Home

documentation

1. www valumegraphics com VGStudio 1 1 Volume Graphics GmbH Wieblinger Weg 92a D 69123 Heidelberg Germany Tel 49 6221 73920 60 Fax 49 6221 73920 88 Printed in Germany First printing July 1999 1999 2001 Volume Graphics GmbH All rights reserved VGL is a trademark of Volume Graphics GmbH The VGStudio software described in this manual is provided under license The software may be used or backed up only in accordance with the terms of the agreement Information in this docu ment is subject to change without notice and does not represent product specification or com mitment on the part of Volume Graphics No part of this publication may be reproduced transmitted transcribed stored in a retrieval system or translated into any language in any form without the express written permission of Volume Graphics GmbH All product names mentioned in this manual are used for identification purposes only and may be trademarks or registered trademarks of their respective companies Registered and unregis tered trademarks used herein are the exclusive property of their respective owners Volume Graphics GmbH makes no claim to any such marks nor willingly or knowingly misuses or mis applies such marks The information provided in this manual is for reference and informational use only and Volume Graphics assumes no responsibility or liability for any inaccuracies or errors that may appear in this documentation Reach
2. OOM mt Mowe m Rotate alt Scale a Clipbox oF Clipplane SEENE view Camera view Fig 82 The context menu in the 3D window Use the Zoom option to open the Zoom menu Out Fig 83 The Zoom Mtono menu of the 3D Actual Pixels window The 3D window may be zoomed in i e enlarged or zoomed out i e reduced These functions may also be applied by using the zoom buttons in the lower right corner of the 3D window The image will then be enlarged or reduced by a preset zoom factor 3 The Fit to Window option allows to zoom the active object so that it is displayed with maximum zoom factor The Actual Pixels option applies a zoom factor so that one pixel in the 3D image of the 3D window will be one pixel on your screen In the following the other options of the 3D view context menu will be explained Move Select this command to move the selected object or object group The Move mode is characterized by the green bounding box around the selected object or group of objects When moving the cursor into the bounding box it will take the shape of one vertical and one horizontal arrow see the table in Chapter 3 1 2 Mouse Usage The object may be moved in the image plane by clicking into the bounding box and dragging the mouse while the left mouse button is pressed The object may be moved forwards or backwards and thus will be enlarged or reduced by clicking into the bounding box and dragging the mous
3. 145 145 136 128 128 128 122 199 slice windows SMP stack of image slices BMP DICOM HDF import JPEG PPM RAW TIFF standard icons starting VGStudio status bar color values gray values stereo images save stereo mode auto checkbox stereo parameters eye distance focal distance interlaced horizontal interlaced vertical red blue red green stereo properties sum along ray algorithm system requirements technical support title bar tool box tool tips tools arrange close disable enable floating maximize minimize tools menu transfer function undo ungroup up vector user interface vgi file VGStudio 200 7 Index 28 99 21 166 166 166 166 169 166 166 166 166 81 21 28 163 163 163 149 149 149 149 149 149 149 149 149 149 77 149 145 20 16 28 59 28 112 58 59 112 114 112 112 113 114 114 76 112 115 64 83 71 143 108 110 162 56 34 166 interface 55 tools 55 view frustum 109 161 view selction icons 81 view selection icons 95 viewing angle 108 159 162 volume graphics 12 Volume Graphics Info file 34 166 volume rendering 12 volumes 166 Analyze 166 DICOM 166 HDF 166 voxel 49 voxel object 47 140 color 136 reference 140 voxel representation 49 voxel resolution 154 what s this icon 81 97 Width 134 window arrange 96 arrange modes 78 cascade 78 maximize 98 minimize 98 new 3D window 78 new slice windows 78 window buttons 59 window
4. Disable Enable Select this command to disable a segment In the Opacity manipulation area a disabled segment will be shown with a gray background the text disabled will be displayed in brackets beneath the segment name In the 3D and the slice windows the seg ment will no longer be visible The same effect may be achieved by mapping the opacity curve to totally transparent A disabled segment s opacity or color mapping may be manipu lated but the results of such a manipulation can only be observed in the 3D and the slice windows when the segment is enabled again Extract Select this command to extract a segment from the original volume object VGStudio s Extract function allows the user to separate parts of a volume data set which are defined by a segment 1 e by a grayvalue range The extract process will generate a new in dependent object in the scene The new object may be manipulated independently from the original object Extract Example Since it is a very powerful and useful feature of VGStudio 1 1 the Extract function will be ex plai 122 ned here by means of an example We will use a CT scan of a human jaw VGStudio 1 1 User s Manual 4 6 Tool Box Classification MOME Object overview oe selection Opacity manipulation area noise t air soft tissue bone l matal Gray values E manipulation area to Fig 119 The CT scan of a human jaw and the Classification tool with three gra
5. Export d Raw volume Load camera trajectory Save camera trajectory Save Mage Print setup Print Fig 187 Select Export Raw volume to export a single volume object as a Raw volume data file The option remains disabled if no object is selected or if the active object is a polygon object or a group of objects A single raw data file will be written to disk in the same data type e g 8 16 32 bit unsigned signed integer 32 bit float or 32 bit RGBA the object was represented in VGStudio For example a data set which was loaded as 16 bit unsigned integer data into VGStudio will be written to disk as 16 bit unsigned integer data The byte order will be the original byte order of your hardware The voxel at position 0 0 0 will be written first x is the inner loop variable y the second loop variable and z the outer loop variable VGStudio 1 1 User s Manual 187 5 Importing amp Exporting Data Vou 77 7 Vam 00 0 Fig 188 The voxel at position 0 0 0 will be writ ten first x is the inner loop variable y the second loop variable and z the outer loop variable After the raw data file was written to disk the following dialog box will pop up Fig 189 VGStudio will ask you whether you want to save a vgi file for the exported volume Click Yes if you want to save a vgi file Volume Graphics Info file for the exported volume Select No to skip this step 188 VGStudio 1 1 User
6. GStudio warning Significant difference between pixel spacing and slice distance detected Do you want to resample dataset Fig 179 Resampling warning Pop up A Warning dialog may come up in case that you import data series with Significant difference in voxel Resolution Press Yes to resample the data The software will calculate additional slices by trilinear resampling This will result in a better 3D image quality However keep in mind that slice images will be generated out of your original data which are not generated by the scanning device The resampling will also result in an additional amount of memory needed by the VGStudio application This process may exceed the available memory installed in your computer depending on your initial image data Press No to skip the resampling process so that only the original image data is loaded However this may result to low 3D image quality 180 VGStudio 1 1 User s Manual 5 1 Importing Data The Data range may be mapped arbitrarily within a maximum data range for the different data types The maximum values will appear as default values when opening the dialog for the first time Pressing the Reset button will restore these default values The maximum data ranges for the different data types that can be handled by VGStudio are listed in the following table Sam ae a cae Sbit ee bit unsigned ri o essas it unsigned s2nic __o _1ouss7s ___ 20 ne 32bit float 16 bit
7. left mouse button while the Ctrl key is pressed or by clicking the object s name in the Scene tree tool with the left mouse button while pressing the Ctrl or the Shift key The bounding boxes of each selected object will be visible when several objects have been selected After grouping a single bounding box around all the selected objects will be displayed You may also use the keyboard shortcut Ctrl G to group the objects For more information see also Chapter 4 6 7 Object Properties Chri u ungroup Two selected objects Selected group Fig 46 Use the keyboard shortcut Ctrl G to group two or more objects After hav ing grouped the objects a single bounding box will be displayed around the selected objects Press Ctrl U to ungroup the objects again Ungroup Select this command to ungroup an object group previously created with the Group command The Ungroup command remains disabled until an object group is se lected You may also use the keyboard shortcut Ctrl U to ungroup objects For more infor mation see also Chapter 4 6 7 Object Properties fe Reminder The clipping of an object group will be reset as soon as you ungroup the object group Create reference Select this command to create a reference of an object A reference is a copy of an object which uses the same classification tool settings color and opacity settings as the original object Due to this special property a reference needs hardly any add
8. 105 Drag the ROI around in the opac ity area Click with the right mouse button into the Object overview area to open a context menu con taining the entries shown in the following figure Object overview Reset Rol Delete all segments Save preset Delete preset Change to levelyvindoyy mode Fig 106 The context menu which opens upon Clicking into the opacity area with the right mouse button The menu option Reset ROI will reset all ROI settings VGStudio 1 1 User s Manual 115 4 VGStudio Interface amp Tools The menu option Delete all segments allows you to reset all segment opacity and color settings to default values which means that all segments will be removed The default opacity ramp is applied and the color is set to white The Save Delete preset options may be used to save or de lete Window Level Opacity and color presets from the Preset selection list See Preset selection within this chapter Opacity manipulation area Advanced mode Classification Opacity manipulation area 5 a serps a Fig 107 The Opacity manipu lation area The Opacity manipulation area contains the following elements e Histogram e Opacity function e Opacity handles e Segment borders e Segment names 116 VGStudio 1 1 User s Manual 4 6 Tool Box Classification Bl Preset selection j NOME Object overview Segment borderline F Opacity ma lation are
9. 6 Reminder For best results while working with scenes including several floating as point data sets you should map the floating point data values of all data sets to the same data range Press the Scan file button to determine the data range included in the data set to be loaded fee Scanning EJ This may take a while b TEL 25 Cancel Fig 180 Use the Scan function to determine the data range Clicking Cancel will stop the scan process but the values determined during the partial scan will be displayed in the dialog VGStudio 1 1 User s Manual 181 5 Importing amp Exporting Data Step 6 Optional preview fee Raw volume preview Mie E4 l MEJE Ej Layer selection Flip views to Miz M Auto scan each layer Hide preview Fig 181 Before starting the import procedure the Raw volume data may be previewed as slice images The Preview window may be used to view your data as slices before starting the import process This may help you to choose the right parameters If you are not satisfied with the results you may always go back to any previous step and change the settings and then check the results again in the Preview window Use the slice selection slider to select the slice to be displayed A region of interest ROI may also be defined To do so grab one of the corners of the blue frame around the region of interest or grab the frame itself by clic
