Materilise Mimics 10.1_handbook

7/22/2019 Materilise Mimics 10.1_handbook

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Introduction

Mimics interfaces between scanner data (CT, MRI, Technical scanner, ...) and Rapid Prototyping, STL file format,CAD and Finite Element analysis. The Mimics software is an image-processing package with 3D visualizationfunctions that interfaces with all common scanner formats.

Additional modules provide the interface towards Rapid Prototyping using STL or direct layer formats withsupport. Alternatively, an interface to CAD (design of custom made prosthesis and new product l ines based onimage data) or to Finite Element meshes is available.

Materialise's Interactive Medical Image Control System (MIMICS) is an interactive tool for the visualizationand segmentation of CT images as well as MRI images and 3D rendering of objects. Therefore, in the medicalfield Mimics can be used for diagnostic, operation planning or rehearsal purposes. A very flexible interface torapid prototyping systems is included for building distinctive segmentation objects.

The software enables the user to control and correct the segmentation of CT-scans and MRI-scans. For instance,image artifacts coming from metal implants can easily be removed. The object(s) to be visualized and/or producedcan be defined exactly by medical staff. No technical knowledge is needed for creating on screen 3Dvisualizations of medical objects (a cranium, pelvis, etc.)

Separate software is available to define and calculate the necessary data to build the medical object(s) createdwithin Mimics on all rapid prototyping systems.

Mimics is a general-purpose segmentation program for gray value images. It can process any number of 2Dimage slices (rectangular images are allowed). The only restriction is the physical memory of your computer.

The interface created to process the images provides several segmentation and visualization tools.

Overview Mimics modules

Mimics consists of five modules. The image below shows the links between the main program and its modules.

Page 1 of 21Introduction

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Mimics

Mimics interactively read CT/MRI data in the DICOM format. Segmentation and editing tools enable the user tomanipulate the data to select bone, soft tissue, skin, etc. Once an area of interest is separated, it can bevisualized in 3D. After this visualization, a file can be made to interface with STL+ or MedCAD. CAD data,imported as STL files, can be visualized in 2D and 3D for design validation based on the anatomical geometry.

Import Module

Import module imports CT and MRI data from a wide variety of scanner formats. The data can be accessed fromCD, optical disk, DAT tapes, 4 mm tapes, etc.

RP Slice Module

RP Slice module provides an interface to Rapid Prototyping systems via sliced files with patented supportstructure generation. The perforated support structures are generated in no time and use less material.

Supported formats:




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Common Layer Interface Files (*.cli)

3D Systems Layer Interface Files (*.sli)

3D Systems Contour Files (*.slc)

STL+ Module

STL+ module provides interface options via triangulated formats.

Supported formats:

STL (ASCII and Binary)

DXF

VRML

PLY

MedCAD ModuleMedCAD module provides a direct interface to CAD systems via surfaces, curves, and objects exported as IGESfiles.

Supported files:

B-Spline (NURB) curves and surfaces exported as IGES

Point Cloud

Simulation Module

The Simulation module is an open platform for surgical simulations. You can perform a detailed analysis of yourdata using the anthropometric analysis, plan osteotomies and distraction surgeries or simulate and explain asurgical procedure for your implant design.

FEA Module

The FEA module provides an interfacing to FEA (Finite Element Analysis) and CFD (Computational FluidDynamics).

Supported formats:

Patran Neutral

Abaqus

Ansys

Fluent

Nastran




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What's new

Basic Mimics module

Upgraded User InterfaceWith the well-organized, intuitive user interface, you can quickly access all relevant tools and functions. Changesto the user interface include a redesign of the graphical elements to conform to Windows XP style, as well as aclearer organization of related functions and options.

Adjust Grayscale

The Adjust Gray Scale toolbar is replaced with a Contrast Histogram. This histogram allows you to do windowinglike before by dragging the two points on the graph horizontally and vertically with the left mouse button.Windowing with the right mouse button is still possible.

Volume Rendering

You can visualize a dataset in 3D without segmentation efforts. This powerful visualization tool instantly gives youa 3D view of your datasets content.

Enhanced Rotation and Translation tools

New tools for Rotating and Translating STLs and 3D objects enable straightforward positioning of the objects inyour project. All you have to do is grab the rotation or translation tool.

New Shortcuts

New shortcuts were added to the software

Extended Clipping

The extended clipping functionalityenables you to manipulate several clipping planes at the same time. It alsogives you greater input on the actual clipping action. These new visualization options expand the possibilities for

General ShortcutsSPACE If you hover with the mouse over a view and

press the spacebar, that view is put to fullscreen. To unzoom to full screen, press thespacebar again.

CTRL +I If you want to make all masks invisible, pressCTRL+I. To make all previous visible masksvisible again, press CTRL+I again.

Scroll wheel With the scroll wheel you can zoom in on theactive view.

Navigation shortcuts for the 3D viewArrows keys Rotate the 3D view left/right and up/downPageUp Rotate the 3D view 30 degrees up

PageDown Rotate the 3D view 30 degrees down

Home Rotate the 3D view with 30 degrees leftEnd Rotate the 3D view with 30 degrees right

SHIFT + keys above Pan the 3D viewALT + left/right Do washing machine rotation




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displaying your 3D images

Convert MedCAD object to mask

MedCad Object like spheres, cylinders and nerves can be converted to a mask.

Add Annotations

With Mimics 10 you can make annotations directly on any object and save this additional information in thedataset. This new functionality ensures efficient communication among all parties involved in the project.

3D Mask Editing

The new 3D mask editing too l allows users to display the 2D mask information in the 3D view and edit that maskin 3D. This tool is very helpful when removing scatter and for easily separating complex structures like vessels.

Delete unselected images from project

After youve imported the images, you can still choose to delete unselected images in the organize image dialog.

MedCAD Module

Fit Centerlines

Using Mimics 10 you can calculate and measure the centreline of 3D object, for example of a vessels. Thisinformation can then be used for clinical trials, diagnostic purposes or for the design of new or custom devices.

FEA Module

New Ansys Format

You can now export you optimized surface mesh as an Element Based Ansys mesh. Starting from this meshformat you can immediately generate your volume mesh in Ansys.

Simulation Module

New Cutting Tool

A new cutting tool was added to the simulation module. By drawing a curve on a 3D object, you can separate theenclosed object from the original 3D object.

Soft-Tissue Module

The Soft-Tissue tool predicts the behavior of the facial tissue with regard to the surgical bone repositioning. TheSoft-Tissue module is based on a biomechanical model of the soft-tissue and it runs on top of the simulationmodule.

Installing Mimics




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We recommend that you close all other applications before installing Mimics. You must have administrativeprivileges to install the software. Place the Mimics CD into your CD-ROM drive. Make sure the artwork faces up.The autorun starts automatically. If the autorun does not start automatically, browse to your CD-drive and chooseautoplay or double-click on MimicsSetup.exe in the Mimics folder.

During the installation the following dialogs will be shown:

STEP 1:

Wait until the progress bar is finished. You will automatically go to step 2.

STEP 2:

Click Nextto proceed.




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STEP 3:

After reading the license agreement, select the I accept the terms of the license agreement bullet and click onthe Nextbutton.

STEP 4:

Select your region and click Next.

STEP 5:




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Choose for the Complete or Custom setup type and select where Mimics will be installed. Mimics will be installedin C:\Program Files\Materialise\Mimics 10.0\ by default. If you prefer another directory, click on the Browse buttonand select an existing directory out of the list. Click Nextto proceed.

