Auto Multi-Select on)
When all editing was performed properly, all layers until -477 are now
stored in Selection 2.
The femur head and the greater trochanter will be grown into new selection
sets. The end result should look like the figure below.

Polyline sets

5. Creation of MedCAD objects

On the great trochanter and on the lower part of the femur we will fit a Free
Form Surface, on the femur head, we will fit a sphere.

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In the Project Management on the Polylines tab, you will find a button Fit
Surface. Choose Selection 2 and press the Fit Surface button. The
following dialog box will appear.

Surface Fit Parameters

You can accept these default values and a Free Form Surface will be fitted
on Selection 2.
Note: Some caution in increasing the number of control points is advised.
The basis of a B-spline is a polynomial and a polynomial has the tendency
to wave. So, if the number of points is too high, the fit on the polyline will
become worse.
Repeat this set on Selection 4.
The Free Form Surfaces are visible in 3D as a shaded surface and in 2D
you will see a cross-section on every layer of this Free Form Surface.
To fit a Sphere on Selection 3, go to the MedCAD menu and select Sphere
> Fit on Polylines. Choose the correct polyline set.
The result of all these fittings should look like following figures:

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Objects fitted on the Polyline sets Imported STL files

6. Visualization possibilities
When a prosthesis is designed, the STL file can be loaded in Mimics. One
can rotate and move this prosthesis to obtain the best fit of the prosthesis
onto the femur and check the design related to the bone structures.
You can import an STL file in the Project Management from STLs tab. Click
the Load... button. Browse to the MedData folder and select the
prosthesis.stl. The STL file will be visible both in 2D (as cross-sections) and
in 3D.
To adjust the position of the STL file, click the Move button to move the
STL file or the Rotate button to rotate it. Both actions can be performed in
2D as well as in 3D.

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Chapter 5: Obturator
In the previous cases we have segmented bone structures, whereas in this
project we are going to make a soft tissue model. An interesting application
is the modeling of the soft tissue around the cavity of the mouth. Such a
model can be used as a mold for obturator prostheses. In the case study
following this introduction we will do just that.
How are we going to model this soft tissue? Since we are only interested in
the area around the cavity, we need to limit the model to the region of
interest. By erasing one layer from the active mask in every direction, the
cavity and the soft tissue around it will be separated from the rest of the
image. This way the region of interest is captured in a 3D box delimited by
the removed layers. Next we perform a region growing that starts in the
region of interest. Because this region is separated from the active mask,
only this area will be put into a new mask after the region growing is done.
From the new mask a 3D model can be calculated which will contain just
the cavity of the mouth and the soft tissue surrounding it.
The topics that will be discussed in this tutorial are:
Case Study
Preparation of the data
o Windowing
o Orientation
o Thresholding
Editing
Region growing
View of the end result

1. Case study
1.1.1 Obturator prosthesis for oncologic patients
Case presented by Dr. L.L. Visch from Daniel den Hoed Kliniek Rotterdam.
The first picture shows the cavity in the mouth of the patient after resection
of a tumor. In order to protect the tissue weakened by irradiation and to be
able to breathe and eat normally, this hole needs to be filled by an implant.

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A CT-scan of the patient was made. The soft tissue around the cavity,
clearly visible on the scans, was modeled. This model served as a direct
mold for the implant.

The implant, called an obturator prosthesis, was cast from the mold in a bio-
compatible silicone.

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Absolutely no surgery was needed to implant the obturator prosthesis. As

the silicone prosthesis is plastic deformable, it can be implanted very easily.
The prosthesis fits the cavity much better than ever could have been
achieved by using conventional impression techniques. These traditional
techniques produce a master of the obturator prosthesis by making an
impression of the cavity in a deformable plastic material.

The prostheses cast from such masters are always less accurate because
of the presence of undercuts (the impression technique is not sensitive to
local internal broadening of the cavity) and can severely damage the
sensitive and vulnerable surrounding tissue.
The soft prosthesis is fixed by means of magnets on a hard dental implant.
This makes it possible to take it out for inspection and to replace it
afterwards.

2. Preparation of the data

2.1 Preparation of the data
In the File menu, select Open (ctrl+O) or click the button . Double click
the obturator.mcs project.

2.2 Windowing
For correct windowing see the windowing procedures in "Mimi" (Case 2).

2.3 Orientation
When the project is loaded, a Change Orientation window pops up.

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In the axial image you see the orientation strings L and R, which stand for
Left and Right respectively. In the coronal and sagittal image several Xs are
displayed instead of the orientation strings. Move the mouse cursor to the
top X in the sagittal or coronal image. The cursor is changed to a hand and
when you right-click, a menu appears with all possible orientation strings.
Select Top. Remark that all other orientation strings are completed
automatically.
Do the same to set the Anterior-Posterior orientation parameter looking at
the image displayed.

You can always change your orientation parameters, going to File >
Change Orientation.

2.4 Thresholding
A reliable way to define an appropriate threshold is to make use of a profile

line (see also Case 2). Press the Profile line button and draw a line in
the axial image over the cavity.

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Profile line over the cavity of the mouth

See the figure above (axial image on position 374) to have an idea where to
place the profile line. You get a profile like shown in the image below. You
can clearly see the transition from the soft tissue to the cavity. Press the
Start thresholding button. To visualize all the soft tissue in the mask, drag
the lowest threshold line to the value 444 (Hounsfield scale). Press again
the End thresholding button and answer yes to the question whether you
want to save the threshold value or not. Close the window.