10. animals If your facility or academic institution receives funding from NIH or if your IRB has DHHS approved assurances on file then you are ob ligated to follow the NIH rules in addition to the FDA rules As a consequence of the regulatory status of the VGStudio products you are reminded of the Login Acceptance Screen reprinted below in which you acknowledge the regulatory status of the product prior to using its functionality Disclaimer VGStudio IS NOT FOR CLINICAL USE VGStudio or data derived from VGStudio may be used only for research and may not under any circumstances be used for clinical purposes Pressing the Accept during the VGStudio installation procedure indi cates your consent NOT to use VGStudio for anything other than re search purposes You are encouraged to contact your governing IRB or clinical risk man ager should you have any additional questions or concerns We hope that this information clarifies your understanding of the regulatory status of the VGStudio product and look forward to continued dialog with you To acknowledge the conditions regulating the use of VGStudio please sign this letter in the space provided below and fax a copy of page 8 and 9 to us at 49 621 181 2634 We wish you continued success in your research activities Volume Graphics GmbH I agree to the above restrictions on the use of VGStudio Customer s Signature Customer s Name Printed Organization VGStudio 1 1
11. in the following table aa a ae aan Sbit O bit et rr ee a signed 32bit 524288 a 32bit float 16 bit Reminder For best results while working with scenes including several floating an point data sets you should map the floating point data values of all data sets to the same data range os es Press the Scan file button to determine the data range included in the data set to be loaded fee Scanning This may take a while b TL 25 Cancel Fig 169 Use the Scan function to determine the data range Clicking Cancel will stop the scan process but the values determined during the partial scan will be displayed in the dialog VGStudio 1 1 User s Manual 171 5 Importing amp Exporting Data Step 9 Optional data preview ie Volume preview OF x Ki e Se nnn nnnm Auto scan each layer Hide preview Fig 170 Before starting the import procedure you may preview your data as slice images The Preview window may be used to view your data as slices before starting the import process This may help you to choose the right parameters If you are not satisfied with the results you may always go back to any previous step and change the settings and then check the results again in the Preview window Use the slice selection slider to select the slice to be displayed A region of interest ROI may also be defined To do so grab one of the corners of the blue frame around the reg
12. s Manual 5 2 Exporting Data VGStudio 1 1 User s Manual 189 6 Appendix 6 Appendix 6 1 VGStudio 1 1 and memory consumption 6 1 1 Memory consumption of voxel data A data set loaded into VGStudio is divided into sub volumes of the size 16x16x16 voxels The dimensions of a data set of the size 252x252x204 will be rounded up to a size of 256x256x208 in memory This is called the Data Size in Memory DSM Every data set in memory needs an additional amount of memory which is needed for performance optimization reasons It is called the Spaceleaping Data SD The SD has the same dimensions as the original data in memory but it allocates only one byte per voxel independent of the data type of the original data In addi tion to the DSM and SD a few kByte additional memory are needed Memory consumption of data set of different data types size 252x252x204 Data type DSM in MB SD in MB Total Size in MB 13 13 26 8 Bit Memory consumption of objects in a VGStudio 1 1 scene Original data DSM SD References of an object few kByte 6 1 2 Rendering large high quality images The rendering of large images VGStudio allows the user to render images up to 4096x4096 pixels which is 64 MB requires large amounts of memory The amount of memory may be reduced by reducing the image size and the oversampling rate 192 VGStudio 1 1 User s Manual 6 2 Limitations and Known Bugs 6 2 Limitations and Known Bugs
13. 2 VGStudio 1 1 on Multiprocessor HardWare sssssecececcsssssceccocsssscccoocosssccecossssssceecssssssececcsesssssecesssssseesoo 21 2 3 Installation Insiru eOe a aa a Ea a Ea aaea EESE EEA EE aN Oi aesa 23 2 4 WG SOU Tl CONS nosne E E E E E A E ENR 24 2 5 Registern VG SCO Us Mites cos saadantestccuausrcl iaee a eeaeee aeia Oaai aaar abea 25 S GEME Starred sesi er E ae e E 27 3 1 Es AUHCHING the Protan irasi E NTT 28 IA KeyDoard USTI eren ce love k in saatenasalenbaniouaan latte tenance teu tau innate ease tameaeede haces 29 Ik Moe Usi esien O Min cabauaeduadeh Wie tata naadaateet i ladaah dane aeiaane 31 3 2 First Steps wuh V GSUUICIO cerra a E coseetneessaueaes 34 Jk M kelODjects Poly son Objects and SCENES airaa a a a a a 47 S22 Rie Mumnanon Mode lis xix ccc csascoasagassacnatautacdooisadcadavssaeaieh a conaneiadgedat vaonagelaccadeutasunnel heroes 50 Dee VGSUIGIO CI DO I csiancuedasasxnosscntcaccudaninctinnes tan codaadnosasansaccedeudesbasnensht uodadauinenanehiadoodarbactogehsaccedaniasnnaclceaced 51 3 3 Exiine VYOGSUdIO a A EE E EEEE A EEE 52 3 4 Image Quality v rsus Speed aoeeoe reneo eaaa N EE E E SEE raea EN E sean AR EEEE NE 53 A VGStu udio Interface amp LOOMS viscisssiscussccvssnsevsbcaesscevesesosesevessnvedsanaswaneecteostsantcssvecesenetaanaswanseevs 55 4 VGStudio 1 1 User s Manual VGStudio 1 1 4 1 Basic Concepts of the VGStudio User Interface cccccccsssssssssccccssssssssssccccccsssssssssscccsscsss
14. Axes amp Instrument properties dialog where you may adjust the display of the grid axes and instrument Fig 48 The Grid Axes amp Instrument properties dialog where you may adjust the display of the grid axes and instru ment Here the index card Grid is dis played Every single grid plane may be enabled or disabled by clicking the checkbox in front of it The grids origins can be defined in scene coordinates The spacing of a single grid cell can be ad justed independently for every direction The number of grid cells in positive and negative direc tion can also be adjusted separately for each axis Click Apply to accept the new settings To reset the values to their default simply click Reset If you want to quit the dialog without accept ing the new settings click Cancel E Gad Ame lnh prin mez Fig 49 The Axes index card in the Grid Axes amp Instrument properties dialog VGStudio 1 1 User s Manual 71 4 VGStudio Interface amp Tools Every single coordinate axis can be enabled or disabled by clicking the checkbox in front of it The coordinate system s origin can be defined in scene coordinates The length of each axis in positive and negative direction can be adjusted separately for each axis Click Apply to accept the new settings To reset the values to their default simply click Reset If you want to quit the dialog without accepting the new settings click Cancel fe Gin Asz 4 aibhae
15. Lit WNN ig Sie ae 4 A y Ka a a ee i rr yi Saeseeeen u TERETE A ERATE IAEA EER TA Se Fig 69 The grid is activated in the scene View Selection 4 4 4 The 3D view window supports two different viewing modes for more information on the 3D view please refer to Chapter 4 5 2 Click the View selection buttons to activate the appropriate mode Camera View Use this button to activate the Camera mode For more information on the Camera mode please refer to Chapter 4 6 9 World View VGStudio 1 1 User s Manual 90 4 4 Icon Bar Use this button to activate the World View mode For more information on the World view mode please refer to Chapter 4 6 8 4 4 5 Window Layout Section EEEE Click one of these icons to select a predefined layout for the windows within the workspace VGStudio uses a Multiple Document Interface MDI The 3D window and the three slice win dows may also be arranged arbitrarily within the workspace by clicking into the title bar of the window and dragging the window to the desired position The arbitrarily arranged windows may be rearranged by clicking one of the window layout buttons HAT hzi t 4 an d We tui i on maiu ac ba pe pe pei pme pe iem np Censinio totes ho ees DENDE E Jg i le Es Fig 70 The VGStudio interface with arbitrar
16. Manual 51 3 Getting Started 3 3 Exiting VGStudio To exit VGStudio click File in the menu bar and select Quit If there are any unsaved scenes VGStudio will ask you whether you want to save them before exiting You may also exit VGStudio by clicking the Close Window button in the upper right corner of the window 52 VGStudio 1 1 User s Manual 3 4 Image Quality versus Speed 3 4 Image Quality versus Speed With every decision you make in VGStudio you make a trade off between rendering speed and image quality As a rule of thumb the higher the quality of the rendered images the slower the rendering speed Additional lights or many semitransparent structures in the image will increase the rendering time As you go through the scene creation process you will probably want to keep the rendering qual ity low in order to increase the rendering speed When you are satisfied with your scene you may increase the rendering quality to see what the scene looks like in its final form Here are some hints on how to adjust parameters in order to achieve optimal settings for per formance or quality Optimal settings for performance e Use the Scatter HQ algorithm e use small result image sizes e g 256x256 e use only front light and disable shadow light source e use oversampling factor of 1 0 e deactivate color rendering e use opaque data structures and avoid transparent data Optimal settings for image quality e Use the
17. Options is used to apply several parameters to VGStudio ig elernek Fig 43 The index card Options in the Prefer ences dialog box e Auto Saving Click the Auto Saving Enabled checkbox and enter the Time Step in min utes i e the regular interval when VGStudio should auto save the scene you are currently working on A file named last vgi will then be saved You may use this file to restore your work after e g a system crash by loading it using the Open command in the File menu VGStudio 1 1 User s Manual 65 4 VGStudio Interface amp Tools CFG File Options If the checkbox Use CFG File is activated VGStudio will load the ap plication settings from the vgstudio cfg file in your VGStudio application folder at every startup If the option Use CFG File is disabled VGStudio will start with its default settings If the checkbox Save CFG File is activated VGStudio will save the application settings to the vgstudio cfg file in your VGStudio application folder every time you exit VGStudio If Save CFG File is disabled VGStudio will not save any new application settings and will use the last vgstudio cfg configuration file at every startup Reminder To restore all preferences to their default settings open the VGStudio application folder and rename or delete the VGStudio 1 1 configuration file vgstu dio cfg New default preferences files will be created the next time you start VGStudio The index card General options is
18. algorithm or background color You may also use the keyboard shortcut Ctrl S to save a scene Print Print Click this icon to print the active window You may select either one of the three slice windows or the 3D window as the active window by clicking the title bar or into one of the win dows You may also use the keyboard shortcut Ctrl P to print the active window Cut dh Cut Click this icon to cut objects within a scene in VGStudio The cut objects will remain in the VGStudio clipboard When you cut objects you cut all related information such as opacity and color along with whatever you cut Note that VGStudio objects cannot be pasted into another program You may also use the keyboard shortcut Ctrl X to cut objects VGStudio 1 1 User s Manual 79 4 VGStudio Interface amp Tools Copy Copy Click this icon to copy selected objects into the VGStudio clipboard When you copy objects you copy all related information such as opacity and color along with whatever you copy Note that VGStudio objects cannot be copied into another program You may also use the keyboard shortcut Ctrl C to copy objects Paste A Paste Click this icon to paste previously copied or cut objects into a scene You may also use the keyboard shortcut Ctrl V to paste objects Undo C e Undo Click this icon to undo your previous action This menu item changes depending on the action you last performed For instance if you have pasted