If you have chosen the Complete setup, you will immediately go to Step 7. If you have chosen the Custom option,you will go to Step 6.

STEP 6:

Select if you want to install the Demo Files or not and click on Next.

STEP 7:




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If you have chosen to install the Demo Files, you can choose where these demo files should be installed. Mimicswill store the studies in a folder C:\MedData by default. If you want to change this directory, select Browse and goto the folder where you want to store your data.

STEP 8:

Program icons will be added to the Programs Folder > Materialise Software. If you want another folder name, thentype a new name or select one from the existing folder list.

STEP 9:




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When everything is filled in like you want, click Nextto proceed. If you want to change or review something, clickBack.

STEP 10:

The Mimics software gets installed. This can take a few moments. This window will close automatically when theprogress bar is finished.

STEP 11:




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Mimics will then ask you if you want to see an overview of what the new features are in Mimics.

STEP 12:

The software is successfully installed. Click Finishto close the installation dialog. Its recommended to rebootyour computer to finalize the installation.

To uninstall Mimics, go to Start > Settings > Control panel > Add/Remove programs . Select Mimics 10.0 andclick the Removebutton. All Mimics folders and the desktop icon will be removed.

Note:The installation of the DICOM Input Application and of the Distractor and Anthropometric template librariesare separate processes. The libraries have to be installed separately in order for the Simulation module tofunction correctly.

Registration

To start Mimics, double click the Mimics icon on your desktop or go via the Start button to Programs,Materialise and choose to start Mimics.

Materialise Software is password protected. When you start Mimics for the first time or when your password hasexpired, a registration dialog will appear. Mimics can be registered with a local license or a floating license.

In the Registration dialog you can display your current license situation, display contact information, requestpasswords and register new modules. To display the Registration dialog, go to the Optionsmenu and choose




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Licenses.

There are two sections in this dialog: the Register new modulessection and the System Informationsection.

Register new modules

There are three different steps when registering new modules:

Step 1: Request passwordYou can request password via the Password request wizard. To start this wizard, click on the Request passwordbutton. When you click on the Contact informationbutton, you will see contact information so you can contactMaterialise if needed.




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Step 2: Enter password

When you have generated a password via the Password request wizard, you can enter this in the Password editbox. Passwords that have been copied to the clipboard can be pasted in the edit box by clicking on the Pastebutton.

Step 3: Register

When the password has been entered in the edit box, you can register the password by clicking on the Registerbutton. You will then see a message that gives you feedback about the registered passwords.

System Information

In the System Information section of the register dialog you can find your SystemID, your CCKey (if filled in) andyou can specify floating license servers.




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System ID

Your SystemID is a unique identifier for your pc. This id is dependant on your hardware and will be used togenerate a password.

CCKeyThe CCKey is a unique identifier for your software license. You can use this key for generating passwords withour on-line password generation system. The CCKey can be found on your Certificate of Authenticity that you willreceive when you buy the software (so evaluators don't have a CCKey). It is optional to fill in the CCKey, but weadvice you to do this because this will facilitate the password generation process.

Floating license server

Via the specify button you can enter floating license servers if needed. This function should only be used whenyou have floating passwords. You can add or change floating license servers by clicking on the Specifybutton in

the System information section.

This will open following dialog:




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In this dialog, all the floating license servers that are used by the software are listed. For each floating licenseserver the IP Address (or hostname), the port and a description are displayed.

To remove a floating license server from the list, select the server and click on the Deletebutton.

To change a floating license server, select the server in the list and click on the Changebutton. To add a newfloating license server, click on theAddbutton. These buttons will open following dialog:

In this dialog you can fill in the IP Address or hostname, IP Port and Description for the floating license server.You can also Browse for a server by clicking on the Browsebutton. With the browse function you can browseyour Network Places, select the appropriate floating license server and by clicking on the OKbutton, the name ofthis server will be filled in automatically.

Show Modules

When you click on the Show Modules button, you will see a list of all the modules that are available for yoursoftware. The name, version, type of license, days left and a comment is displayed for each module.

If you haven't got a password for a certain module, there will appear n/a as number of days left and "no licensefound for this module" will be displayed under the comments section.




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Password Request Wizard

When you start the password request wizard, you can choose how you want to request your passwords. You canchoose between Online password request, Request passwords via E-Mail and Request passwords via Fax.

If you have bought our software, if you have already received your Card of Authenticity and if you are connectedto the Internet, we advice you to use the Online password generation. This way you will receive your passwordsinstantly.




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Online Password Request

When you have chosen to generate passwords online, you will be asked to fill in your CCKey and E-Mail addressif this data hasn't been entered before. You can find your CCKey on your Certificate of Authenticity.

You will receive this Certificate of Authenticity when you buy the software. This card contains a unique CCKey

that identifies the license you have bought. This CCKey can be used to generate your own passwords via theonline password system.

If you have filled in the required information you can click on the Finish button and you will automatically bedirected to the correct webpage. First you will have to choose your language by clicking on one of the flags.




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You can find more information about web passwords by clicking on the How does it work? link.

When you have chosen your language you will go to the second screen where you have to fill in your CCKey. Ifyou have entered your CCKey in your software when asked, this key will already be filled in automatically.




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To continue click on the Loginlink. In the next screen you will have to fill in information about the software youare requesting passwords for. When this is done, you can request a regular password or an emergencypassword. This password will be sent to you by E-Mail.

If you request a regular password and you receive a message that some of the information was not correct andthat you will be contacted by Materialise, you can generate an emergency password if needed. This passwordcan be used for a week and should be requested when your password has expired and you really need tocontinue working with the software.

Request Passwords via E-MailWhen you choose to request a password via E-Mail, you will see a window where you have to fill in your contactdata. Fields with an exclamation mark behind them have to be filled in. When you have filled in the correctinformation and click on the Finishbutton, your E-Mail software will start and a new mail will be shown with all theinformation needed for us to generate a password.

Once you have filled in your contact data, this information will be saved. So next time you request a password,you won't have to fill in your contact data again.




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Request Password via Fax

When you choose to request a password via Fax, you will see a window where you have to fill in your contactdata. Fields with an exclamation mark behind them have to be filled in. When you have filled in the correctinformation and click on the Finishbutton, a document will be shown with all the information needed for us to

generate a password. This document can then be printed and faxed to us.Once you have filled in your contact data, this information will be saved. So next time you request a password,you won't have to fill in your contact data again.

Using help

Mimics provides Help so that you can get useful information while you are working. The help pages contain adescription of each command and dialog box, and explains procedures for most tasks. To get help, press F1 orselect Help | General Help from the menu bar. The Help window consists of a tabbed window showing a tree oftopics at the left side and a preview window at the right side. If the page is not displayed completely, maximize thehelp window or scroll with the scroll bars.




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You can search for the correct help page in 4 different ways:

Browse through the tree by clicking on the book icons and page icons.

Click on an underlined item in the preview page to jump to the help page about that item. The tree will beupdated accordingly.

Select the Index tab and type the first few letters of the topic you're looking for. The corresponding itemswill be highlighted in the list while typing. Click the Display button to view the item that is highlighted.

To search very quickly all pages about a specific topic, click on the Search tab and fill in the name of thetopic. Click the List topics button to show a list of all help pages about the topic. Click on an item in the listto view the page.

To hide the contents window. Once it's hidden you can show it again by clicking again on thisbutton.

To display the previous page.