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3. Editing
In the axial image, go to position 387,00. Press the Edit masks button .
The edit toolbar is displayed on your screen. Your cursor has become a
little square. If not, go to Type and select a square from the drop down list.
Notice that the length and the width of the square are displayed and can
also be altered. The easiest way to change the size is to press the control
key and your left mouse button simultaneously and to move to the right/left
to make the square bigger/smaller.

The three modes available are listed below. To make a mode active, just
click in the little circle on the left of the mode or press the first letter of the
desired mode. When the edit mode is not yet selected and you use the
shortcuts between parentheses below, the edit toolbar appears and the
associated mode is activated.
Draw (Ctrl + D): Every pixel that lies within the shape of your
cursor, while pressing the left mouse button, will get the color of
your active mask. In other words, you add pixels to the active mask
by going over the pixels with the square.

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Erase (Ctrl + E): This mode is the opposite of the draw mode. You
remove all the pixels from the active mask by moving the square
(keeping the left mouse button pressed) over the pixels in the
image.
Threshold (Ctrl + T): This mode is used to set a local threshold.
This means that if you apply a local threshold in a particular area of
one image, this threshold doesnt apply to other images in the
project. Remark that the threshold weve set in the beginning of this
case was global and it applied to every image in the dataset.
When you activate this mode, a box with the two default threshold values is
displayed on your screen. To set a local threshold, press one of the two
arrow buttons and double click on a threshold value. After you have
changed the value, press Enter. When moving the square over the image
while pressing the left mouse button, every pixel that comes to lie within the
square and has a threshold within the threshold range you set, will be
added to the active mask. On the other hand, all the pixels that were
already part of the active mask and that dont have a grey value within the
range will be removed from that mask.

For the current case we are only going to use the draw and the erase
mode. In the Simon case we already illustrated the threshold mode.
Working on the axial image in position 387 activate the Erase mode (Ctrl +
E) and set a very large square (for example, 200 by 200). Press your left
mouse button and wipe off all the color in the image. Be sure not to forget
any pixels! Close the Edit toolbar.

Notice in the sagittal image that one layer is shown in grey values. In the
figure below, the sagittal image is displayed and the arrow points to the
layer that has been removed from the active mask (the slice indicator is
moved down to see this).

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To see the result of erasing the mask in one layer, we will now perform a
region growing . Select the axial image at a position lower than 387,00,
(= the position of the image we removed from the active mask). Press the
Region Growing button, a window will be displayed on the screen.

Check both the Multiple Layer and Leave Original Mask checkboxes and
click on an arbitrary position in the active mask. You see that all the images
at a position lower than 387,00 are put into a new mask (yellow mask in
figure below). Close the region growing toolbar.

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Why are the images above this position not included into the new mask? As
you already know, a region growing looks for pixels that are connected to
each other and puts them into a new mask. But, because we have
disconnected the lower images from the higher ones, we have limited the
area of the region growing. This will be the trick we will use to get our region
of interest into a separate mask.
How will we proceed? In the same way as above, we are going to erase a
complete layer from the active mask on every side so that our region of
interest is completely surrounded by these removed slices. After we
perform a region growing within that region, we should have the oral cavity
and the surrounding tissue in one mask, like we wanted.

Activate the axial image. Go to position 362,00 and press Ctrl +E (or press
the Edit masks button and select the erase mode). Make a big square and
erase all the pixels from the active mask. Take a look at the sagittal image.
Two horizontal lines are shown in grey values. The top and the bottom of
our box are now defined.

To set the left and right boundaries of the box, you have to remove two
layers from the mask in the sagittal image. Try to visualize the situation and
make sure you understand why we will now operate in the sagittal image.
Erase all pixels from the active mask at position 126,49 (left boundary) and
42,05 (right boundary) in the sagittal image. In the axial image two vertical
lines in grey values are visible.
To close our box, a separation still has to be made on the posterior side.
Activate the coronal image and remove all pixels from the active mask at
position 76,61. In the axial image the removed layer is visible. Setting a
boundary on the anterior side is not necessary. In figure 5-10 you can see
the boundaries of the obturator on the yellow mask.

4. Region growing
Now that the box is delimited by the layers removed from the active mask, a
region growing can be performed to get the obturator into a new mask. Go
to an axial image that has a position between 362,00 and 387,00. This is to
make sure that the starting pixel for the region growing lies within the region
of interest. Press the Region growing button and click in the axial image
within the box.

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Boundaries of the obturator in the axial image.

The obturator is now within a new mask. In the figure below you clearly see
the obturator within the active (blue) mask from the axial and the sagittal
viewpoint.

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Axial and sagittal view of the obturator

Because we disconnected the pixels of the obturator from the other pixels in
the original mask, the region growing was confined to the region of interest.

Press the Calculate 3D button and select the mask of the obturator.
Choose custom quality and press the Calculate button. The processing of
the 3D model is started.
To visualize the 3D image, make the axial image active and press the 3D

View button .
Note that the model will always be visualized in the sagittal view, unless you
select to view it in a fourth pane in Options > Preferences > Visualization
> View. On the right of the 3D object you see a toolbar and a button where

you can select some predefined viewpoints for your 3D model . If you
press the bottom view you should obtain a model as shown in figure 5-12.

You can also enable transparency using the button.