19. an object into your scene the text reads undo paste object and the object will be removed from the scene when you select this command You may undo the last 100 actions and commands Only one exception will destroy the undo history You may also use the keyboard shortcut Ctrl Z to undo your last command Reminder The undo history will be destroyed in case of deleting an object You a57 have to select the undo command immediately after the delete command to undo a delete process Redo k Redo Click this icon to redo your previous Undo action This menu item changes depending on the last Undo action For instance 1f you have undone the pasting of an object the text reads redo paste object and the object will be pasted into the scene again when you select this com mand You may also use the keyboard shortcut Ctrl Y to redo your last Undo command 80 VGStudio 1 1 User s Manual 4 4 Icon Bar 4 4 2 Object Manipulation Section VGStudio provides five object manipulation modes translation rotation scaling clipbox and clipplane All five modes allow interactive object manipulation The mode can be selected by clicking the icons in the icon bar after you have selected an object st De Object manipulation can also be applied by using the Object properties tool which allows the user to type in exact translation rotation clipping and scaling values For more information on the Object properties tool please refer to Chapter
20. button or the Alt key and the left mouse button is pressed When several objects are selected only isotropic scaling is supported Group the ob jects first if you need to perform unisotropic scaling for several objects at a time For more information on the Scale mode see also Chapter 4 6 7 Object Properties Clipbox Select this command to box clip the selected object or object group along the axes of its bounding box The Clipbox mode is characterized by the cyan bounding box with squared handles 1 e active areas on each side of the selected object or group of objects When moving the cursor into the active area a scissors will appear next to the cursor see the table in Chapter 3 1 2 Mouse Usage The object may be clipped by clicking one of the han dles of the bounding box and dragging the mouse along the desired clip direction while the left mouse button is pressed Group the objects first if you want to clip several objects at a time For more information on the Clipbox mode see also Chapter 4 6 7 Object Properties Clipplane Select this command to clip the selected object or object group by an arbitrary clipplane The Clipplane mode is characterized by the cyan bounding box with a normal vector on one side of the currently selected object When moving the cursor into the bound ing box a scissors will appear next to the cursor see the table in Chapter 3 1 2 Mouse Us age The object may be clipped along an arbitrary clipplane by m
21. default the ROI covers the whole opacity area The background of the opacity area will be white Fig 101 The ROI covers the entire opacity area When defining a ROI the background of the opacity area will be gray while the ROI has a white background Fig 102 Once you have de fined a ROI the opacity area will be displayed in gray and the ROI in white The ROI may also be set for a single segment by clicking with the left mouse button into the appropriate segment of the color area in the Object overview section Ms Fig 103 Set a ROI for a single segment only 114 VGStudio 1 1 User s Manual 4 6 Tool Box Arbitrary ROIs may be defined by moving the mouse cursor to one of the four borders of the opacity area The mouse cursor will change as shown in the images below which indicates that the manipulation of the ROI is possible When the mouse cursor changes click the left mouse button and drag the ROI border in the desired direction The appropriate border value will be displayed while changing the ROI Object overview Object overview 1 4616 sjana Fig 104 Change a ROI by dragging the ROI s borders to the desired position A ROI may be moved in the opacity area like a magnifier Click with the left mouse button into the ROI and drag the ROI around while keeping the left mouse button pressed The appropriate border values will be displayed while moving the ROI Object overview Fig
22. enable 69 image quality exiting VGStudio 52 optimal settings export 62 image slices import wizard exporting data 165 197 import exporting Raw volumes 197 add file extract function 128 Analyze data extract segment 128 data type selection 172 extracted segment DICOM data export raw data 132 file order feedback 17 file selection file menu 60 file type first steps 34 file type selection floating tools 113 guess button front light source 50 148 HDF data ambient 148 image size selection diffuse 148 internal data representation GNU zip 172 184 manipulation of object coordinate system gray values 163 non isotropic voxel dimensions grayvalue range 123 optional data preview grayvalue segment 125 polygon data grayvalue segmentation 125 preview function grid 12 Raw volume data axis amp instrument properties 72 region of interest properties 73 remove file from list group 70 ROI and Skip selection group objects 143 scan file guess button 173 186 skip function handle sort function active 111 voxel resolution apply color 136 import stacks of image slices delete 127 138 import tool insert 123 127 138 importing data move 124 importing Raw volume data set color 139 browse help data type selection e mail 16 file name Volume Graphics sales 16 file selection Volume Graphics technical support 16 guess button Volume Graphics web site 16 header size help menu 79 image size histogram 122 133 internal data representation disable 134 manipulation o
23. entries will show that the tool is enabled A tool which was just enabled will appear at the bottom end of the tool box You may also arrange the tools in an arbitrary vertical order within the tool box by clicking into their title bar with the left mouse button and then dragging them to the desired position within the tool box while the left mouse button is pressed Tools can also be dragged out of the toolbox by clicking into their title bar with the left mouse button and then dragging them to the desired position outside the tool box The tools are then floating tools which are independent of the main application window Tools dragged out of the VGStudio 1 1 User s Manual 107 4 VGStudio Interface amp Tools tool box will stay on top all the time Inside the tool box the tools have a fixed size If you need to enlarge or reduce the windows e g for better handling you first have to drag them out of the tool box Most tools can be resized when they are located outside the tool box by clicking into the frame of the corresponding window and then dragging the mouse until the desired size is reached When placing the tool back into the tool box it will be reduced or enlarged to its default size The tool will be resized to the size defined by the user once it is dragged out of the tool box again When you deactivate all tools the tool box will shrink so that the whole window can be used as workspace Activate a tool to expand the too
24. from the bottom upwards However these orientations represent the default settings The whole scene may be rotated or moved with help of the World view tool All axes or planes orthogonal to the axes in VGStudio have a consistent color coding The x axis and planes orthogonal to the x axis are displayed in red the y axis and planes orthogonal to the y axis in green and the z axis and planes orthogonal to the z axis in blue For easy identification all sections in the windows of the tool box related to the coordinate axes are also marked accord ing to this color scheme VGStudio 1 1 User s Manual 47 3 Getting Started Fig 31 Color coding of axes and orthogonal planes However the user may change the coordinate system used to display slice images in the three orthogonal slice windows to a left handed coordinate system Left handed coordinate systems are mainly used by medical applications Please refer to Chapter 4 3 3 Setting Prefer ences An object loaded into a scene will be placed in the scene s origin 0 0 0 with its center not with its origin An object may be moved or rotated arbitrarily within the scene as shown in the follow ing example Scam 90 ee Fig 32 An arbitrarily rotated object is moved to scene position 200 200 200 48 VGStudio 1 1 User s Manual 3 2 First Steps with VGStudio VGStudio is able to handle and render objects or data sets in voxel and polygonal representation In tradition
25. functions to the data for both opacity and color The opacity transfer function can be adjusted in the graph which is shown in the Opacity manipulation area VGStudio 1 1 User s Manual 109 4 VGStudio Interface amp Tools Classification oe selection MONE Object overview opaque Opacty manipulation area Gray values Color manipulation area kx Pree bright grayvalues Fig 93 The Opacity manipulation area of the Classification tool The default transfer function maps the darkest grayvalues to transparent and the brightest gray values to totally opaque The default color mapping is set to white The default mappings may be manipulated arbitrarily Thus the Classification tool allows the user to apply any transparency level or color to any grayvalue within the data set The examples below show what the images will look like when you change the opacity values Default Reduce noise Soft tissue Remove soft tissue semi transparent Reminder Exceptions occur in case of RGBA color data e g colored TIF JPEG BMP or PPM images or RAW RGBA data No color mapping will be possible for color data The color intensity is used as grayvalue in the classification tool for color data 110 VGStudio 1 1 User s Manual 4 6 Tool Box The classification tool can be used in two different modes Level Window mode and Advance mode Level Window mode provi
26. layout icons 81 96 window menu 78 workspace 98 world view 77 96 105 158 default view buttons 159 move mode 159 reset 160 rotate mode 159 scene viewer 159 viewing angle 159 zoom 160 world view mode 72 108 x ray algorithm 145 zoom 100 101 105 106 160 actual pixels 101 106 fit to object 101 fit to window 106 in 100 101 106 out 100 101 106 VGStudio 1 1 User s Manual 7 Index VGStudio 1 1 User s Manual 201
27. remain unchanged Select the objesit to import Megnetc resonance study of hes Fig 40 Select the objects to be imported and click OK VGStudio 1 1 User s Manual i 4 3 Menu Bar Save Object Select this command to save the currently selected object only The object will be saved in its default settings no scene relevant settings such as position rotation or clipping will be saved with the object Only the object s voxel resolution will be saved Use the Save or Save As command to save an object with all scene parameters Import Select this command to import objects and data of different data types into VGStu dio VGStudio supports image stacks of TIFF JPEG BMP PPM DICOM and RAW Im ages as well as RAW data volumes un signed 8 16 32 bit Integer 32 bit Floating Point and 32 bit RGBA HDF volumes Analyze volumes and DICOM data Polygonal data can be imported in OFF file format For more information on how to import images please refer to Chapter 5 1 Importing Data Import DICOM images Select this command to import DICOM volume data or image files into VGStudio Use the file dialog to select one or several data files For more informa tion on how to import images please refer to Chapter 5 1 6 Importing DICOM Data Export Select this command to export the currently selected object For more information on how to import images please refer to Chapter 5 2 Exporting Data Save Image Select this command
28. representation chosen by the user see Chapter 5 2 Exporting Data If you save your current work to a vgi file all the conversion information will be saved along with all the other scene specific data The next time the vgi file is loaded the conversion will be carried out automatically 160 VGStudio 1 1 User s Manual 5 1 Importing Data 5 1 2 Importing Stacks of Image Slices To import a stack of images click File in the menu bar and select Import Then click Image Slices in the Import menu to open the Image Slices Import Wizard The Image Slices Import Wizard will guide you through the whole import process step by step Click the Next or Previous buttons to go through the different steps of the import process The different steps will be explained in the following Step 1 File type selection le Import tool OF x Fileselection Please select the files containing the slices and specify the proper order You can change the fileorder by using dragfdrop or the sortbutton Filetype Ir Sort a Add Remove P x RAW Data Tiff Images JPEG Images Previous Mest cancel FPM Images BMP Images DICOM Images HOF Images Fig 159 Select the file type in the Import tool window Select the File type from the File type list You may choose between RAW data TIFF JPEG PPM BMP DICOM and HDF images VGStudio 1 1 User s Manual 161 5 Importing amp Exporting Data Step 2 Fil