To display the page that was shown before clicking the Back button.

To print the current page.




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The different views

In the default configuration the images appear in a four-dimensional engineering view. The images in the top rightview are called the axial images (XY-view or Top-view) and are surrounded by a red border. The upper left view(surrounded by an orange border) shows the coronal images that are the images resliced in the XZ-direction

(Front-view). The lower left view (surrounded by a green border) shows the sagittal images that are the imagesresliced in the YZ-direction (Side-view). The lower right view (surrounded by a light-green border) shows the 3Dview.

These windows can be resized by moving the edge between the images (Click and drag to move this edge).

The other images that can be shown are:

Alignment image (if available)

X-ray image

Title Bar

The title bar displays some information about the project:

The name of the project is displayed first (unless you have chosen to hide the patient name) and after the patientname, the compression of the project is displayed. There are several different types of compression possible:

Image ColorAxial RedSagittal GreenCoronal Orange3D view Light-greenParallel Yellow (these images are only visible after performing an online reslice)Cross-sectional Blue (these images are only visible after performing an online reslice)

Page 1 of 27The different views

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Menu Bar

Almost all functions can be accessed via the menus of the menu bar. Corresponding to some of these functions,you will find buttons on the toolbars.

3D Toolbar

The 3D toolbar is displayed at the right side of the 3D view.

Toggle transparency

You can show the 3D object opaque or transparent. Click on the button in the 3D toolbar to toggle betweenopaque and transparent view.

Displayed in title bar: Case:

Lossless Compression No compression was used while importing and JPEG compression was notused during saving

CT Compressed CT compression was used while importing and JPEG compression was notused during saving

MR Compressed MR compression was used while importing and JPEG compression was notused during saving

Lossy JPEG Compressed No compression was used while importing and project was saved withJPEG compression

Lossy JPEG & CTCompressed

CT compression was used while importing and project was saved withJPEG compression

Lossy JPEG & MRCompressed

MR compression was used while importing and project was saved withJPEG compression




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You can change the transparencyof the 3D objectand make objects transparent. Drag the Transparency slider atthe bottom of the 3D properties dialog. If the slider is all the way to the right, the 3D surface is opaque and nothingbelow the surface can be visualized. If the slider is all the way to the left, the 3D surface is completely transparent.

Clipping

Clipping allows you to visualize the section in which you are interested. It can be used, to evaluate the grayvalues on the section boundaries or to look inside the model to get a better comprehension of the geometry. Thesection can be made along the different planes, axial, coronal and sagittal. Several clipping planes can be

activated at the same enabling you to isolate the part of interest.

To enable clipping click on the Enable/Disable clippingbutton . The settings of the clipping can be changedin the clipping tab:

Active

By default one axial clipping plane is active. To make more planes active, make sure to check the active icon .

The position of the clipped plane in the 3D view corresponds with the position of the active axial, sagittal orcoronal image. Scrolling through the 2D images updates the clipped plane in 3D. Also navigation on the clipped3D is possible by clicking on visible parts on the 3D. When you rotate the 3D along the clipped plane, the visibility

Transparency off Transparency on

Clipping in the AxialPlane

Clipping in the SagittalPlane

Combined axial andsagittal clipping plane




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automatically reverses.

Type

As stated above you can select multiple clipping planes. For each view you can define two clipping planes. Foreach of the clipping planes, you can choose which objects need to be clipped. You can choose this by selecting

the clipping plane in the list and changing the selections in the dropdown menu . All objects areselected by default.

Clip

By default the direction of the clipping plane is defined by the viewing angle. The direction of the clipping plane

can be locked by selecting a clip direction. Click on the clip icon to lock to a clipping direction or to unlock.

Lock

The location of the clipping plane is locked to the slice position. To unlock the clipping plane from the slice

position, disable the lock icon . When the lock icon is disabled, you can determine the location of the clippingplane with the slider at the bottom of the clipping tab.

Texturing

You can also choose between three texturing methods:

When choosing No texturing, only the 3D Object is clipped and you can see inside the 3D Object. When choosingObject Texturing, a texture corresponding with the 2D slice is placed in the contours of the 3D Objects. Whenchoosing Full slice texturing, the 3D Object is not clipped, but the whole 2D slice is visible in the 3D window.

Note:This technique is only available in OpenGL and direct3D rendering (not in software). To check yourrenderingoption, go to Option | Preferences and select the OpenGL or Direct3D rendering option in the 3D

Clipping along two axial and a sagittalplane

Clipping along the axial and sagittalplane

No texturing Object texturing Full slice texturing




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settings. To accelerate the performance of clipping, activate the hardware acceleration in the same dialog.

Volume rendering

Volume rendering allows you to quickly visualise your 2D image data as a 3D object without any segmentation.The 3D object is build up out of the voxels representing the dataset. The transparency of the voxels is determinedbased on their grey value.Volume rendering is a pure visualisation tool and cannot be used for anything else (e.g.exporting).

You can find the interface for the volume rendering in the volume rendering project management tab:

Defining the opacity

This interface shows a histogram which represents the gray values or Hounsfield units of the dataset. Thetransparency of the gray values is set by the opacity lines on the histogram. The higher a line is positioned themore opaque the voxels within that range will be visualised.

In the first column the line representing the low Hounsfield values is positioned to the bottom. Subsequently thevoxels are represented transparent. In the second column the line is positioned higher which makes the voxels

opaque.




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Defining the color

The graph below the histogram defines the color of the rendered voxels. You can choose a color for each point inthe graph by right-clicking on the points and choosing Change Color. Mimics will then create an interpolatedshading between the different control points. The same system for adding, moving and deleting bullets is availableas for the opacity line.

Predefined settings

On the bottom of the volume rendering interface you find a dropdown list with predefined settings. The predefinedsettings are optimized for CT image and allow you to quickly select bone, soft-tissue or both

You can save your current setting as a predefined setting by clicking on the save button. To delete yourpredefined setting, select it from the dropdown box and click on the delete button.

Show reference planes

It is possible to show in the 3D view the reference planes of the current position by clicking on the Show

Reference Plane button . The reference planes take over the colors that belong to the different views:

The reference planes that have to be shown can be selected in the 3D tab of the Preference settings. Only thereference planes of the views that are displayed can be shown in the 3D view.

Move a point Position a point click left and drag the point to its new position

Add a point Click left on a line to add an extra point

Delete a point Right click on a point and select delete to delete a point

Axial RedCoronal OrangeSagittal GreenCross Sectional BlueParallel Yellow




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Select 3D view

When you click on Select 3D View button , a list with all possible default views is displayed. Selecting an itemfrom this list will position the 3D object according to the selected position.

Rotate view

The rotate function is only available on a 3D object. There are different ways to select the rotate function:

right-drag with your mouse button

use the arrows-keys for precise rotation

use Home / End to rotate 10 degrees Left / Right

use Page Up / Page Down to rotate 10 degrees Up / Down

right-click in the 3D view and select Rotate Viewfrom the context menu

click on the Rotate Viewbutton in the toolbar




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select View > Rotate Viewfrom the menu bar

Toggle visibility

By toggling the colored cubes in the 3D toolbar, you can make the 3D objects, with the corresponding color,visible or invisible. For every 3D object in the project there is a corresponding cube.

Indicators in the views

On the different views you can see intersection lines, tick marks, slice positions and orientation strings. To hidethe intersection lines, tick marks or slice positions, select its entry in View menu > Indicators. Select again itsentry to show it again. If you never want to see one or more indicators when loading a project, select Preferencesfrom the Options menuand go to the Visualization tab. In this dialog you can make your selection of theseindicators.