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5. View of end result

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Chapter 6: Manual Import
In this case we will show you how you can use the manual import function
to import any image data you want. The topics that will be discussed in this
tutorial are:
Importing images
Manual Import
o Parameters
o Preview the images
o Choosing the right parameters
Convert the images

1. Importing images
The goal of this chapter is to teach you how to import images with the
Manual Import option and convert them to a Mimics project. Select Import
Images from the File menu. An Import Project Wizard will be displayed
where you need to point to the "MedData\Import3" directory (STEP 1)

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There are 3 ways to import images, depending on their file format:

automatic, semi-automatic and manual import. Only the manual import will
be explained in detail, because the other ways are more straightforward to
use and are mentioned already in the tutorial Case 2.
Note: When you press the Next button, all the project files listed will be
converted. Select only the files you want to convert and leave the others
unselected.

2. Manual import
2.1 Manual import
In the first step of the wizard, browse to the following path:
\MedData\convert\. The images will be selected automatically. Select the
Manual Import button and press Next. A new window is displayed on your
screen. The most important parameters are explained in the next
paragraph.

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2.2 Parameters
2.2.1 File header size
The file header size is calculated automatically, based on the file size, the
resolution of the images and the pixel type.
Typically a file contains both a file header and the image itself (in some rare
cases also a footer is present). The file header can contain information
about pixel size, patient data, The image is a matrix of pixels. The
horizontal (or vertical) image size is equal to the number of pixels in that
direction.

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2.2.2 Structure of a file

Common sizes of images are: 256 * 256
512 * 512
1024 * 1024
The number of bytes per pixel depends on the type of the pixel. Some
examples of pixel types and their respective sizes (note that these types
can be either signed or unsigned, however, this does not affect their size):
Byte: 1 byte
Short: 2 bytes
Long: 4 bytes
Float: 4 bytes
Image size = horizontal image size * vertical image size * number of bytes
per pixel
In this example, the images have a resolution of 256*256. If you fill these
values in, you will see that Mimics will set the file header size to 8432 bytes.

2.2.3 Exam information

Fill in an appropriate name for the patient name. This will be the name that
is used for your project.

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2.2.4 Image information

In the Image Information frame you see that the value for the image size is
still 512*512. Correct the size to 256 * 256 pixels. The default values for the
other parameters are correct in this case.

2.2.5 Pixel properties

Select Signed Short for the parameter Type and Low Byte First for the
parameter Byte Swapping.

2.3 Preview the images

Press the Show Preview button and take a look at the images to check
whether the parameters we filled in were correct.
On the left side, the first of the 8 images is displayed. Scroll through the
images by moving the arrow on the right (or use your mouse wheel if you
have one). For each image a histogram is displayed that gives you
information about the range of grey values that are present in the image
and their respective quantity.
If you want to know the amount of all the different grey values in the entire
dataset (and not just in one image), you have to press the Sample button

on the right. Notice that the title of the middle frame has changed to
Sampled. What if you have a very large dataset? Dont worry, you can
restrict the amount of images that is used for this calculation. For example,
fill in the number 2 for the interval. Now only 4 images are taken into
account, namely the first, the third, the fifth and the seventh image.

Press the OK button to close this window.

2.4 Choosing the right parameters

Lets experiment a little bit with the different parameters. The examples will
help you fill in the right parameters when the image does not look like you
expected it to.

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File header size: Set the file header size back to zero. Select the
Show Preview button. Notice that all the pixels are shifted. Fill in
the correct value and click the Update button to adjust the preview.
Pixel Type: Select Unsigned Short for the pixel type and preview
the images. Remark the loss of information due to the restriction to
positive grey values. Select the correct type and click the Update
button to adjust the preview.
Byte Swapping: Choose High byte first for the byte swapping and
preview the images. You can see that there are local distortions all
over the image, because the data is read in the wrong order. Fill in
the correct value and click the Update button to adjust the preview.

Influence of the file header size

Influence of the pixel type (signed/unsigned)

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Influence of the byte swapping (high first/low first)

3. Convert the images

If the images look good in the preview, click the OK button in the Manual
Conversion Options window. In the wizard window you should see the
name of the patient and some other information about the data. Select the
project you want to convert and check the box. Press the Open button, the
project will be saved in the default folder (usually MedData). A Mimics
project is created from the data and it will be opened automatically showing
you the Change Orientation window.

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Chapter 7: Simulation
Tutorial
In the Simulation Tutorial we will explain some of the functions that are
available in the Simulation module. We will start with a dataset of a skull
with a hole in it and explain how to do the segmentation, how to calculate
the 3D, how to cut, split and reposition a custom implant. The Simulation
module has to be licensed to be able to conclude this tutorial.
The topics that will be discussed in this tutorial are:
Opening the Project
Windowing
Thresholding
Region Growing
Calculating a 3D
Cutting
Splitting
Mirroring
Repositioning

1. Opening the project

In the File menu, select Open (Ctrl+O). Browse to the directory where you
have installed the extra Tutorial Files and double click the
Skull_with_hole.mcs file.

2. Windowing
For correct windowing see the windowing procedures in "Mimi" (Case 2).

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3. Thresholding
Go to an axial image where the skull is visible (for example, at position
18.94). Press the Profile line button and draw a line over the bone. The
figure below shows a profile line and the corresponding profile dialog box.
Press Start thresholding and drag the threshold line to a value of about
1250 (Grayvalue scale). End the thresholding and save your settings. Close
the dialog box.

Profile line over the bone (upper image) and the corresponding profile
dialog box

4. Region Growing
Now we will use the region growing tool to separate the skull from the
artifacts and noise in the images:

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Click the Region Grow button or press Ctrl + R.

Set the Source to Green (if this is your base mask) and Target to
New Mask. Check the Multiple layer box.

Click the left mouse button on one point of the skull. The skull has
now been grown into a new mask.