29. the creation process of new grayvalue segments Color mapping will only be applied to a segment Color mappings will not be interpolated across seg ment borders You may apply a color to each color handle on both sides of a segment border VGStudio 1 1 User s Manual 131 4 VGStudio Interface amp Tools Classification fone Selection MOME Object overview E manipulation area Fig 133 A color is applied to segment 2 VGStudio allows the user to insert the maximum number of one color handle per grayvalue This provides a maximum degree of freedom by applying an arbitrary color mapping Press the right mouse button within the color manipulation area to open the context menu Fea tures such as Copy Paste segment color Set segment color Set interval color or Set handle color may be disabled this depends on the position you click with the right mouse button within the Color manipulation area Inzert handle Delete handle Set handle color Set interval color Set segment color Copy segment color r Paste segment color Import segment color Export segment color Save preset Helene de Fig 134 The context menu of the Change to levelAvindow mode Color manipulation area il e Insert handle Select this command to generate a new color handle in the Color manipula tion area e Delete handle Select this command to remove a color handle in the Color manipulatio
30. the same relative position as in the first reference Reminder The new offsets of the smart create reference procedure will be reset to ar its default values as soon as you deselect the object aoe Select All Select this command to select all objects in the scene You may also use the keyboard shortcut Ctrl A to select all objects Deselect Select this command to deselect all selected objects in the scene You may also use the keyboard shortcut Alt D to deselect all objects Select Inverse Select this command to invert the active objects in the scene You may also use the keyboard shortcut Alt I to generate an inverse selection VGStudio 1 1 User s Manual 137 4 VGStudio Interface amp Tools 4 6 3 Render Properties The Render properties tools allows you to control the rendering relevant settings of VGStudio 1 1 The rendering algorithm may be selected as well as the resolution of the resulting image and the image rendering quality Renderer properties Rendering algorithm Scatter Ht Result image size width 256 height 256 Rendering qual color IY oversampling 2 0 li Motion smoothing enable F factor 2 Perspective rendering ere r Fig 139 The Render proper ties dialog Rendering algorithms In VGStudio 1 1 you may choose between six different rendering algorithms Use the Rendering algorithm section to select one of the following alg
31. to Chapter 4 6 7 Object Properties Scale Select this command to scale the selected object or object group The Scale mode is characterized by the dark blue bounding box with squared handles 1 e active areas on each side of the selected object or group of objects A rectangular shape will appear next to the cursor when moving it into the active area see the table in Chapter 3 1 2 Mouse Usage The object may be scaled along the x y or z axes by clicking the handle 1 e the active area on one side of the bounding box and dragging the mouse while the left mouse button is pressed Isotropic scaling may be performed by clicking into the bounding box and moving the mouse up or down while the middle mouse button or the Alt key and the left mouse button is pressed When several objects are selected only isotropic scaling is supported Group the ob jects first if you need to perform unisotropic scaling for several objects at a time For more information on the Scale mode please refer to Chapter 4 6 7 Object Properties Clipbox Select this command to box clip the selected object or object group along the axes of its bounding box The Clipbox mode is characterized by the cyan bounding box with squared handles 1 e active areas on each side of the selected object or group of objects When moving the cursor into the active area a scissors will appear next to the cursor see the table in Chapter 3 1 2 Mouse Usage The object may be clipped by c
32. to activate or deactivate the Camera view tool For more information on the Camera view tool please refer to Chapter 4 6 9 Polygon properties Select this command to activate or deactivate the Polygon properties tool For more information on the Polygon properties tool please refer to Chapter 4 6 6 Object properties Select this command to activate or deactivate the Object properties tool For more information on the Object properties tool please refer to Chapter 4 6 7 VGStudio 1 1 User s Manual 4 3 Menu Bar 4 3 7 Window Menu Click Window to open a pulldown menu containing the following entries Window Mew slice windows Mew 30 window HI Arrange mode 0 LH Arrange Mode 1 kd Arrange Mode 2 HH Arrange Mode 3 Cascade Fig 54 The Window menu e New slice windows Select this command to open the three slice windows within VGStu dio s workspace The menu entry remains disabled as long a these windows are open in the workspace e New 3D window Select this command to open the 3D window within VGStudio s work space The menu entry remains disabled as long a these windows are open in the workspace e Arrange modes and Cascade Click one of the Arrange modes 0 to 3 to choose a prede fined layout for the windows within the workspace VGStudio uses a Multiple Document Interface MDI The 3D window and the three slice windows may also be arranged arbitrar ily within the workspace by clicking into the title ba
33. to save a rendered image or a slice image to a file Sup ported file formats are TIFF JPEG BMP or PPM The rendered 3D image or one of the three slice images may be saved To save an image select one of the four windows in the workspace by clicking into the image View window 3D Scene view Camera view or one of the three slice windows and then selecting Save Image in the File menu Reminder The size width and height in pixels of a saved image is independent of a sal the applied zoom factor in the 3D or slice windows car ey 1 The size of a saved slice image is the original size of the cross section of the volume data set When saving a slice image only the cross section of the actual volume data set will be saved No bounding box cross sections or instruments will be saved in the image The size of a saved 3D image is the size width and height which is adjusted in the Render properties tool When saving a 3D image the full scene as shown in the 3D window will be saved including all instruments active bounding boxes coordi nate axes or grids To remove the bounding box of an object use the Deselect option in the Edit menu Print Setup Select this command to access the standard print options dialog box Print Select this command to print the active window You may select one of the three slice windows or the 3D window as the active window by clicking the title bar or into one of the windows You may also use the key
34. us on the Internet e mail support volumegraphics com world wide web http www volumegraphics com 2 VGStudio 1 1 User s Manual VGStudio 1 1 AS SSS S d DIICS a i E j r i Development Team Thomas Ginther Christoph Poliwoda Christof Reinhart Joachim Meiiner tetan Roth Christian Gosch Dirk Reinbach Martin Bergtold 2000 Volume Graphics GmbH All rights reserved Render engine YGL amp 2 1 YGL i 5 a registered trademark of Volume Graphics GmbH Germany Web http s www evo Email vgstudio ivolumegraphics com Volume Graphics Solutions about Voxels VGStudio 1 1 User s Manual VGStudio 1 1 Table of Contents i NEFOGUCTION CO VG SOU CIO Liersen a a E 11 1 1 Volume Graphics and VGStudio Ll sisisiscirssiissspaiidssikoieitenneenias oanien saias ainean aaa airain eao 12 1 2 Example Images Rendered by VGStudio 1 1 USersS eeccccccccossssssssssesceececocoosoosssssescecececosssossssssssssssssceee 13 1 3 ADOUE this Wlanial ccicacccccaciscesescacccseanaresesncesscenascesosedseascaassesasactseuesteesesescsedesssadsoesabactsdssscessesesssadeassracassensaes 14 1 4 Conventions Used in this Mamnilall occssccsccsssccccdvescossiacesesssncdisveieccucussetedeussanstececdsusiensssuadetedenssedesessaascdensiecese 15 1 5 Where to Get Additional Hel Pisiin aiaia 16 1 6 Feedback inisenisi a a a a Aa a a 17 2 Teala onn E 19 2 1 System Reguire MENIS iasoer aare a aeae aa ae a aa a aai eie 20 2
35. used to apply several parameters which define the appearance of VGStudio 66 ig Puslerences Fig 44 The Preferences dialog box with the General options index card selected Slice window mode The three orthogonal slice windows see Chapter 4 5 1 Slice Windows and Multiplanar Reformatting will show the slices in a right handed coordinate system if the Slice window mode is set to standard The three orthogonal slice windows will show the slices in a medical style if set to medical mode Most medical applications use left handed coordinate systems to present slice data to the users Classification tool mode VGStudio will startup either with the default Classification tool or in Window Level mode depending on which mode is set in this dialog VGStudio 1 1 User s Manual 4 3 Menu Bar 4 3 4 Object Menu Click Object to open a pulldown menu containing the following entries Object Enable wt Move Shitt Ctrl h m Rotate Shitt ctr R ml sale Shitt Ctrl S a Cliphox Shitt Ctri 8 Clipplane Shitt Ctrl C Reset Croup Ctrl Ungroup Ctr Create Reference Ctri R Fig 45 The Object menu Disable Select this command to disable an object or object group A disabled object will not be displayed in the scene No action can be applied to a disabled object you first have to enable it again To do so select the object in the Scene tree tool by clicking it and then se lecting the Enable option in the Object menu Th
36. 0 61 98 147 33 31 69 85 106 56 99 56 99 78 96 21 61 81 48 142 144 143 32 84 142 143 142 143 manipulation icons menu origin polygon reset selection voxel object group change name disable enable ungroup object manipulation icons object overview 31 84 116 define Region of Interest ROT delete all segments reset Region of Interest ROT object properties clipping position rotation scale Object relative mode Off file format opacity opacity curve copy paste reset reset to default reset to full opaque reset to full transparent opacity function opacity handles opacity manipulation area delete handle histogram insert handle move handle opacity function opacity handles segment borders segment names open a scene optimal settings image quality performance paste paste opacity curve performance optimal settings pixel polygon object TI 155 2 122 114 122 123 125 142 142 143 84 119 119 122 121 150 157 151 151 153 102 196 114 127 128 127 127 127 127 123 123 124 127 122 127 124 122 122 122 122 61 82 53 53 64 83 47 128 53 49 140 VGStudio 1 1 User s Manual polygon properties polygonal representation position preferences Dicom imports path HDF imports path images path objects path polygons path raw imports path scenes path preferences dialog box directories index card options index car
37. 00 y Jo 000 ie o 000 Rotation aoe 0 000 Standard Reset Apply Fig 147 The Advanced dialog of the Rotate index card The Advanced dialog provides you with an interface where you may enter absolute rotation values for the selected object The absolute rotation is defined by a normalized vector in the 3D space and a rotation angle around this vector Non normalized vectors may also be entered They will be normalized when the values are applied Type in the x y or z coordinates to define the vector around which you want to rotate the image or use the up and down arrows to increase or reduce the x y or z values Type in the absolute rotation angle around the axis defined by the x y or z value or use the up and down arrows to increase or reduce the rotation angle Press the Reset button to reset the orientation of the selected object to its original value Press the Apply button to activate the new values entered in the rotation dialog Scaling When the Scale index card is selected the bounding box of the selected object will be displayed in dark blue the color of the Scale mode VGStudio 1 1 User s Manual 145 4 VGStudio Interface amp Tools Object properties Pos Rotate Scale clip scaling m 17 000 E Ne Ii 00 2 f 000 i O00 Ii 100 i O00 Resolution 2 2 l A N E Reset Apply Fig 148 The Scale index cad of the Object properties d
38. 4 6 7 Object Selection and Deselection Before any object manipulation can be applied you have to select an object or a group of ob jects A bounding box around an object will indicate that the object is selected This means that the object is the active object to which actions may be applied When loading an object into VGStudio the object will automatically be the active object indicated by a green bounding box around the object You may deselect an object by selecting another object by clicking into the scene outside an object s bounding box or by clicking Deselect in the Edit menu alternatively you may also use the keyboard shortcut Alt D Click an object to select it A bounding box will appear around the ob ject Click outside an object s bounding box or press Alt D to deselect an object The bounding box around the object will disappear Fig 59 Select or deselect an object A bounding box around the object indicates that an ob ject is selected VGStudio 1 1 User s Manual 8 4 VGStudio Interface amp Tools Move n Click this icon to move the selected object or object group The Move mode is characterized by the green bounding box around the selected object or group of objects When moving the cursor into the bounding box it will take the shape of one vertical and one horizontal arrow see the table in Chapter 3 1 2 Mouse Usage The object may be moved in the image plane by clicking into the bound