Tick MarksThe set of red tick marks to the left of the sagittal and coronal images reference the position of each axial image inthe study. The set of green tick marks below the axial images reference the position of each sagittal image in thestudy. The set of orange tick marks to the left of the axial images reference the position of each coronal image inthe study.




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In the View menu, the preference setting for tick marks can be temporarily overruled. If you prefer another settingpermanently, go to Options > Preferences > Visualization.

Intersection Lines

In the View menu, the preference setting for intersection lines can be temporarily overruled. If you prefer anothersetting permanently, go to Options > Preferences > Visualization . The relation between the different views isindicated by the colors of the intersection lines (dashed or full colored lines over the view). When you move to anew position, the intersection lines will be updated and show you your current position in the data set. They are in

the matching color of the corresponding view. Notice the red horizontal line across the sagittal and coronalimages. It references the exact location of the axial image.

When you move to a new position, the intersection lines will be updated and show you your current position in thedata set.

After performing an online reslice, you will see 3 blue dashed or full lines and a yellow dashed or full line in theaxial image. The middle blue line references the exact location of the cross-sectional image (surrounded by a blueborder). The most left blue line reference the exact location of the cross-sectional image at the left top corner ofthe cross-sectional grid. The most right blue line reference the exact location of the cross-sectional image at theright bottom corner of the cross-sectional grid. The yellow line reference the exact location of the parallel imagethat is displayed.

Color Table

Note:You can choose between dashed or full lines in the Visualization tab of the Preference window.

Slice Position

In the view that contains the scanner images, the slice position is indicated in the lower left corner and the imagenumber is indicated in the lower right corner. In the other views, the slice position is indicated in the lower rightcorner.

Orientation strings

tick marks on tick marks off

Axial RedCross-section Blue (only visible if the project is resliced in Reslice Layout)

Parallel Yellow (only visible if the project is resliced in Reslice Layout)

Sagittal Green

Coronal Orange

Image Numbering

Axial Increasing from bottom to top

Sagittal Increasing from the right to the left side of the patient

Coronal Increasing from posterior to anterior




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The colored letters located on each view shows the orientation of the images.

P: Posterior

A: Anterior

L: Left

R: Right

T: Top

B: Bottom

Looking at the images you can verify if they are correct, if not you can easily change them in the ChangeOrientation window going to File > Change Orientation.

The Context Menu

If you right-click with your mouse on any of the views, you will see the context menu. The functions in the contextmenu can differ, depending on the location you click on: if you right-click on an image, on the 3D view, on a 3Dobject, a STL, a CAD object, ...

There are several easy shortcuts available from the default context menu:

1-Click Navigation

1-click navigation is very easy. By clicking once on an image (e.g. the axial image) with your left mouse button allimages are immediately updated to show the same point. Navigation is also possible from the 3D image.

Pan view

Every image and 3D view can be panned or moved. When you select the pan function, the cursor will change to across-shaped double arrow. There are different ways to select the pan function:

hold down the SHIFT key, right-drag your mouse button

right-click in an image or in the 3D view and select Pan Viewfrom the context menu

click on the Pan View buttonin the toolbar

hold down the SHIFT key in combination with the arrows-keys for precise rotation

Pan View Enables the panning mode

Zoom Enables the zoom mode

Unzoom Unzooms the view

Zoom to full screen Zooms the view to full screen

3D Window Enables the 3D view in the window




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Hold down the SHIFT key in combination with Home / End for quick Left / Right panning

select View > Pan Viewfrom the menu bar

Rotate view

The rotate function is only available on a 3D object. There are different ways to select the rotate function:

right-drag with your mouse button

use the arrows-keys for precise rotation

use Home / End to rotate 10 degrees Left / Right

use Page Up / Page Down to rotate 10 degrees Up / Down

right-click in the 3D view and select Rotate Viewfrom the context menu

click on the Rotate Viewbutton in the toolbar

select View > Rotate Viewfrom the menu bar

There are two different modes when rotating the 3D view. When your mouse cursor is in the middle of the 3Dwindow and you then hold down the right mouse button, the 3D view turns about a vertical axis when you move

the mouse left and right. The 3D view tilts around a horizontal axis if you move the mouse up and down.When your mouse cursor is at the side of the 3D window and you then hold down the right mouse button, the 3Dview rotates around an axis perpendicular to your screen when moving the mouse.

Zoom

Allows to Zoom in at a user defined rectangle. Click on the left mouse button to indicate a corner of the zoomrectangle, drag and release to indicate the opposite corner. Can be used on every image.




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There are different ways to select the zoom function:

hold down the CTRLkey, right-drag your mouse button

right-click in an image or in the 3D view and select Zoom from the context menu

click on the Zoom buttonin the toolbar

select View > Zoom from the menu bar

Note:The behaviour of zooming is different in Reslice Layout.

Zoom to fixed factor

Allows to Zoom in at a defined factor. Click on the arrow and choose from the drop-down list the factor you wantto zoom with: your cursor becomes a lens.

Zoom to full screen

Allows you to display a view on the whole screen. Click on the Zoom to full screen button and the cursor willchange to a magnifying glass. Then click on an image. To return to a normal view, click again on the Zoom to fullscreen button.

When you hover with the mouse over a view and click on the spacebar the view is put to full screen. To unzoompress the spacebar again. You can also zoom to full screen by by invoking the context menu by right-clicking onthe view.

Unzoom

Changes the display scale to show the whole image. You need to select the function first and then left-click on theview on which you want to apply the function.

Project Management

Zoom tofull

screen onaxial view




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The project management gives you an overview of all the objects in the project. You can hide the project menu by

toggling the project management button in the main toolbar .

Masks

The project management consists out ofcontainers which hold a number of tabs.Each tab stands for a kind of objects inMimics. It lists the available objects in theproject. On the bottom of a tab you have a

toolbar with the most common functions.On the toolbar you typically find a create, adelete and a properties button. The lastbutton on each toolbar is always the action

button . This button lists all the functionsthat can be performed on the selectedobject.

Besides object based tabs there are threedifferent tabs on the bottom of the projectmanagement. The contrast tab allows you toadjust the gray scale of the images. Thevolume rendering tab shows a histogram of

the dataset and a line which allows you toset the opacity of the voxels. The clippingtab lists the possible clipping planes andtheir settings.

When the containers are docked in theproject management they have a fixed size.To enlarge them you can undock them byleft-clicking on the pointed top of thecontainer and dragging the containeroutside the project management.

The same counts for the different tabs. Youcan left-click on the tab and drag the taboutside the container. Tabs can as well be

dragged to another container




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A mask is a collection of pixels where all actions (editing, region growing, ..) and calculations (3D calculations,STL, ..) are based on.

List of the created masks

Functions on masks

Properties

The mask properties gives numerical information about the gray values in the selected mask:

Name Name of the mask. By clicking on the name of the mask, it can be renamed.

Visible

Lists if the mask is visible or not by means of glasses.

Lower Threshold Lower Threshold setting of the mask.

Higher Threshold Higher Threshold setting of the mask.