5. Calculating a 3D
Go to the Project Management by clicking its icon and choose the
Masks tab.
You'll see all created masks listed with their respective threshold. Selecting
one mask will make it active and it will appear in the Active Mask field in the
visualization toolbar automatically. It is possible to hide/show a mask by
clicking on the glasses.

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Click on the Calculate 3D button.

The "Calculate 3D Models" Dialog box is displayed. Here you can mark
(with a green dot in the column called Selected) which masks you want to
visualize and calculate the 3D by clicking on the Calculate button.
Select the "Skull" mask if it is not already selected and click on the
Calculate button.

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6. Cutting
After the calculation of the 3D you will see a 3D representation of the Skull
mask. To be able to make a cut that fits well, make the skull transparent by

clicking on the button and choose to view the skull from the Right
view. Now you can pan and zoom so you can see the hole clearly.

If you then zoom and pan, you can clearly view the hole in the skull through
the intact side.

This way we can easily draw around this hole. To do this, select the Cut
with Polyplane tool from the Simulation menu (CMF/Simulation -> Cut ->
With Polyplane). You will see following dialog:

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Select the 3D from the skull in the Objects to Cut list. The New button is
already enabled so we can immediately start drawing a cutting path. Do this
by clicking several times with your left mouse button around the hole like
below. To end the drawing, double click with your left mouse button.

You can see that a cutting path has been added to the cutting path list. You

can now make the 3D opaque again by clicking on the button. You can
then rotate the 3D to determine if the cut went through the whole skull or
not:

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As you can see, it would be best if we adjust the depth of the cutting path.
You can do this by clicking on the Properties button while the cutting path
is selected. This will open the cutting path properties dialog:

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Adjust the Depth of the cutting path from 20.0mm to 30.0mm and enable
the Closed checkbox (this will close the cutting path). Click on Preview to
view the result. When you are happy with the result, close the Cutting Path
Properties by clicking on the OK button. Enable the Keep Originals
checkbox (since we want to keep the original 3D) and finish the cut by
clicking on the OK button of the Cut with Polyplane tool.
You can see in the 3D objects list that a new 3D object was added.

7. Splitting
The next step is to split the two cut parts of the newly generated 3D. To do
this, go to the CMF/Simulation Menu and choose Split.

Select the freeform object, choose to keep all parts and disable the Keep
Originals checkbox. You can then click on Preview to preview the split and
then on OK to apply the split.

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As you can see, two different objects were created and have been given a
different color.
You can make the largest part invisible since we will only need the small
part to fix the defect in the skull.

8. Mirroring
To mirror the part to the other side of the 3D, we will need a mirror plane.
The Mimics simulation module generates a default sagittal plane, but we
will have to adjust this plane a bit to make sure it's suitable for this dataset.
To do this, go to the Simulation Layout (by pressing F5 or by going to the
View menu, choose Layouts and then Simulation Layout). Then make the
original skull visible and go to the CMF/Simulation menu and choose
Measure and Analyse .

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You can see in the right dialog that you can change the Sagittal Plane. Click
on the Change button and adjust the Sagittal plane (by dragging the white
points with your left mouse button) in the axial images to make sure the
sagittal plane goes through the center of the nose.

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After this, close the Measure and Analyse tool by going to the Simulation
Menu and choosing Measure and Analyse again. Then mirror the part by
going to the Simulation Menu, from the advanced Tools select Mirror.
Select the correct part and mirror plane and disable the Keep Originals
checkbox and click on the OK button to apply the mirroring.

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As you can see, the part is mirrored, but not correctly positioned. We will
reposition this part in the next section of the help.

9. Repositioning
To reposition the part, got to the CMF/Simulation menu and choose
Reposition. This will open following dialog:

Select the Mirrored part and start the repositioning. The easiest way to do
this, is to first reposition the part with the mouse and then do some fine-
tuning with the parametrical translation and rotation tools.
So click on the Move with Mouse button and reposition the part. You can
translate the part by dragging the center point with your left mouse button
and rotate the part by dragging the corners of the selection box with your
left mouse button. Keep in mind that you can also reposition in the 2D views
so this makes it a lot easier to get a real nice fit. During repositioning it is
also possible to scroll through the axial images to make sure the fit is
optimal on all slices.

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When you are happy with the fit, you can click on the Analyze Motion
button to see the final translation and rotation of the part.

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To apply the reposition, click on the OK button. If you have a license for
STL+, you can then export the part and the skull to STL files and continue
working on the custom implant in your design software.

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Chapter 8: FEA Tutorial
In the FEA Tutorial we will explain the work-flow for making a FEA analysis
on a model of the Femur. We will start with a dataset of a Femur and
explain how to do the segmentation, how to calculate the 3D, how to
remesh the 3D and how to assign materials to the 3D. The FEA and STL+
module have to be licensed to be able to conclude this tutorial.
The topics that will be discussed in this tutorial are:
Opening the Project
Calculating a 3D
Remeshing the 3D
Creating the volume mesh based on the remeshed 3D
Material Assignment
Exporting the Volumetric Mesh

1. Opening the project

In the File menu, select Open (Ctrl+O). Browse to the directory where you
have installed the extra Tutorial Files and double click the Femur.mcs file.

2. Calculating a 3D
There is already a Yellow mask available in this dataset that will be used to
calculate a 3D object. In the Calculate 3D dialog select the High quality
setting and click on calculate.

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3. Remeshing the 3D
In the next step we will remesh the 3D to make it optimal for FEA purposes.
Start the remesher by going to the FEA menu and choose Remesh. You
will notice that there are two 3D models, select the yellow 3D model. The
FemurShaft model will be used in the non-manifold assembly tutorial.