39. GStudio 1 1 User s Manual 4 5 The Workspace ton is pressed to change the camera position By using two slice images the user will gain full 3D control over the camera position Grab one of the viewing angle handles and drag the View frus tum so that it becomes wider or more narrow This will change the viewing angle of your cam era The changes of the camera position will become visible in all images 1 e all slice images and the 3D window simultaneously m Ta a i J L A F Es ai Ay Aa i L q x oak a ytd Fig 87 Reduce or enlarge the view frustum by dragging the handles The up vector the up direction defined in scene coordinates of your camera may also be ad justed by clicking with the middle mouse button or with the left mouse button while holding the Alt key pressed into a slice window and dragging the mouse up or down while the middle mouse button is pressed This will rotate the rendered image around the viewing vector Fig 88 Rotate the image around the viewing vector The length of the viewing vector is of no importance VGStudio 1 1 User s Manual 105 4 VGStudio Interface amp Tools While moving the camera the slice images will show the three cross sections through the volume data with the appropriate handle either in camera position or the look at handle as the center of the three sections The active handle which marks the center of the slice sections will be dis played in r
40. Level Window mode Select this command to switch the classification tool into Level Window mode 4 6 2 Scene Tree The Scene tree shows all objects included in the scene It also shows the object type and the hi erarchical organization of objects in groups of objects The Scene tree may be used to select one or several objects in the scene Select a single object in the scene tree by clicking it with the left mouse button Use the Shift or Ctrl modifier to select several objects Keep the Ctrl key pressed VGStudio 1 1 User s Manual 133 4 VGStudio Interface amp Tools and select several objects in the Scene tree by clicking the objects with the left mouse button Keep the Shift key pressed and click a second object in the scene tree e g the last object in the row All objects in between the two selected objects will then also be selected Scene tree Cene tree EI amp group 1 o E gp jaw vol 1 a EF jaw vol 1 teterence 1 section 0 H ai jaw vol 1 fcopy 1 Gg wet x29 plane off 1 Fig 136 The Scene tree shows all objects that are included in the scene The following symbols are used in the Scene tree tool Object type Enabled Disabled Scene Object Voxel objects Polygon objects Reference of a voxel object Group of objects Age amp A e amp Section of an Object Sections Each data set in VGStudio s Scene tree contains a single section as default An object may con
41. Manual 2 5 Registering VGStudio 1 1 2 5 Registering VGStudio 1 1 To be eligible for technical support as well as receive information on bug fix updates and fea ture upgrades you must register your copy of VGStudio To register press the Create registra tion form button in the License dialog please refer to Chapter 4 3 8 Help Menu License update fill in the required information and send the registration form to Volume Graphics either by fax mail or e mail If you change your address after registering you may call or e mail us so we can update your record or send us a standard post office change of address notice See Chap ter 1 6 Feedback for more information on how to contact Volume Graphics directly VGStudio 1 1 User s Manual 25 26 2 Installation VGStudio 1 1 User s Manual 3 Getting Started This chapter explains how to get started using VGStudio by introducing some basic program concepts It covers the following topics e Launching the program e First steps with VGStudio e Exiting VGStudio e Image quality versus speed 3 Getting Started 3 1 Launching the Program To launch VGStudio MAX 1 0 for Windows open the Start menu Select the option Programs Volume Graphics VGStudio 1 1 You may also double click on a vgi File e g in your Win dows Explorer to start VGStudio 1 1 You may drag a vgi file on the VGStudio 1 1 icon to start VGStudio 1 1 with the appropriate file loaded automatically To launch
42. Object properties dialog 4 6 8 World View The World view tool is used to steer your view on the scene The position rotation and the viewing angle may be manipulated In the World view tool an overview of the current scene is displayed in form of the bounding boxes of each object or group of objects PE D p m k y Scene viewer he Viewing ange tt fao Fig 153 The World view tool of VGStudio 150 VGStudio 1 1 User s Manual 4 6 Tool Box You activate the World view tool by pressing the World view mode button in the icon bar or by clicking World view mode in the Scene Menu All changes can be observed in the 3D view window Changes in the World view tool will not affect the scene itself Click the Move button to activate the World view tool s Move mode wt oh The Move mode is characterized by the green color of the scene coordinate system axes in the World view tool The scene may be moved in the image plane by clicking into the Scene viewer area with the left mouse button and dragging the mouse while the left mouse button is pressed The scene may be moved forwards or backwards by clicking into the Scene viewer area and dragging the mouse while the middle mouse button or the Alt key and the left mouse button is pressed Using the Shift modifier in Move mode allows you to move the scene in vertical or horizontal direction Click the Rotation button to activate the World view tool s Rotate mo
43. Scatter HQ or Scatter Gradients algorithms e use large result image sizes e use oversampling factor of 3 0 or more e activate color rendering VGStudio 1 1 User s Manual 53 4 VGStudio Interface amp Tools This chapter will guide you through the various functions of VGStudio Before you actually start working with the program you should familiarize yourself with the various parts of the interface In this chapter the following parts of the interface will be explained in detail e Menu bar e Tool bar e Tool box e Slice windows e 3D window e Status bar 4 VGStudio Interface amp Tools 4 1 Basic Concepts of the VGStudio User Interface 4 1 1 2D slices and 3D images In the past working with volume or voxel data meant working with stacks of 2D image slices Radiologists got tenths of images from a CT scanner and viewed them slice by slice along the scan axis to get a 3D impression of the data Thanks to the upcoming computer technology radi ologists now have the possibility do use MPR Multi Planar Reconstruction image slices which means that they can view image stacks not only along the scan axis but also along all three axes of a voxel data set VGStudio overcomes the limitations of simple 2D image viewing It provides full 3D visualization and analysis functionality In addition VGStudio supports the MPR tech nology The VGStudio user interface includes a 3D view window as well as the 2D image view ing windows
44. Soft tissue is displayed in yel low the bone tissue in white VGStudio 1 1 User s Manual 43 3 Getting Started Fig 25 The 3D image after a color has been assigned to one of the segments The grayvalue segmentation allows to set up independent grayvalue ranges where opacity and color can be customized without affecting other segments A single segment may for example be extracted see Chapter 4 6 1 Classification Tool disabled or enabled by clicking with the right mouse button into segment 1 shown in the Opacity manipulation area A context menu will then open where you may for example select Disable segment to disable segment 1 The next functions explained here are the Clipbox and Clipplane functions Rotate the jaw into a position as shown in the following figure Fig 26 The 3D image in Rotate mode indicated by the red frame 44 VGStudio 1 1 User s Manual 3 2 First Steps with VGStudio Click the Clipbox icon in the icon bar The Clipbox mode is characterized by the cyan bounding box with squared handles 1 e active areas on each side of the selected object or group of objects When moving the cursor into the active area a scissors will appear next to the cursor as it is shown in the figures below Clip the object by clicking the active area on one side of the bounding box and dragging the mouse in ward while keeping the left mouse button pressed Fig 27 The 3D window in Clipbox mode indicated by the cy
45. User s Manual 1 Introduction to VGStudio 1 1 This chapter will help the user in getting accustomed with the program and its functions and gives an Overview of some basic concepts the user should keep in mind when using the program This chapter covers the following topics e Volume graphics and VGStudio e About this manual e Conventions used in this manual e Where to get additional help e Where to send feedback 1 Introduction to VGStudio 1 1 1 1 Volume Graphics and VGStudio 1 1 Volume rendering or to use a more general term volume graphics is a sub specialty of 3D computer graphics which deals with the discrete representation and visualization of objects rep resented as sampled data in three or more dimensions Volume graphics differs from traditional 3D graphics in that 3D graphics primarily deals with the representation of object surfaces whereas volume graphics deals with the representation of both object surfaces and interiors In volume graphics for example sample points such as CT or MRI scans are taken from the real world assigned color and transparency levels and are then projected directly onto the computer screen Image Slice Fig 1 Color and transparency levels are assigned to CT or MRI scans and are then projected directly onto the computer screen In recent years the popularity of volume graphics has grown considerably A few years ago volume graphics was still limited by the large amount of c
46. VGStudio 1 1 for Linux Unix enter the command vgstudiomax at the command prompt You may add a vgi file as command line option to start VGStudio MAX with the appro priate file loaded automatically C gt vestudiomax vgi file Example C gt vgstudiomax demo vgi You may drag a vgi file on the VGStudio icon to start VGStudio with the appropriate file loaded automatically Reminder When starting the program for the first time you have to enter your ani name and the license key For more information on the installation procedure see So Chapter 2 Installation After having launched the program the VGStudio application will appear on your screen with its startup screen The startup screen will disappear after a few seconds or upon pressing a key on your keyboard or a mouse button The VGStudio interface consists of seven main elements Title bar Menu bar Icon bar Slice windows 3D window Tool box Status bar 28 VGStudio 1 1 User s Manual 3 1 Launching the Program at Si ad ie a itt wl ia a foi i gs a i r 7 aie 1 al J a k Fig 4 The VGStudio interface after startup All the functions included in VGStudio are accessed either by selecting options in the main menu by clicking buttons in the icon bar by using the tools in the toolbox or via context menus which you open by clicking into an element with the right mouse button 3 1 1 Keyboard Usage Most VGStud
47. a Classification Preset selection l MONE Object overview Opacity manipulation area Segment 1 a Gray values Color manipulation area NUA Bi eooo o o mnl Fig 20 For grayvalue segmentation move the cursor to the right side of the Opacity manipulation area and drag the blue line The shape of the cursor will change as shown in the figure above Drag the blue line which ap pears on the left hand side of the Opacity manipulation area while keeping the left mouse but ton pressed The grayvalues to the left and right of the blue line will be displayed while dragging the line Drag the line to a grayvalue between 1300 and 1400 You can always move the line by dragging it to the left or right while keeping the left mouse button pressed VGStudio 1 1 User s Manual 41 3 Getting Started Classification Preset selection rove Object overview Opacity manipulation area Segment Segment 2 qos Gray values Color manipulation area NLA lt Fig 21 The blue line marks the border be tween two grayvalue segments The blue line will mark the border between two grayvalue segments Two segments have been created The left segment includes the noise air fat and muscle grayvalues the right segment includes the bone structure and metal objects To reduce the noise add a new handle in the left segment as you did before by using t