New Creates a new mask with a default threshold

Delete Deletes the selected mask

Properties Gives numerical information of the selected mask

Duplicate Duplicates the selected mask

Clear Clears the contents of the selected mask, the threshold of the mask is kept

Calculate 3D Opens the Calculate 3D window

Action Lists the available function on the selected mask




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3D objects

List of the created 3D reconstructions

Minimum value Minimum gray value in the selected mask

Maximum value Maximum gray value in the selected mask

Average value Average gray value from the selected mask

Standard deviation

Number of pixels Amount of pixels in the selected mask

Mask volume The volume of the mask

Scale The scale you are working in: GV (Grayvalues) or HU (Hounsfield Units).




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Functions on 3D reconstructions

Properties of a 3D Object

When you click on the Properties button in the 3D Objects list, following dialog box will open:

Name Name of the 3D, by clicking on the name of the 3D, it can be renamed.

Visible Lists if the 3D is visible or not by means of glasses.

Contour Visible Lists if the contour of the 3D object is visible on the 2D images or not by means ofglasses. You can change the visibility of the contours by clicking on the glasses.

Transparency Lists the transparency settings of the 3D, possible options are: opaque (= nottransparent), low, medium and high. Change the transparency by clicking on the

icon in the transparency column. To see your objects transparent, the transparencybutton has to be enabled.

Quality Quality which was set before calculation, possible options are: low, medium, high,custom.

New Creates a new 3D. The Calculate 3D window appears.

Delete Deletes a 3D.

Properties Gives the properties of the calculated 3D object.

Move

Activates the handles to move the STL to a new positions

Rotate Activates the handles to rotate the STL around its axis

Action Lists the available functions on the selected 3D object




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Mimics displays the name, color and transparency of the object. The volume, surface, outer dimensionalparameters and the number of points and/or triangles are also shown, which give a good idea if reducing of thefile for further applications is needed.

You can change the transparency of the 3D objectand make objects transparent. Drag the Transparency slider atthe bottom of the 3D properties dialog. If the slider is all the way to the right, the 3D surface is opaque and nothingbelow the surface can be visualized. If the slider is all the way to the left, the 3D surface is completely transparent.

In order to see the 3D object transparent, you need to click the Toggle transparency button in the 3D toolbar.

If the Detailsbutton on the 3D Properties dialog is selected, some measurements of the 3D object are displayed.

Opaque 3D Transparent 3D




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Move and Rotate button

When the simulation module is licensed, two new buttons will appear on the 3D tab of the project management:Moveand Rotate. These buttons allow you to rotate and/or move one or more 3Ds.

RotateWhen you select a 3D object and click on the Rotatebutton, rotation handles will appear around the 3D object.You can now rotate the 3D objects around the X, Y or Z axis of the project by grabbing one of the colored rotationhandles. You can also rotate the object around an axis perpendicular to the camera by grabbing the outer ring ofthe rotation tool. To change the rotation center select the center of the tool and move it to its new position.

The rotation value is shown in the status bar.

Move

When you select a 3D object and click on the Move button, translations arrows appear. To translate the 3D objectgrab a translation arrow and move the mouse. To translate the object parallel to the viewing plane, grab and movethe middle of the tool.

The translation value is shown in the status bar.




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Polylines

List of the created Polyline sets

Functions on Polyline sets

STLs

Sets Name of the polyline. By clicking on the name of the polyline, it can be changed.

Visible Lists if the polyline is visible or not by means of glasses.

Based On Tells on which mask the polylines were calculated. If the set is grown out of anotherset, it is independent of a mask.

New Creates a new polyline set. The Calculate Polylines window appears.

Delete Deletes a polyline set

Duplicate Duplicates the selected polyline set

Color Changes the color of a polyline set

Polyline growing The polyline Growing tool provides the capacity to create several sets of polylines.

Action Lists the available functions on the select polyline set




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List of created Objects

Functions on Objects

Name Name of the object. By clicking on the name of the object, it can be changed.

Visible Lists if the object is visible or not by means of glasses.

Contour Visible Lists if the contour of the object is visible on the 2D slices or not by means of

glasses. You can change the visibility of the contours by clicking on the glasses.Transparency Lists the transparency settings of the STL, possible options are: opaque (= not

transparent), low, medium and high. Change the transparency by clicking on theicon in the transparency column. To see your objects transparent, the transparencybutton has to be enabled.

Load Loads an STL file into the project.

Remove Removes an STL file from the project.

Properties Displays the properties of the selected STL file.

Export STL Saves the selected STL file (with its current position).

Move When the Move button is enabled, you can move the STL in the 2D views and the 3Dview.

Rotate When the Rotate button is enabled, you can rotate the STL in the 2D views and the 3Dview.

Action Lists the available functions you can perform on the selected STL

Transform Opens the transformation dialog:

In this dialog, you can enter a transformation matrix, invert the transformation matrix ifneeded and apply it on the selected STL file.

You can also load a transformation matrix file, written out by Mimics when reslicing or




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Measures

List of the created Measurements

Functions on Measurements

Curves

cropping a project or when doing an STL registration.

Type The type of measure, represented by its corresponding icon. Possible measuresare: a 2D or 3D distance, a 2D or 3D angle or a density measure. These are thesame measures that are available in the tools toolbar and are represented in the listwith the same icon.

Visible Lists if the measure is visible or not by means of glasses.

Value Depending on the type of measure this value can represent a distance (mm), anangle (in degrees) or a mean density (HU or grey values).

Deviation The deviation in Hounsfield units or grey values for a density measure.

Area The area in mm of a density measure.

New Shows a menu from where you can choose the type of measure. Possiblemeasures are: a 2D distance, a 3D distance, a 2D angle, a 3D angle or a densitymeasure. These are the same measures that are available in the tools toolbar.

Delete Deletes one or more measures.

Properties Shows the properties of the selected measurement.

Locate Updates all views to show to selected measure. Only angle and distance measurescan be located.

Action Lists the available function on the selected measurment




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A reslice curve allows you slice the images in a different direction. To draw a reslice curve, select Online Reslicefrom the File menu.

The resliced images can only be viewed when the Reslice layout is chosen in the View menu.

List of the created Curves

Functions on Curves

Annotation

List of the created Annotation

Name Name of the reslice curve. By clicking on its name, it can be changed.

Visible The active reslice curve is indicated by means of glasses. In the Reslice layoutthe images corresponding the active reslice curve will be shown.

Cross-Section Length(mm)

The cross-section length determines the width of the cross-section images. Thislength is set to optimal by default, but can be altered by double-clicking on theOptimal text. This way you can specify an exact cross-section length.

Note:To return to the Optimal setting after you have specified an exact length,set 0 as the value of the cross-section length.

New Opens the reslice curves toolbox to draw a new curve.

Delete Deletes one or more reslice curves.

Name Name of the annotation. The name is generated automatically based on theobject on which the annotation is attached




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Functions on Annotations

Adjust grayscale

The mapping of pixel values into gray levels is specified by the level and the width of the line on the histogram.The amount of available gray values levels is dependent on your display setting. When your display setting is seton true color (24-bit or 32-bit) you will be able to map the pixel values onto 128 gray levels.

You can change the window by grabbing one of the points or the line and move it with the left mouse button. Youcan as well define the position of the points by filling in a value in the Minimum and Maximum field.

Visible The visibility of the annotations is set by means of the sunglasses

Object Lists the object to which the annotation is attached

Text Shows the content of the annotation

New Activates the annotation cursor. Click with your mouse on the object on which you

want to attach an annotation. The annotation properties dialog will open in whereyou can add your comments.

Delete Deletes the selected annotation

Properties Opens the Annotation Properties dialog

Locate Updates all views to show to selected annotation.