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The remesher will open with the part already loaded in an inspection scene:

There are several Shape parameters available to measure the quality of the
triangles. For this example we will use the height/base parameter. This
parameter measures the ratio between the height and the base of a triangle
and normalizes the value. A perfect equilateral triangle has a quality of 1
and a very bad triangle has a quality of 0. In the quality parameters
section select Height/Base(N) from the Shape measure dropdown box.

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In the Histogram parameter section make sure the current measure is set
to Shape measure.

This quality histogram shows the amount of triangles that have a certain
quality.
Then drag the green slider to 0.30. This is the quality threshold we will use
for our project. Below the histogram you can see three values:
Value 1 is number of triangles that have a quality below the
minimum quality threshold. Since the minimum quality threshold is
0 in our project, there are 0 triangles with a lower quality
Value 2 is the number of triangles that have a quality between the
minimum and maximum threshold. In this case we have 15.124
triangles. We will try to increase the quality of all those triangles.
Value 3 is the number of triangles that have a higher quality as our
quality threshold. In this case 32.168.
For more information about the remesher in general and quality in specific,
please have a look in the help pages under the FEA module.

3.1 Remeshing Protocol

Below is a description of the remeshing protocol that you can use to remesh
the Femur. The values given are those used for the Femur example and will
have to be adapted if your part has a different scale (i.e. geometric error,
maximum triangle size).
The protocol can be divided in three big steps:
1. Reduce the amount of detail
2. Reduce the amount of triangles of your object
3. Improve the quality of the triangles of your object
4. Reduce the amount of triangles while preserving the quality
5. Remove extra shells

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In between these steps measures will be taken to make sure that the object
has no intersecting triangles and has no bad edges.
STEP A: Because the 3D object will be used for FEA only, you can reduce
the amount of detail by applying a smoothing to the 3D object. In the

remeshing tab select the smooth icon .

Left click on the 3D model and select the 3D model from the context menu:

st
Perform a Lapacian (1 order) and use the following parameters: Smooth
Factor 0.7, 3 iterations and check Use compensation.
Step B: The 3D object contains too much triangles for an FE Analysis. To
reduce the amount of triangles, go to Fixing -> Reduce (or use the

reduction icon in the remeshing toolbar ). Left click on the 3D model to

select it and use following parameters Method: normal, Flip threshold angle:
15, Geometrical error: 0.2, iterations 5.

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STEP C: In this step we will improve the quality of the mesh. As already
explained we will use the Height/Base (N) Shape measure. Make sure the
Shape measure is put on Height/Base(N) and check if Current measure
is set on Shape measure.

To improve the quality, go to Remeshing -> Auto Remesh (or use the Auto

remesh icon in the remeshing toolbar ) and use the following

parameters: quality threshold: 0.4, geometric error: 0.2, control triangle
edge length OFF, Number of iteration: 4.
Most triangles now reach the desired quality but the edge lengths are still
diverse. In order to get a more uniform mesh we can limit the Maximum
edge length. To get an idea of the edge lengths present in the mesh select
the inspection parameter Smallest edge length or Largest edge length.

In the Histogram parameters section put the Current measure to

Inspection measure. The histogram will now show the selected inspection
measure. In the example below you see the Largest edge length
distribution.

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You will notice that most of the triangles have a larger edge length smaller
than 5mm. To remove the outliners we will perform the Auto Remesh
algorithm again limiting the maximum edge length to 5mm.
Go to Remeshing -> Auto Remesh and use the following parameters:
quality threshold: 0.4, geometric error: 0.3, 4 iterations, control triangle edge
length ON, Maximum edge length: 5.

STEP E : The mesh still contains groups of small triangles. These can be
removed using the quality preserving reduce triangles. Go to Remeshing
-> Quality preserve reduce triangles (or use the Quality preserving triangle

reduction icon in the Remeshing toolbar ) and use the following

parameters: Quality threshold 0.4, number of iterations 3, Max Geometry
error 0.3 mm, Max edge length 5 mm.

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STEP F: Call the self-intersection test. Go to Fixing -> Mark self-

intersecting triangles. No intersections should be found.
STEP G: Once you have an adequate surface mesh, you can create your
volume mesh. Go to Remeshing -> Create Volume Mesh (or use the icon in

the Remeshing toolbar ). Fill in the dialog with the following parameters:
Method: Init and Refine, control edge length ON, Maximum edge length: 5,
Shape measure: Height/Base (N) and Shape quality threshold: 0.3.

To visualize your volume elements, go to the 3D View Window and in the

Active Scene Tab, right-click on Standard Section Y and select Show.

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Check Clip ON and adjust the position of your section .

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STEP H: You can convert your Tet-4 elements to Tet-10 volume elements.
In order to do so, go to Remeshing -> Convert Volume Mesh or select the

icon in the Remeshing tab . Select you entity by clicking on your part
and select the conversion type Tet4 to Tet10.

STEP I: Check the quality of your mesh by going to Remeshing -> Analyze

Mesh Quality or by clicking on the icon in the Remeshing tab . Select

your volume mesh and check Analyze volume mesh ON. Select the shape
measure Height/Base (N) and fill in the quality threshold you want to
achieve, in this case 0.3. Select Mark bad triangles, in case you want to
visualize the surface triangles in the region of the volume elements with a
quality inferior than the value specified in Shape quality threshold and set
the element growth to 2. Define a histogram interval of 0.1.

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After clicking on Apply, you can find the results of the quality analysis in the
log window.
When you are satisfied with the quality of the mesh, close the Mimics
remesher. You will then return to Mimics and the volume meshes will be
automatically loaded in the 3D Objects and FEA mesh tabs in the Project
Management. These meshes can then be exported to your FEA software.