48. a Segment 1 qaamen z 5 a r ra a Gry values ani i E p F pacity function f Fig 108 The different elements of the Opacity manipulation area The grayvalue histogram of the active data set is displayed in the background of the opacity ma nipulation area You may zoom in or zoom out on the histogram or disable the histogram by clicking with the right mouse button into the Opacity manipulation area and then clicking His togram in the context menu Another menu will then open where you may select the appropriate function Disable Enable histogram Zoom in Zoom out or Zoom reset The default opacity mapping function will look like shown in the following figure The opacity function looks like a linear ramp from the opacity handle at the lowest darkest grayvalue with zero opacity to the opacity handle at the brightest grayvalue with maximum opacity Opacity manipulation area Gray values Fig 109 The default opacity mapping function The opacity function may be adjusted to any arbitrary shape New opacity handles may be in serted by clicking the desired position with the middle mouse button or with the left mouse but ton while keeping the Alt key pressed You may also insert a new handle by using the context menu which you open by clicking into the Opacity manipulation area with the right mouse button Click the desired position with the right mouse button and then select Insert handle in the context menu VGStud
49. al 3D graphics polygon graphics objects are represented as mathematical models Surfaces are subdivided into many small triangles or polygons which are assigned colors tex tures and levels of transparency or opacity P i Yoel Vaelume Element Fig 33 Objects in polygonal representation left and voxel representation right Volume graphics is a sub specialty of 3D computer graphics It deals with the discrete represen tation and visualization of objects represented as sampled data in three or more dimensions A volume voxel data set is a three dimensional array of voxels The term voxel is used to character ize a volume element it 1s a generalization of the notion of pixel that stands for a picture ele ment A volume data set usually contains values that have been obtained by some type of 3D scanning or sampling device or by a simulation process Typical sampling devices are x ray CAT MNR PET SPECT and Confocal Laser microscopy Each voxel consists of a position and a value The voxel position is a three tuple that specifies a position within the three dimensional voxel array The origin of the volume data set is considered to be the center of the first voxel 1 e the voxel with coordinates 0 0 0 The first coordinate of the voxel position represents the column the second coordinate represents the row and the third coordinate repre sents the image or slice Columns rows and images are numbered starting from 0 The voxe
50. al objects have been selected After grouping the objects a single bounding box around all the selected objects will be visible You may also use the keyboard shortcut Ctrl G to group objects See also Chapter 4 6 7 Object Properties Ungroup Select this command to ungroup an object group previously created with the Group command The Ungroup command remains disabled until an object group is se lected You may also use the keyboard shortcut Ctrl U to ungroup objects See also Chapter 4 6 7 Object Properties Reminder The clipping of an object group will be reset as soon as you ungroup the object group 136 Delete Select this command to delete any selected object in the scene Note that you can undo a deletion process by selecting the Undo command defined earlier Remember that you have to select the Undo command immediately after having deleted the object You may also use the Del key to delete an object Duplicate The Duplicate option is the fastest possibility to generate and use a copy of an object You may also use the keyboard shortcut Ctrl D to duplicate objects In contrast to the Copy and Paste command the Duplicate command does not use the clipboard The cop ied object will be placed directly into the scene where it can be used immediately When du plicating an object VGStudio places the object directly above the original object The relative position will be used as default offset If the new object is moved i
51. ales department by sending an e mail to info volumegrapics com or one of our sales representatives VGStudio 1 1 User s Manual 1 6 Feedback 1 6 Feedback We are very interested in your comments on VGStudio Many of VGStudio s changes and 1m provements over the years were based upon user requests and input If you have comments or feature requests please send them to us via the World Wide Web http www volumegraphics com e mail vgstudio volumegraphics com You may also send a letter or fax to the following address fax number Volume Graphics GmbH VGStudio Product Manager Wieblinger Weg 92a D 69123 Heidelberg Germany Tel 49 6221 73920 60 Fax 49 6221 73920 88 VGStudio 1 1 User s Manual 17 18 1 Introduction to VGStudio 1 1 VGStudio 1 1 User s Manual 2 Installation This chapter gives general information on installation requirements and on the installation itself Each section provides the users with instructions for both Windows and Unix operating systems Find the section that is appropriate for your operating system This chapter covers the following topics e System requirements e Installation instructions e Registering VGStudio 2 Installation 2 1 System Requirements This section lists the minimum system requirements for Windows and Unix users Refer to the section that 1s appropriate for you Also see the section on VGStudio and memory usage in the Appendix Windows Micros
52. alues Group the objects first if you want to clip several objects at a time Object properties pos Rotate Scale cip Cippo He 0 000 256 O00 T 80 000 82 000 E i 0 000 244 000 Fig 149 The Clipbox index card of the Object properties dialog Press the Reset button to remove the clipping of the selected object Press the Apply button to activate the appropriate parameters Clipplane Select this command to clip the selected object or object group by an arbitrary clipplane The Clipplane mode is characterized by the cyan bounding box with a normal vector on one side of the actual object The object may be clipped along an arbitrary clipplane by typing VGStudio 1 1 User s Manual 147 4 VGStudio Interface amp Tools in the values for the arbitrary clipplanes in the Clipplane dialog of the Clip index card The clipplane will be disabled if several objects are selected Group the objects first if you want to clip several objects with one clipplane at a time Object properties pos Rotate Scale cip Clipplane normal m T E O00 Jo 000 0 000 Clipplane origin m 56 000 E4500 22 000 Clipplane distance Distance 256 000 Clipbox Reset Apply Fig 150 The Clipplane index card of the Object properties dialog The arbitrary clipplane is defined by the clipplane s normal vector and the distance between the clipplane and the origin of the c
53. an bounding box and the scissors displayed next to the cursor when moving it into an active area Remove the clipping by dragging the handles outward or by clicking the Undo button kj Most features included in VGStudio 1 1 can be undone After you have removed the clipping the 3D image should look like the following image VGStudio 1 1 User s Manual 45 3 Getting Started Fig 28 The 3D view in Clipbox mode after the previous clipping has been undone Click the Clipplane icon to activate the Clipplane mode F The Clipplane mode is characterized by the cyan bounding box with a normal vector on one side of the currently selected object When moving the cursor into the bounding box a scissors will appear next to the cursor The object may be clipped along an arbitrary clipplane by dragging the mouse up and down while the middle mouse button or the Alt key and the left mouse button is pressed Press the middle mouse button while positioning the mouse inside the active area and drag the mouse down to move the clipplane inward Drag the mouse inside the active area while keeping the left mouse button pressed to rotate the clipplane in any arbitrary direction Liven muses dpan while MOO MOU Gis DS Seo Fig 29 Move the object along an arbitrary clipplane by dragging the mouse up or down while the middle mouse button is pressed By dragging the mouse inside the active area while the left mouse button is pressed the clipplan
54. andle in the menu Reset opacity curve Select this command to open the following menu Detault Full transparent Full opaque Default Select this command to apply the default opacity function to the appropriate segment Full transparent Select this command to set the opacity to totally transparent Full opaque Select this command to set the opacity to totally opaque Copy opacity curve Select this command to copy the current segment s opacity curve into the clipboard Use Paste opacity curve to paste the copied opacity settings to another object or segment Paste opacity curve Select this command to paste a previously copied opacity curve to another object or segment New segment Select this command to generate a new segment Use the following menu to decide on which side of the current segment the new segment is to be generated 1 e either on VGStudio 1 1 User s Manual 121 4 VGStudio Interface amp Tools the left hand side or the right hand side At lett side At right side Cut segment Select this command to cut the current segment Use the following menu to decide which segment should be expanded when cutting the current segment Expand lett neighboor Expand right ne ighkboor Delete segment Select this command to delete the current segment Use the following menu to decide which segment should be expanded when deleting the current segment Expand lett neighboor Expand right neighboor I
55. arameters a ua ph focal distance 700 eye distance RE W auto Fig 143 The Stereo properties dialog VGStudio 1 1 User s Manual 141 4 VGStudio Interface amp Tools Select one of the following rendering modes in the Stereo parameters listbox e Red green red on right eye e Red blue red on right eye e Interlaced v ertical e g for autostereoscopic 3D displays VGStudio 1 1 supports the D4D display The D4D is a flat autostereoscopic 3D display the new type of computer output device for true 3D visual representation of data or other three dimensional information Information on the D4D can be found on http kastor inf tu dresden de D4D e Interlaced h orizontal e g for HMD devices Select a stereo mode in the listbox to activate stereo rendering Use the Swap checkbox to swap between left and right images By changing the Focal distance and Eye distance values you may adjust the stereo projection parameters Simply type in the appropriate value or use the up and down arrows to increase or reduce the values If the Auto checkbox is activated a default relation of 30 1 between focal distance and eye dis tance will be applied While a stereo mode is activated images will be saved as stereo images when the Save Image option in the File menu is selected 4 6 6 Polygon Properties Select a polygon object in the scene and use the Polygon properties tool to adjust the polygon rendering mode for the select
56. ay also use the keyboard shortcut Ctrl C to copy objects e Paste Select this command to paste previously copied or cut objects into a scene You may also use the keyboard shortcut Ctrl V to paste objects e Delete Select this command to delete any selected object in the scene Note that you can undo this action by using the Undo command explained above You must however undo your action immediately after having deleted the object You may also use the Del key to de lete an object e Duplicate The Duplicate option is the fastest possibility to generate and use a copy of an object You may also use the keyboard shortcut Ctrl D to duplicate objects In contrast to the Copy and Paste command the duplicate command does not use the clipboard The copied object will be placed directly into the scene where it can be used immediately When dupli cating an object VGStudio places the object directly above the original object The relative position will be used as default offset If the new object is moved its offset to the original object is used as offset for every new duplication process This procedure is called smart duplicate Reminder The offset adjusted during a smart duplicate will be set to its default E a value zero as soon as the duplicated object is deselected or another object is se r 5 lected ae e Select All Select this command to select all objects in the scene You may also use the keyboard shortcut Ctrl A to