Action Lists the available actions on the selected annotation




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Instead of defining the contrast yourself, you can choose one of the predefined scales from the dropdown box.

You can change the gray scale also interactively by pointing at an image of interest and dragging the right mouse

button. The cursor will change into . Move the mouse down to increase the width of the gray scale - thislowers the contrast within the soft tissue. Move the mouse up to decrease the width of the gray scale - thisheightens the contrast within the soft tissue. Move the mouse to the right to increase the level of the gray scale -this darkens the soft tissue. Move the mouse to the left to decrease the level of the gray scale - this lightens the

soft tissue. When you are satisfied with your gray scale, release the mouse button. All the images are updatedimmediately with the new gray scale.

Volume rendering

The volume rendering tab shows a histogram of the dataset and a line which allows you to set the opacity of thevoxels. To visualize the volume rendered 3D select the volume render button in the 3D toolbar. You can find moreinformation about volume rendering in the section about the 3D toolbar.

Clipping

In the clipping tab you can define the different clipping planes and their options. To activate clipping select theclipping button in the 3D toolbar. You can find more information about clipping in the 3D toolbar section




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Shortcut Keys

General Shortcuts

Shortcuts on files

Shortcuts on the views

F1 Open the Online HelpCTRL + Z Undo last actionCTRL + Y Redo last actionCTRL + F Enable/Disable the Navigation ToolbarCTRL + I Makes all mask invisibleCTRL + SHIFT + M Enable/Disable the Movie export

Alt + F4 Exit MimicsSPACE If you hover with the mouse over a view and press the spacebar; that view is put to

full screen. To unzoom to full screen; press the spacebar

CTRL + O Open a fileCTRL + P Print a fileCTRL + S Save a fileCTRL + N Close a file

ArrowUp Go to next slice

ArrowDown Go to previous slicePageUp Go 10 slices upPageDown Go 10 slices downCTRL + L Make slice indicators visible/invisibleRight mouse button Adjust gray scale: Move the mouse horizontally while keeping the buttons pressed to

change the level of the gray scale. Move the mouse vertically to change the width ofthe gray scale.

SHIFT + Right mousebutton

Pan: Move the mouse while keeping the buttons pressed to pan.

CTRL + Right mouse buttonZoom: Move the mouse vertically while keeping the buttons pressed to zoom in andout.




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Shortcuts on the 3D view

Shortcuts on the layouts

Shortcuts on Segmentation functions

Region Growing

Edit

Shortcuts on text fields in dialogs

Shortcuts on Movie Tool

Arrow keys Rotate the 3D view left/right and up/downPage Up Rotate the 3D view 10 degrees downPage Down Rotate the 3D view 10 degrees up

Home Rotate the 3D view 10 degrees leftEnd Rotate the 3D view 10 degrees rightSHIFT + keys above Pan the 3D view

ALT + left/right Do washing machine rotation

F2 Image LayoutF3 3D LayoutF4 Reslice LayoutF5 Simulation Layout (if the simulation module is licensed)

CTRL + R Start the Region growing function

CTRL + E Open the edit toolbar and go in edit mode

While in edit mode:D DrawE EraseT Draw with local thresholdCTRL + drag left mousebutton

Resize the edit cursor

SHIFT + Left mouse button Temporarily release the edit-tool and do 1-click navigation.

CTRL + C Copy

CTRL + X CutCTRL + V Paste

CTRL + SHIFT+ M Start the movie toolSHIFT+ F8 Start Recording / Stop RecordingSHIFT+ F9 Pause Recording




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Shortcuts on Polylines

CT Gray scale

CT images are a pixel map of the linear X-ray attenuation coefficient of tissue. The pixel values are scaled so thatthe linear X-ray attenuation coefficient of air equals -1024 and that of water equals 0. This scale is called theHounsfield scale after Godfrey Hounsfield, one of the pioneers in computerized tomography. Using this scale, fatis around -110, muscle is around 40, trabecular bone is in the range of 100 to 300 and cortical bone extendsabove trabecular bone to about 2000.

The pixel values are shown graphically by a set of gray levels that vary linearly from black to white. Mimicsdisplays the CT images using up to 256 gray levels if your display setting is true color (24-bit or 32-bit), 128 graylevels if your display setting is 256 color palette, but as few as 32 gray levels if your display setting is high color(16-bit). The mapping of pixel values into gray levels is specified by a level and a width. A gray scale is centeredabout its level.

For example, a level of 0 specifies that water will be displayed as mid-gray. The extent of the gray scale isspecified by its width. The default gray scale used by Mimics allows you to see the full range of tissue from air inthe maxillary sinus to the densest of cortical bone, but subtle differences in the soft tissue cannot be visualized. Ifyou narrow the gray scale, you can better visualize subtle differences in the soft tissue or trabecular bone, but atthe cost of forcing cortical bone to be in one gray level: white. Narrowing the gray scale can help you locate themandibular canal if it is not easily seen with the default gray scale.

CTRL + U Update polylines




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File Menu

The file menu contains the following items:

You will also find the corresponding buttons in the toolbar.

Open project

Open an existing project by selecting File > Open projectfrom the menu bar or by clicking its button on the Main Toolbar. When you clickon the black arrow on the Open project button, a list of previously opened projects appears.

The Open project dialog displays your folders containing Mimics files (*.mcs) on the left side of the window.

Folders for the floppy-, Compact Disc and zip-drive are also displayed when they are installed. Click on a folder to see the list of Mimics filesin that folder. Use the arrows on the scroll bar if the patient you wish to view is not displayed. Open a study by clicking once its line in the listand then the Open button or by double-clicking its line.

There are two different modes in the Open project window. The first mode allows you to easily browse on your harddisk. The second mode

will show you more information for each project. You can switch between these modes with the button.

Note:The first mode will be disabled when the Hipaa preference, Hide file name, is enabled. To change the Hipaa preferences go topreferences, you can change the Hipaa settings in the General section

Page 1 of 74File Menu

2/3/2014file://C:\Users\Mark\AppData\Local\Temp\MimicsTemp_15_52_05\~hh66DD.htm


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List of studies

Functions

Browse tree Displays the browse treePatient Displays the patient nameStudy ID Shows the study IDStudy Date Shows the study dateFile Displays the file name

Add directory to Favorites Adds the current

Make default Makes the selected folder your default

Delete folder To delete the selected folder from the list of favorites.

Browse To select a new directory in order to see the reformatted CT studies the folder contains. You willbe asked if you want to add the folder to the list of favorites.

Delete study To delete the selected study from your computer.

Search in Subfolders Shows all the projects in the folder and subfolders

Switch view Switches between the two browse modes.

Sort by column Quickly sort the studies by a column by clicking on the column header

Change column order Change the order of the columns by dragging the column header to the left or the right

Open Click on the Open button after selecting a study or double-click on a study to open it

Cancel Closes the Open dialog box




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List of favorites

Click on a folder to see the images within the folder. The path of the selected folder is shown at the top.

Right-click on a folder to display the following context menu.

Reduce Images

High-resolution images can contain a lot of noise and this means that a noisy 3D is obtained. When you want to filter the noise within theimages or want to speed up the segmentation functions, use a voxel reduction. The reduce Images window (see picture) is shown whenloading data sets that require more memory than available or when the preference setting Always ask to reduce images when loading (onthe General tab page) is selected. Based on the amount of images and the pixel size, the necessary amount of memory is calculated andcompared with the total amount of memory (RAM). If more memory is needed than available, a reduction is proposed.