4. Material Assignment
When you have created a volumetric mesh from your remeshed object, you
can perform the material assignment in Mimics. You can see the mesh
listed in the FEA mesh tab.

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Note: We will use grayvalues for this tutorial, so if you are working in
Hounsfield units, please change this by going to the Options menu, choose
Preferences and change the Pixel Unit in the General tab.
With the FEA mesh of the Femur selected, click on the Materials button.
Mimics will display a message that the grayvalues for this mesh have to be
calculated before you can do a material assignment. Choose Yes to
continue. After the calculation you will see following dialog box:

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Mimics shows for each grayvalue the amount of elements that were
assigned that particular value. We will then convert this grayvalue to
material properties. In this tutorial we will use the uniform method.
STEP A: If the uniform method is not selected, click on the radio button
next to Uniform.
STEP B: Enter the number of materials in the edit box. We will use 10
materials for this tutorial. The FEA module will now divide the range of
grayvalues that occur in the volume mesh into 10 equally sized intervals
that each represents a material. You can see this discretization by choosing
the Materials histogram. Select Limit to Mask: Green 2. The limit
assignment to mask intercepts the deviation in the boundary elements due
to the partial volume effect. As boundary voxels typically represent multiple
tissues by excluding these voxels, the material assignment will become
more accurate.

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STEP C: Enter a density expression to convert the grayvalue of each

material to a density. For this tutorial we will use following expression:
Density = -13.4 + 1017 * Grayvalue.
STEP D: Choose to write out only the E-Modulus material properties in the
exported file by deselecting the selection boxes before Density and Poisson
Coefficient. We will use following expression for the E-Modulus: E-Modulus
= -388.8 + 5925 * Density.
STEP E: Check the values for the materials that will be assigned in the
material editor:

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STEP E: Press the OK button to assign the materials to the FEA mesh. The
elements of the FEA mesh will be colored according to their materials:

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This volumetric mesh can then be exported together with the material
assignment (in this case only the E-Modulus).

5. Exporting the Volumetric Mesh

The volumetric mesh, together with the material assignment can be
exported to Ansys, Patran Neutral and Abaqus files and can then be used
to do FEA analysis on the mesh. To export the mesh go to the FEA menu
and choose Export. Then go to the FEA tab, add the correct mesh to the
export list, choose the required format and export directory and click on the
OK button.

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Chapter 9: CFD Tutorial
In the CFD Tutorial we will explain the workflow for creating a 3D model of
the throat that is suitable to do a CFD analysis on. This tutorial will explain
how to link between Mimics and Fluent. We will start with a dataset of a
head and explain how to do the segmentation of the airway, how to
calculate the 3D model and how to remesh the 3D model. The FEA module
has to be licensed to be able to follow this tutorial.
The topics that will be discussed in this tutorial are:
Importing the images
Doing a segmentation
Calculating a 3D Object
Remeshing the 3D Object
Exporting to a Fluent mesh
Importing the mesh in Fluent

1. Importing the images

In the File menu, select Import Images. Browse to the directory where you
have installed the extra Tutorial Files and go to the Airway directory.

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The images in the Airway directory will be selected automatically, so click

on the Next button to accept this selection.
In the next step you will see the properties of the project. Make sure that the
skip images setting is 0 and that you use CT as compression method. By
clicking on the Convert button, the images will be imported and a Mimics
project will be created in your default working folder.

2. Doing a segmentation
After the import of the images, we can start doing a segmentation of the air
in the throat. Create a new mask with a lower threshold value of 1024HU
and an upper threshold value of 500HU.

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As you can see, this will create a mask that contains all the air in the
project. We will now cut of a part of this segmentation to make sure we only
have a small part of the throat. To do this, go to the segmentation menu,
choose Edit Mask and choose the erase function. Make sure that your
cursor is big enough by pressing the CTRL key and drag the left mouse
button. Then go to axial slice 48.30/10.80 and remove the green mask from
that slice with the manual editing tools. Then do the same for the axial slice
92.70/55.20.

Before manual editing After manual editing

Before manual editing After manual editing

Next we will isolate the throat from the other parts in the dataset. To do this,
go to axial slice 63.30/25.80, then go to the segmentation menu and choose
the Region Growing tool. Select the Green mask as the source mask and a
new mask as the target mask. Then click with the left mouse button on the
throat as indicated on the screenshot below.

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3. Calculating a 3D Object
This will result in a second mask that only contains the throat. You can now
calculate a 3D Object. To do this, go to the segmentation menu and select
the Calculate 3D Object item.
Select the Yellow mask from the list, choose Custom Quality and then click
on the Options button. This will open the Calculate 3D Parameters dialog
where you should use the same settings as below:

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This will result in following 3D:

This 3D Object is quite coarse because we are not using any smoothing.
We will do this smoothing in the Remesher to make sure that we can
contain the sharp edges at the top and bottom of the throat.

4. Remeshing the 3D Object

This 3D Object now has to be remeshed in the Mimics Remesher. To do
this, go to the FEA menu and choose Remesh. This will show following
dialog:

Make sure your interface is looking like the screenshot below:

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4.1 Mark inlet and outlet

Go to the Mark toolbar and select the mark smooth region . Left
click on the inlet to mark the area. Then Right click on the marked area and
select separate -> Move to new surface.

Perform the same procedure on the outlet. Press the Esc key to unselect
the mark tool.

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To rename the surfaces go to the database tab. Browse to the Surface list
of the Yellow 3D. You can rename the surfaces by double clicking on the
name.