57. ayed in the Opacity manipulation area may be changed To do so simply click the name with the left mouse button and type in the new name Opacity manipulation area Segment 1 Seqmen 2 Fig 117 Change the segment name in the Opac ity manipulation area by clicking the name with the left mouse button and then typing in the new name Press the right mouse button within the Opacity manipulation area to the context menu Fea tures such as Copy opacity curve Paste opacity curve Cut segment and Delete segment may be disabled this depends on the position you click with the right mouse button within the Opac ity manipulation area In the context menu of the Opacity manipulation area you will find the following functions 120 VGStudio 1 1 User s Manual 4 6 Tool Box Insert handle Delete handle Reset opacity curve Copy opacity curve Faste opacity curve Hew segment Cut segment Delete segment Disable segment Extract segment Histogram Change to levelAvindow mode Fig 118 The context Save preset menu of the Opacity ma Delete preset nipulation area Insert handle Select this command to generate a new opacity handle in the Opacity ma nipulation area The handle will be inserted at the position you click with the right mouse button Delete handle Select this command to remove an opacity handle from the Opacity ma nipulation area Click the handle to be removed with the right mouse button and then select Delete h
58. b Delete segment b Disable segment Extract segment Histogram b Fig 120 To extract a segment click into the segment with the right mouse button and select Extract segment from the context menu In the Opacity manipulation area click into Segment 2 named soft tissue with the right mouse button Select Extract segment in the context menu After the extraction process only the extracted soft tissue segment with a grayvalue range from 659 to 1443 will be shown in the Classification tool Classification one selection MOME Object overview Opacity manipulation area Gray values e manipulation area I Fig 121 After the extraction process only the soft tissue segment will be shown 124 VGStudio 1 1 User s Manual 4 6 Tool Box In the Scene tree and in the Object selection box the new object will be displayed with the fol lowing name soft tissue extracted of CT scan of a human jaw 1 Scene tree scene tree aie CT scan of a human jaw ha ai soft tissue extracted of CT scan of a human jawe 1 Fig 122 In the Scene tree the newly created object will be displayed The newly created object only includes the soft tissue and may now be manipulated independ ently from all other objects in the scene like any other object It may be positioned rotated scaled or clipped the opacity and color mapping may also be changed In our example the soft tis
59. ble one at a time depending on the mode you are currently working in If you are working in World view mode indi cated in the 3D view window with the text scene view you may switch to Camera mode and vice versa Axis Select this command to activate or deactivate the axes within a scene A small check mark in front of the menu item indicates that the axes are activated The axes can be custom ized within the Grid Axes amp Instrument properties dialog which you open by clicking Properties in the Scene menu see below Grid Select this command to activate or deactivate the grid within a scene A small check mark in front of the menu item indicates that the grid 1s activated The grid can be custom ized within the Grid Axes amp Instrument properties dialog which you open by clicking Properties in the Scene menu see below Instrument Select this command to activate or deactivate the 3D cursor within a scene A small check mark in front of the menu item indicates that the instrument is activated You can move the cursor around in the three slice windows The cursor position and the appropri ate gray or color values are displayed in the status line of the VGStudio user interface The instrument can be customized within the Grid Axes amp Instrument properties dialog which you open by clicking Properties in the Scene menu see below VGStudio 1 1 User s Manual 4 3 Menu Bar e Properties Select this command to open the Grid
60. board shortcut Ctrl P to print the active window VGStudio 1 1 User s Manual 61 4 VGStudio Interface amp Tools Reminder The Print option will scale the printed image so that it fits best to the page When printing a slice image only the cross section of the actual volume data set will be printed No bounding box cross sections or instruments will be printed When printing a 3D image the full scene as it is shown in the 3D window will be printed including all instruments active bounding boxes coordinate axes or grids To remove the bounding box of an object use the Deselect option in the Edit menu e Quit Select this command to exit VGStudio Note that if there is an open scene that you have not yet saved VGStudio will ask you whether you want to save your changes prior to exiting You may also use the keyboard shortcut Alt F4 to exit VGStudio e Lust of the last four edited scenes 4 3 2 Edit Menu Click Edit to open a pulldown menu containing the following entries Edit EY undo group object Ctrl z2 fal edar hob passihE Cte y Cut Ctr Copy ctrl E FA Paste Ctre Delete Duplicate Ctrl D Select All Ctrl 4 Deselect Alt D Select Inverse AR Preferences Fig 41 The Edit menu e Undo Select this command to undo your previous action This menu item changes depend ing on the action you last performed For instance if you have pasted an object into your scene the text reads undo paste object and t
61. but in those instances when there are differences most often with key commands the manual will list both commands VGStudio 1 1 User s Manual 15 1 Introduction to VGStudio 1 1 1 5 Where to Get Additional Help Check the table of contents or the index whenever you need to locate information on a particular function If you cannot find the information there are other ways to get help Please also refer to Chapter 2 5 Registering VGStudio 1 1 16 Installation amp Information Card Provides latest information on the current VGStudio 1 1 release and information on the installation procedure for your operating system Volume Graphics Web Site The Internet is a quick way to get answers to your questions You can use the Volume Graphics web site at www volumegraphics com as a technical sup port resource E Mail Send an e mail to Volume Graphics at vgstudio volumegraphics com Volume Graphics Technical Support lIf none of the resources mentioned above provides the answer you can contact the Volume Graphics technical support by sending an e mail to vgstudio volumegraphics com or one of our sales representatives Please be at your com puter and have your registration number available when you call Volume Graphics Sales Our friendly and knowledgeable sales personnel can answer basic questions about product capabilities and give information on other Volume Graphics prod ucts which may fit your needs You may contact our s
62. camera position look at point up vector and viewing angle For more information see Chapter 4 6 9 VGStudio users will be able to perform an arbitrary data walkthrough when activating the Cam era view mode A camera may be placed into any position within the scene or even within a data set The viewing direction and viewing angle may also be chosen arbitrarily VGStudio 1 1 User s Manual 103 4 VGStudio Interface amp Tools Up vector Camera position Scene with data set Fig 54 The Camera view mode allows you to view your data from inside You may adjust all camera parameters shown here according to your needs The camera symbol will appear in all slice images after having activated the Camera view mode The camera symbol looks as follows Fig 85 The camera symbol as it is dis played in the slice images Several handles are included in the camera symbol The Camera position handle is marked with a small circle The Look at point is marked by the tip of the viewing vector The two front edges of the View frustum are the viewing angle handles i View frustum i Camera gt position X Look at point l Viewin angle handle i Fig 86 All camera parameters may be changed by dragging the handles Each handle may be manipulated by using the mouse To do so click the camera handle in one of the slice images with the left mouse button and then drag the handle while the left mouse but 104 V
63. d Preset selection preview auto scan checkbox region of interest print print setup PROCESSORS properties axis grid instrument quit Raw volume import wizard redo reference region of interest registering Volume Graphics remove handle render properties motion smooting rendering algorithms result image size rendering in monochrome in true color rendering algorithms maximum projection scatter scatter gradients scatter HQ sum along ray x ray rendering quality rendering speed representation polygonal voxel resampling reset VGStudio 1 1 User s Manual 7 Index 77 150 49 151 65 66 116 180 192 180 192 196 180 192 195 63 82 63 21 77 145 53 49 49 178 190 195 70 108 reset opacity curve resolution area result image size ROI rotate advanced dialog standard dialog rotation absolute save save as save image save object scale scatter gradient algorithm scatter algorithm scatter HQ algorithm scene axes grid menu origin tree utilities icons view viewer Scene relative mode segment apply color create new cut delete disable enable extract generate segment borders segment color copy export import paste set segment name change select all select inverse selection of an object setting preferences shadow light source ambient diffuse slice selection box 127 154 146 119 69 87 107 151 153 152 153 61 82 61 62 62 70 88 107 153 145
64. de w The Rotate mode is characterized by the red color of the scene coordinate system axes in the World view tool The scene may be rotated around the x or y axes of the image plane in the Scene viewer window by clicking into the Scene viewer area with the left mouse button and dragging the mouse while the left mouse button is pressed The scene may be rotated around the viewing direction by clicking into the Scene viewer area and moving the mouse while the middle mouse button or the Alt key and the left mouse button is pressed Using the Shift modifier in Rotate mode allows you to rotate the scene around the vertical or horizontal axes of the image plane Click one of the six Default view buttons to view the scene either from the front back left right top or bottom TETIT The distance between the observer and the scene s center which can be adjusted in Move mode will remain unchanged when one of the Default view buttons is pressed Drag the Viewing angle slider to the left or right or type in the desired value to adjust the view ing angle By clicking into the Scene viewer window with the right mouse button you open the following context menu VGStudio 1 1 User s Manual 151 4 VGStudio Interface amp Tools When clicking Zoom the following menu will be opened Zoom F Move Rotate Reset Fig 154 The context menu of the Scene viewer area The Scene viewer window may be zoomed in or out Cl
65. delete the selected preset Keep in mind that default Presets can not be deleted 112 VGStudio 1 1 User s Manual 4 6 Tool Box Object overview Advanced mode The Object overview section of the Classification tool is divided into two parts i e the opacity area which shows the grayscale to opacity mapping function and the color area which shows the color mapping a Color area Fig 98 The Object overview section is divided into two parts i e the opacity area and the color area As the name says the Object overview section provides the user with an overview of the entire grayscale and opacity range as well as the color settings of the selected object To display the grayscale and opacity range of the active object click with the left mouse button into the opacity area of the Object overview section The values will disappear as soon as you release the mouse button Object overview Fig 99 When clicking into the opacity area of the Object overview section the gray scale and opacity values of the active ob ject will be displayed The Object overview section may also be used to define a Region of Interest ROD within the opacity area The ROI will be displayed enlarged in the Opacity manipulation area of the clas sification tool VGStudio 1 1 User s Manual 113 4 VGStudio Interface amp Tools Fig 100 Define regions of interest in the Object overview section of the Classification tool By