This function groups voxels together when loading the study. A reduction value of 1 means no reduction; every single voxel will be loaded. Areduction of 2 will group 4 voxel together (2 in the X-direction and 2 in the Y-direction) as 1 voxel with as gray value the mean gray value ofthe 4 voxels. The maximum allowed reduction is 5. Since pixels are grouped together, the noise is filtered out and all segmentation toolswork faster.

Save project

Saves the Mimics project.

Save project As

Allows you to save the project with another name.

Help Opens the help pages on the Open project subject

Rename To change the name of the folderRemove To remove the folder only from the list of favorites. The folder will not be removed from your computer.




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When saving the project, you can choose to compress it. The compression algorithm used is a lossy JPEG compression. Using this option

will reduce the size of the project.You can choose between three different quality presets for the JPEG compression:

When saving a project, it is possible to compress the images in the project with a lossy JPEG compression. This way you can reduce thesize of your projects. It is possible to choose between three quality presets:

High Quality Low Compression

Medium Quality Medium compression

Low Quality High compression

The higher the compression factor is, the smaller your files will become, but the worse your image quality will be.

When you have done a reduction on the images during loading or importing, you can also choose to keep the reduction when you are savingthe project.

Close project

Closes the Mimics project. If necessary, the program will prompt you to save it.

Import STL file

Loads an STL file into the project. It will appear in the Project Management, STL tab and in the 3D window.




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Note: You can only load an STL file if a project is open, the function is disabled if no project is opened.

STL LibraryThe STL library allows you to create a library with STL files on your hard drive that is easily accessible from Mimics. The first time you usethe STL Library, Mimics will ask where you want to create this library:

We recommend creating a new folder on a hard disk with a lot of free space. After you have selected the directory where the STL library willbe located, you will see following interface:




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The interface is divided in two parts: the left part will show a directory tree of your library. If you select an STL in the tree, you will see theproperties for that STL in the right part. If you select a directory in the tree, you will see a list on the right of all the STLs that are found in thatdirectory.

You can extend the library in two ways:

You can copy STL files in the STL library folder via the Microsoft Explorer. You can also create new directories or remove files viathis way. The changes will be visible the next time you open the STL library in Mimics or when you click on the Refresh button.

You can create new folders and import STL files in the library by clicking on the appropriate buttons in the STL library interface.

When you select one or more STLs in the tree or in the list on the right and click the Load button, the selected STLs will be loaded inMimics.

You can also adjust the Name, Manufacturer, Product Line and Description when viewing the properties of an STL by clicking on the fields.These changes will be saved to a small XML file in the STL library.

Import images

To start the Import Images wizard, first close all projects and than select Import imagesfrom the File menu. The wizard will start with STEP1.

Selecting images to import

The first step is to choose the source directory of the images to import. You can click immediately on the drive or folder in the favorites

column or you can browse for the drive or folder in the Windows Explorer tree. When you look for images on an optical disk or tape, youneed to browse to the folder SCSI adaptor. Click on the + sign in front of SCSI adaptor to see the list of optical drives. Click on the opticaldrive and browse to the folder with the images.

As soon as you select the source directory, all images within the directory are displayed at the right side and are immediately selected. ClickNextto continue the conversion.




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Favorites

The following folders will be listed as favorites when starting the Import images wizard for the first time.

To add a new folder as favorite you need to browse for that folder in the Windows Explorer tree and click the Add favorite button in thetoolbar. Right-click on a favorite folder (except for the Browse folder) to delete or rename the folder. Each favorite folder can be dragged toanother place in the list.

Filename

This window displays all the files in the selected Source Directory. All images are automatically selected. To restrict the selection you canhold down

the CTRL key and left mouse button to select the images one by one

the shift key and left mouse button to select the first and the last image in your selection

Import Toolbar

Manual import

If Mimics does not recognize the image format, check the Manual import option before clicking the Next button. This option allows you toimport any type of images by providing Mimics all the image information yourself. For more details, go to the Manual import page.

Browse To browse through the folders on your computer.

DIA To display the images received via a DICOM network (if the Dicom Input Application module isinstalled and licensed).

Floppy To display the images stored on a floppy disk (if a floppy drive is available).

CD To display the images stored on a CD (if a CD drive is available).

Add the selected folder to the Favorites column

Select all the images/projects in the Filename window

Displays a window with extra information about the images to import

Rebuild the DIA database in order to display recently received images

To merge 2 or more image sequences of one patient

To delete images within the DIA folder

When there is a DICOMDIR file available in the folder, you can toggle between viewing the studies as specified in theDICOMDIR or viewing the files.

Select this button to display the images in the subfoldes

To dump images from a tape




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Selecting studies to convert

In this window information is shown about the studies you are going to convert. All studies that are selected will be converted and for thosestudies, a Mimics file will be made in the default working folder. To unselect a study, click on the checkmark in front of each study. Click theConvertbutton to start the conversion.

Notice that when you click the Backbutton, you are able to add some more studies to the list. In this way you can perform a batchconversion.

If multiple image sequences of the same patient are displayed, this means that not all image parameters are equal. The differences arehighlighted in bold. To merge one or more sequences to one Mimics project, select them by using the SHIFTkey and left mouse button, and

click the Mergebutton . Merging sequences in not allowed when the patient name, pixel size or image orientation is different.

Note: Mimics checks for several parameters during the import of images. If one of these parameters are different, Mimics splits the data setin different parts. The parameters that Mimics checks for are: height, width, pixel size, gantry tilt, orientation, label, patient information, studyinformation and reconstruction center of the images.

Study

In this area you can find information (number of images, type of compression, pixel size...) about the study to convert. You can also select

which studies should be converted by changing the checkmark in the Convert column.

Skip Images

You can choose to skip images during the import, by selecting one of the studies (the selected study will be colored blue) and then choosehow many images to skip. In the screenshot above, the first sequence has a skip images setting of two. This means that only image0,image3, image6, image9, ... will be imported.

Compression

There are different types of image compression to choose:

CT: this compression is typically used for the removal of background noise for CT-images. It is a lossy compression and changesthe grayvalue of all the voxels with a grayvalue between 0 and 200 to 0

MR: this compression is typically used for the removal of noise for MR-images. It is a lossy compression and sets the grayvalue ofall the voxels with a grayvalue between 0 and 10 to 0.

Lossless: when choosing lossless compression, nothing is changed to the voxels of the images

Note:for technical CT images it is best to use the lossless compression.

Invert Table Position

When this option is active, the table position will be inverted during import. This function allows you to set the Bottom and Top of a patient onthe Bottom and Top of the screen.

Selecting studies to open

Select in this window the study you want to open in Mimics. If the data contained only one study, step 3 will be skipped and you will goautomatically from step 2 to the next step.




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Changing orientation and gantry tilt sign

If one of the orientation parameters is unknown, a window Change orientation is displayed on top of the images. You need to fill in themissing orientation strings, indicated by an X, before you can proceed. To do this, right-click on the X and choose one of the remainingorientation characters.

When the patient has been scanned at an angle (see picture) a Gantry tilt window will pop up after the import. The gantry tilt is the angle ofthe scanning plane relative to a vertical plane. The sign of the gantry tilt can be positive or negative, but there is no convention for this. Thismeans that the absolute value of the gantry tilt is known, but the sign is not. A decision about the correct sign has to be made by visualinspection of the images in the YZ or sagittal view. You can change the sign by clicking the Switch button. If you're not sure about thecorrect sign, contact the radiologist. Click the Closebutton to save the correct sign.