4.2 Smoothing
We will first do a smoothing operation. Since we dont want to lose the
sharp edges at the in and out surface, we will only select the wall surface.

In the remeshing toolbar select the smoothing tool. To select the wall
surface, press left-click on the mantle and select wall from the list.

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Make sure the Wall is listed as Entity. Click on apply to Smooth the surface.

4.3 Improve quality

Next we will improve the quality of the triangles. Make sure that Skewness
(N) is selected as Shape measure in the Quality parameter section. In the
Histogram section the Current measure should be set to Shape measure:

Set a value of 0.4 as the maximum quality measure. As you can see we
have 186 triangles with a quality that is below 0.4.
Hint: The skewness parameter in the Mimics remesher and the Fluent
softwares are inverses. So a quality of 0.4 in the Mimics Remesher is
actually a quality of 1-0.4=0.6 in Fluent.
We will try to remove these with the Auto Remesh operation. Use following
settings and click on OK:

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Then apply the Auto-Remesh operation again with following settings:

This will result in following 3D Object and quality histogram:

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As you can see, there are no more triangles with a quality below 0.4.

4.4 Sharp Geometry

Next we will check for sharp geometries in the part. To do this, select from
Inspection measure list the sharp geometry measure. Make sure to put
the Current measure to Inspection measure and drag the green slider to
0.8:

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Now click on the Mark bad button to select the sharp geometry and click on

the Expand Marked Area button .

We will refine the mesh where sharp geometry is occurring. You can do this
by calling the auto Remeshing algorithm again and by setting a maximum
edge length of 0.5mm. Make sure to select marked only.

Now, we want to smooth the parts where sharp geometry is occurring, but
we dont want to change the sharp edges of the in and outlet surfaces. In
the groups section enable the Groups and the Show All checkmarks and

set the Boundary level to 1. Select the Shell button on the mark
toolbar, hold the Ctrl key and left click on the in and outlet surfaces.

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Select again the Smoothing function , make sure the Marked triangles
are selected and click on apply.

Click on the Unmark button in the mark toolbar again to unmark all
triangles.
Go again to the Quality parameter in the quality histogram and you will see
that a couple of bad triangles were created during the previous operations.
Remove them by using the Split Based Remeshing algorithm again with
following settings:

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When you are satisfied with the quality of the mesh, close the Mimics
remesher. You will then return to Mimics and the remeshed surface mesh
can then be exported.

5. Export the mesh to Fluent

Now you can export the remeshed 3D object in Mimics to a Fluent mesh.
To do this, go to the Export menu and choose Fluent. Select the remeshed
3D and click on add:

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Click on OK to export the mesh. In the surface split dialog select Use
current surface split, this option will preserve the naming of surface split
you did in the Mimics remesher.

Click on OK to finish the export.

6. Import the mesh in Fluent

You can then import this fluent file in fluent by using following parameters:

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Chapter 10: Non-manifold

Assembly Tutorial
The non-manifold assembly Tutorial explains step by step how to obtain
matching surfaces between the bone and an implant. First we will register
the femoral head prosthesis on the Femur. Secondly we will use the cutting
tools of the simulation module to perform an ostectomy of the femoral head.
In the Mimics re-mesher we will combine both the femur shaft and the
implant to ensure perfectly coinciding nodes between them. The Simulation,
FEA and STL+ module have to be licensed to be able to conclude this
tutorial. In case you do not have the simulation module you can skip the
Ostectomy of the femoral neck and still perform the remeshing part of the
tutorial.
The topics that will be discussed in this tutorial are:
Opening the Project
Calculating a 3D
Registration of the implant
Ostectomy of the femoral neck
Remeshing the femur and implant
Creating a volume mesh
Exporting the remeshed 3D models

1. Opening the project

In the File menu, select Open (Ctrl+O). Browse to the directory where you
have installed the extra Tutorial Files and double click the Femur.mcs file.

2. Calculating a 3D
There is already a yellow mask available in this dataset that will be used to
calculate a 3D object. Select the yellow mask and click on the Calculate 3D
icon in the Masks toolbar. In the Calculate 3D dialog select the High quality
setting and click on calculate.

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3. Registration of the implant

3.1 Import the STL
In the file menu select import STL (or go to the STL tab in the Project
Management and click on Load STL from the tabs toolbar. in the
toolbar of the STL tab). From the TutorialData folder load the Implant.stl.

3.2 Point registration

The Point registration will be used to bring the implant nearer to the Femur.
Indicate a start points on the STL and their corresponding end point on a
3D model or in the 2D views. Mimics will then calculate the transformation
matrix that should be applied to have the best fit between the start and end
points and applies the transformation matrix on the selected STLs.
In the registration menu select the Point Registration. Click on Add point,
add a start point on the top of the implant head and put the corresponding
end point on the femur head. Place a second set of points on the end of the
implant neck and in the middle of the Greater Trochanter top. Position the
last set of points on the end of the prosthesis and place the corresponding
end point in the middle of the femur shaft in the sagittal view.

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3.3 Reposition the implant

The position of the implant can be fine tuned using the reposition tools. In
the STL tab select the implant and click on the move tool . In the move
dialog select Move along inertia axis from the dropdown box.
By grabbing one of the arrows you can move the implant in the direction of
the selected arrow.

The position of the implant can be verified in both, 2D and 3D views. To

visualize the implant in 2D enable the contours by selecting the sunglasses
in the contour column of the STL tab.

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To make the implant visible in the 3D view enable the transparency from
the 3D toolbar . The transparency setting of each individual 3D object
can be changed by toggling the transparency mode in the 3D and STL tab.
Left click on the transparency setting to change to another level of
transparency

4. Ostectomy of the femoral head

To remove the femoral head we will use the polyplane cut from the
Simulation module. From the CMF/simulation menu select cut, polyplane
cut . In the simulation dialog select the 3D model of the bone, yellow.
To perform the cut click once on the top of the femoral neck, turn the 3D
and double click on the bottom. This will create a cutting plane as shown in
the images below:

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The orientation of the cut can still be modified. Hover over the center of the

red arrow, when the cursor changes into the reposition icon , hold the
left mouse button. By moving the mouse you can change the orientation of
the cutting plane.

Hold the left mouse button to change the orientation of the cutting plane
To finalize the cut the cutting plane should go completely through the bone.
Therefore the depth needs to be increased. In the cut with PolyPlane dialog
click on properties. In the properties dialog change the depth to 50 mm.

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Click on Ok, to finish the cut.

The cut will create a new 3D model, PolyplanCut-Yellow. To split this
model, go the CMF/simulation menu and select split. In the Split dialog
select the PolyplaneCut-yellow 3D model and select largest part. In this
way you will only preserve the shaft of the femur.

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5. Remesh of the femur and

implant
The femur and the implant now have to be remeshed in the Mimics
Remesher. To do this, go to the FEA menu and choose Remesh. This will
show the following dialog:

Select both the implant and the shaft of the femur and click on Ok. The
Mimics remesh will open showing three tabs, 3D view, inspection scene of
the implant, inspection scene of the femur.
We will first combine the femur shaft and the implant. The combined mesh
will then be remeshed and split afterwards.

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5.1 Create non-manifold assembly

To make sure that the common surface between the implant and the bone
are identical we will combine both meshes into one mesh.
Go to the 3D view and select from the Remeshing menu -> Create non-
manifold assembly (or use the Create non-manifold assembly icon in the

remeshing toolbar ).

As Main entity select the femur shaft by left clicking on the femur. Now click
on Intersecting entity and select the implant. Click on Apply to combine
both meshes

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5.2 Create Inspection scene

To be able to optimize the combined mesh we will need to create an
inspection scene. From the remesh toolbar select the create inspection

scene tool . Select the non_manifold_assembly and click on apply.

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5.3 Sharp triangle filter

First we will remove the sharp triangles using the sharp triangle filter. To
reduce the amount of triangles, go to Fixing -> Reduction (or use the

reduction icon in the fixing toolbar ). Left click on the 3D model to

select it and use following parameters Filter distance: 0.2, Threshold angle
15, Filter mode: Collapse.

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5.4 Smooth Femur Shaft

Because the 3D model of the femur will be used for FEA only, you can
reduce the amount of detail of its outer surface by smoothing it. In the

remeshing tab select the smooth icon . Left click on the shaft to select
the surface and use following parameters Smooth factor: 0.7, Number of
iterations: 6.
Then click Apply.

5.5 Reduce
The 3D model contains too many triangles for an FE Analysis. To reduce
the amount of triangles, go to Remeshing -> Reduction (or use the

reduction icon in the remeshing toolbar ). Left click on the 3D model to

select it and use following parameters Method: normal, Flip threshold angle:
15, Geometrical error: 0.1, iterations 5, enable preserve surface contours.

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5.6 Auto remesh

In the next step we will optimize the triangle shape. In this tutorial we will
use the Height/Base shape measurement. Select the Height/Base (N)
measure from the shape measurement dropdown box.
In the histogram drag the upper slider to 0.3, this is the quality needed in
order to generate a volume mesh.

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To Auto Remesh the 3D object, make sure that the shape parameter is
selected as current measure. Go to Remeshing -> Auto Remesh (or use

the Auto remesh icon in the remeshing toolbar ) and use the following
parameters: quality threshold: 0.3, geometric error: 0.1, 3 iterations, control
triangle edge length OFF.

After this operation the mesh will still contain triangles with divergent
triangle sizes. To create a uniform mesh you can limit the maximum edge
length.

Call again the Auto remesh function and apply it with following
parameters: quality threshold: 0.3, geometric error: 0.1, 3 iterations, control
triangle edge length ON, Maximum edge length 5 mm.

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5.7 Quality preserving triangle reduction

The mesh still contains groups of small triangles. These can be removed
using the quality preserving reduce triangles. Go to Remeshing ->
Quality preserve reduce triangles (or use the Quality preserving triangle

reduction icon in the Remeshing toolbar ) and use the following

parameters: Quality threshold 0.3, number of iterations 3, Max Geometry
error 0.3 mm, Max edge length 5 mm.

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You now obtained a uniform mesh with the desired quality.

5.8 Creating a volume mesh

Now that your surface mesh has an adequate quality, you can create your

volumetric mesh. Click on the Create Volume Mesh icon in the

Remeshing tab. Select your entity by clicking on your non-manifold
assembly. Select Init and Refine as method and check Control edge length
ON, specifying a value for Maximum edge length of 5. In Shape measure
select Height/Base (N), define a Shape quality threshold of 0.3 and click on
Apply.

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To visualize your volume elements, go to the 3D View window and in the

Active Scene Tab, right-click on Standard Section Y and select Show.

Check Clip ON and adjust the position of your section.

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Close 3-matic to revert to Mimics.

6. Exporting the remeshed 3D

models
Now you can export the remeshed 3D objects in Mimics to a Patran neutral,
Abaqus or Ansys file. To do this go to the Export menu and choose the
correct format to export the mesh. Select the FEA meshes and click Add.
To export, click OK:

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