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Note:the orientation strings can still be changed after loading the project by selecting Change Orientation from the File menu. But thischange results in the loss of all your segmentation. The gantry tilt sign cannot be changed anymore after the project is loaded.

Reading Tiff and Bitmap images

When you select images in Bitmap or Tiff format an extra window will be displayed on the screen after clicking Nextin the first Import imagesWizard window. In this Bmp/Tiff Import window you need to fill in some image related coordinates before a conversion can be performed.The radiologist should provide this information.

Filenames

The data you want to import can be seen here.

Files Sorting

Sorts the images numerical or alphabetical.

The sort order can be changed interactively by selecting an image in the list and clicking the Up or Down arrow in the Move box. The imagewill be moved up or down one position in the list.

Image Information

Image size This value (0 - 65535) represents the horizontal and vertical size of the input image(s) in pixels.Common values are 256, 320, 512 and 1024.

Note: If Mimics displays the error message that your images are not the same size when you want toimport them, you have to change the size of these images manually in an image-editor, likePhotoshop.




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Exam Information

Show Preview

The Show Previewbutton, allows you to check the used parameters before conversion. When changing a parameter, click the Updatebutton to update the Preview.

Import table position from This option allows you to convert Bitmap or Tiff images with a variable slice distance. After selectingthis option, the first table position and a slice distance parameters will become disabled. You need tobrowse to a text file by clicking on the button with the yellow folder. The text file should contain 2columns. The first column should list all the file names (with extension) and the second column all thecorresponding table positions. In between these 2 columns there need to be a TAB. By selecting thistext file, Mimics will put every image on the right table position, even if the distance is variable. If youselected more files than written in the text file, he will give you the message "Not all files could beassigned a table position". If you click OK, Mimics will proceed and makes a Mimics project with allimages on the correct table positions.

In order to make a text file very quickly, first make an Excel sheet and then export from within Excel to

a text document with a tab in between the 2 columns.

First Table position This option defines the table position for the first image slice of the first input file.

Always try the default value, i.e. a table position of 0, except for the case in which two conversionsteps are necessary. In this case you have to ensure the correct distance between the imagesconverted in the first step and the images converted in the second step. This can be arranged byfilling in the correct value for this parameter.

Slice distance This option defines the distance in mm between all image slices converted at once, whether they arestored in one file or not.

Pixel size This option defines the actual size of one image pixel in mm. The software always assumes that thepixels are square!

Gantry Tilt This option defines the angle of the scanning plane relative to a vertical plane. It is very important toknow whether a patient has been scanned with a gantry tilt (angle different from 0) or not. Althoughthe MIMICS software has been adapted to support data scanned with gantry tilt, interpolations and 3Drepresentation will have an inferior quality due to the gantry tilt. It is advised not to use a gantry tilt.

Patient Name Fill in the Name of the patient

Institute Name Fill in the Name of the Institute

Orientation Fill in the Orientation string of the patient. If unknown, fill in the default XXX, the orientation can alsobe changed after the conversion.

Note:A correctly filled in orientation is very important. If filled in incorrectly, a mirrored model might bethe result.




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The slider at the right side of the image makes it possible to scroll through the different images. The Contrast toolbar on the bottom allowsyou to change the contrast.

The contrast is immediately optimized to the values of the image(s). Values can be examined image by image or can be sampled throughthe complete data set. The user can define the sampling interval. By moving the contrast sliders, you will also see two vertical lines movingon the histogram. These lines indicate the interval of the values that will be taken in to account. Values below this user minimum will beconverted to black, values above the user maximum will be converted to white. This will not only lead to an increased compression on theimages but makes it also easier for the user to define proper values during the conversion operation.

Manual import

When selecting the Manual impor toption in the Import Images wizard and clicking the Nextbutton, the following window appears.

If you select only one file for doing a manual import, you will see another window. With this window you can import several images that aregrouped in one file.




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As you can see, the only difference with the regular manual import window is that you can define how many images are grouped in the fileand what the header size is between each image.

Multiple Files Sorting

The multiple files sorting tab is only active when more than one file is selected and allows sorting the images numerical or alphabetical.

The sort order can be changed interactively by selecting an image in the list (e.g. PUMP8.XP) and clicking the Up or Down arrow in theMove box. The image will be moved up or down one position in the list.

File Structure

Exam Information

Example

numerical sorting CT0, CT1, CT2, CT3, CT4, CT5, ....CT9, CT10, CT11, CT12, ...

alphabetical sorting CT0, CT1, CT10, CT100, CT101, ...

File Size This field gives the file size.

File header Size This value represents the position (number of bytes) of the first image pixel. This header sizeis calculated automatically by Mimics. If needed, you can adjust the value manually.

A way to calculate this value :

file size = header size +(number of images in one file *horizontal size *vertical size *number of bytes used by one pixel) +inter image header size *(number of images in one file -1)

therefore :

header size = file size -(number of images in one file *horizontal size *vertical size * number of bytes used by one pixel) -inter image header size * (number of images in one file - 1)

Only active when only one file is selected :

Number of images per file This value represents the number of image slices available within one file.

The defaultvalue is 1.

Inter-image header Size When a file contains more then one image, general structure is mostly a header with generalinformation at the beginning of the file, followed with an image and then between every twoimages a short description of each slice. This option represents the number of bytes to be

skipped between every two images read from the same file.Only active when one file is selected.

Patient Name Fill in the Name of the patient

Institute Name Fill in the Name of the Institute

Slices Indicate the type of slices: axial, sagittal or coronal.

Orientation Fill in the Orientation string of the patient. If unknown, fill in the default XXX, the orientation can also bechanged after the conversion.

Note:A correctly filled in orientation is very important. If filled in incorrectly, a mirrored model might be




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Image Information

Pixel properties

the result.

Horizontal and Vertical

image sizeThis value (0 - 65535) represents the horizontal and vertical size of the input image(s) in pixels.Common values are 256, 320, 512 and 1024.

Import table position from This option allows you to convert Bitmap or Tiff images with a variable slice distance. After selecting thisoption, the first table position and a slice distance parameters will become disabled. You need tobrowse to a text file by clicking on the button with the yellow folder. The text file should contain 2columns. The first column should list all the file names (with extension) and the second column all thecorresponding table positions. In between these 2 columns there need to be a TAB. By selecting thistext file, Mimics will put every image on the right table position, even if the distance is variable. If youselected more files than written in the text file, he will give you the message "Not all files could beassigned a table position". If you click OK, Mimics will proceed and makes a Mimics project with allimages on the correct table positions.

In order to make a text file very quickly, first make an Excel sheet and then export from within Excel to atext document with a tab in between the 2 columns.

First Table position This option defines the table position for the first image slice of the first input file.

Always try the defau lt value, i.e. a table position of 0, except for the case in which two conversionsteps are necessary. In this case you have to ensure the correct distance between the imagesconverted in the first step and the images converted in the second step. This can be arranged by fillingin the correct value for this parameter.

Slice distance This option defines the distance in mm between all image slices converted at once, whether they arestored in one file or not.

Pixel size This option defines the actual size of one image pixel in mm. The software always assumes that thepixels are square.

Gantry Tilt This option defines the angle of the scanning plane relative to a vertical plane (see figure).

Pixel type This option is a string representing the different formats available for

Documents

Materilise Mimics 10.1_handbook