66. der lined letter or by using the cursor keys to highlight it and then pressing lt Enter gt Menu items that appear in gray are currently not available In the following sections you will find a description of each of these menus in the order in which they appear in the menu bar 4 3 1 File Menu Click File to open a pulldown menu containing the following entries i Hew Ctrl hy pe Open Ctrl O LA DAVE Cirl s Dave aS Fiz Merge object Save object Import b Import DICOM images Export b Save Image Print setup 48 Print Ctrl F Gui AR F 4 1 Ewgtwgdenowdemomatcheda wagi Id atemmedica datadata raw mr head vai joo imnedica data Wata_ravy Waciatumar gi hice GStudioidata medicalicthead vi Fig 39 The File menu VGStudio 1 1 User s Manual 59 60 4 VGStudio Interface amp Tools New Select this command to create a new scene Note that selecting this entry will close the scene you are currently working on After you have created a scene you can save it by using the Save command The scene can be accessed again using the Open command Both commands are described below You may also use the keyboard shortcut Ctrl N to create a new scene Open Select this command to open an existing scene You may load Volume Graphics Info files vgi extension as well as old info files info extension by selecting the desired file and clicking Open or by simply double clicking the file in the Ope
67. des an easy to use interface which allows to apply a simple Opacity ramp with a defined width and center Window leveling is mostly used and well known in the medical community Advanced mode allows the user to apply arbitrary opacity functions which can not be generated by using a simple ramp Both modes are described in this chapter The Classification tool consists of several elements e Preset selection In Advanced mode In Level Window mode e Object overview e Level Window area e Opacity manipulation area e Opacity manipulation area e Color manipulation area Preset selection The Preset selection contains a set of predefined Window Level Opacity and color settings Clicking the Preset selection will show several predefined settings Clicking one of these presets changes the Window and Level settings or the opacity function in the classification tool to the preset values You may apply the various presets to see which works best for displaying the vol ume Classification Preset selection NONE z Preset selection ma preset Ramp T Bone T Tissue CT Lung CT Liver CT Sbdomen T Bone Tizsue CT COLOR 2 ee MR Heacd Fig 95 Select a classification tool preset from the pull down list VGStudio 1 1 User s Manual 111 4 VGStudio Interface amp Tools The following presets for medical users are included as default and therefore may not be re moved from the preset list Ramp Inverse Ramp CT Bo
68. dio 1 1 User s Manual 183 5 Importing amp Exporting Data 5 1 5 Importing ANALYZE Data VGStudio is capable to import data stored in the Analyze file format Select the Import Analyze volume option in the File menu to load Analyze volume data files into VGStudio More information on the Analyze file format can be found under the following internet address http www mayo edu bir analyze AnalyzeFileInfo html 5 1 6 Importing DICOM Data Select the Import DICOM image option in the File menu to load DICOM volume data or im age files into VGStudio Use the file dialog to select one or several data files The Dicom import dialog will pop up Select a study and acquistion to be imported Press OK to load the data or Cancel to abort the operation le vgstudio_exe Please select study and acquisition number Patient CT Example an OK Details Cancel Fig 183 The Import Dicom files window A Warning dialog may come up in case that you import DICOM image series with non equal slice distances or in case that the slice distance is more than three times the pixel resolution lel GStudio warning E4 Significant difference between pixel spacing and slice distance detected Do you want to resample dataset Fig 184 Resampling warning Pop up within the slices Press Yes to resample the data The software will calculate additional slices by trilinear resampling This will result in a better 3D image q
69. direction by clicking into the bounding box and dragging the mouse while the middle mouse button or the Alt key and the left mouse button is pressed The whole bounding box may be used as active area to apply the appropriate action Using the Shift modifier in Rotate mode allows you to rotate the object e1 ther around the vertical or horizontal axes of the 3D window image plane For more information on the Rotate mode please refer to Chapter 4 6 7 Object Properties Fig 61 The 3D window in Rotate mode indicated by the red bounding box and the ball with arrows dis played next to the cursor when moving it into an ac tive area VGStudio 1 1 User s Manual 83 4 VGStudio Interface amp Tools Scaling Click this icon to scale the selected object or object group The Scale mode is characterized by the dark blue bounding box with squared handles 1 e active areas on each side of the selected object or group of objects A rectangular shape will appear next to the cursor when moving it into the active area see the table in Chapter 3 1 2 Mouse Usage The object may be scaled along its x y or z axes by clicking the handle 1 e the active area of one side of the bounding box and dragging the mouse while the left mouse button is pressed Isotropic scaling may be performed by clicking into the bounding box and moving the mouse up or down while the mid dle mouse button or the Alt key and the left mouse button is pressed When several obj
70. e Enable and Disable menu options will toggle in the object menu 1 e will only be visible one at a time Enable Select this command to enable a previously disabled object or object group To enable an object select a disabled object in the Scene tree tool by clicking it and then select ing the Enable option in the Object menu The Enable and Disable menu options will tog gle in the object menu 1 e will only be visible one at a time Move Select this command to move the selected object or object group The Move mode is characterized by the green bounding box around the selected object or group of objects When moving the cursor into the bounding box it will take the shape of one vertical and one horizontal arrow see the table in Chapter 3 1 2 Mouse Usage The object may be moved in the image plane by clicking into the bounding box and dragging the mouse while the left mouse button is pressed The object may be moved forwards or backwards and thus will be enlarged or reduced by clicking into the bounding box and dragging the mouse while the middle mouse button or the Alt key and the left mouse button 1s pressed The whole bound ing box may be used as active area to apply the appropriate action For more information on the Move mode please refer to Chapter 4 6 7 Object Properties Rotate Select this command to rotate the selected object or object group The Rotate mode is characterized by the red bounding box around the selected objec
71. e The shadows appear to be bent The shadows rendered by VGStudio 1 1 are bent due to the lighting model used in VGStu dio s renderer This behavior will be corrected in one of the next VGStudio releases e Windows NT 4 0 crashes when visualizing very large amounts of data Under certain conditions Windows NT 4 0 with Service Pack 5 or lower may crash when visualizing very large data amounts using up almost all available memory RAM Swap on your system To correct this fault install the latest Windows NT 4 0 Service Pack e VGStudio 1 1 crashes during printing on a Linux system VGStudio 1 1 crashes when printing on a Linux system where no valid printer is configured Please refer to your Linux distribution s manual and set up a printer VGStudio 1 1 User s Manual 193 6 Appendix 194 VGStudio 1 1 User s Manual 7 Index 3D instrument 3D window about VGStudio active areas active handle axis axis properties background color bounding box camera mode camera position default view buttons look at point up vector view frustum viewing angle camera position camera symbol camera view camera position look at point up vector view frustum viewing angle camera view mode Center CFG file CFG file options classification classification tool color manipulation area object overview object selection opacity manipulation area clipboard clipbox clipping clipplane distance normal vector origin color apply co
72. e divided into five main categories Standard icon section D ce lad d E ie Object manipulation section E w Sok Scene utilities section he 1 E View selection section E Window layout tools section H E od H What s this section Lti 4 4 1 Standard Icon Section New L New Click this icon to create a new scene Note that selecting this command will close the scene you are currently working on After you have created a scene you can save it by using the Save command The scene can be accessed again using the Open command Both commands are described below You may also use the keyboard shortcut Ctrl N to create a new scene 78 VGStudio 1 1 User s Manual 4 4 Icon Bar Open al Lar Open Click this icon to open an existing scene You may load Volume Graphics Info files vgi extension as well as old info files info extension by selecting the desired file and clicking Open or by simply double clicking the file in the Open info file dialog You may also use the keyboard shortcut Ctrl O to open an existing scene Save Save Click this icon to save your work You should save your work frequently throughout the scene creation process Saving a scene will generate a Volume Graphics Info file vgi exten sion The vgi file includes data relevant information such as the file name and path data type file type file size and data mapping as well as scene relevant information such as light settings rendering
73. e of 1 every second voxel will be skipped in the selected direction To skip voxels in z direction remove the appropriate files from the list of selected files see step 1 and step 2 The Preview function allows you to preview the new settings 168 VGStudio 1 1 User s Manual 5 1 Importing Data Step 8 Internal data representation Biel Es le Import tool Load as Mow specify the data representation the application should use to handle the volume unsigned Skit Resolution saa eee p E YE E T E Data range mapping Scan File Jo to 255 Scan Ro maps to o Bet E to 258 Preview Cancel Fig 167 Specify the data representation The data type may be changed while loading data into VGStudio e g a 32 bit floating point data set on your hard disk may be mapped to a 16 bit integer data representation In this case this would reduce the amount of memory needed for visualization by a factor of two Any data type may be mapped to any other data type The only exception are RGBA data sets He Reminder RGBA data cannot be mapped to any other data representation Also ae monochrome data types may not be mapped to RGBA data VGStudio 1 1 User s Manual 169 5 Importing amp Exporting Data unsigned 8bit unsigned 8bit signed 8bit signed 8bit unsigned 16bit unsigned 16bit signed 16bit may be mapped to signed 16bit unsigned 32bit unsigned 32bit signed 32bit signed 32bit 32bit float 32b
74. e quality Higher over sampling values may enhance the image quality again In scenes that include objects with different scaling values you should scale up all objects so that the smallest ob 146 VGStudio 1 1 User s Manual 4 6 Tool Box ject will have an effective scaling value of at least 1 0 Clipping When the Clip index card is selected the bounding box of the selected object will be displayed in cyan the color of the Clip mode The index card Clip provides the VGStudio user with two different interfaces to clip the selected object in the scene 1 e the Clipbox dialog and the Clipplane dialog Use the Clipbox Clipplane toggle button to switch between the two modes All parameters in the Clipbox or Clipplane dialogs are in object voxel coordinates Clipbox Select this command to box clip the selected object or object group along the axes of its bounding box The Clipbox mode is characterized by the cyan bounding box with squared handles 1 e active areas on each side of the selected object or group of objects a small scissors will appear next to the cursor when you place it on one of the handles The object may be clipped by typing in the position of each of the six clipplanes on the Clip index card Use the two values for each coordinate axis to apply a clipplane to all sides of the selected object Type in the values for the clipplane position or use the up and down arrows to increase or reduce the clip plane position v
75. e selection E Import tool OFX Fileselection Please select the files containing the slices and specify the proper order You can change the fileorder by using drag drop or the Sortbutton Jwodaksakoyv 20000 tit Jovogtaksakoy woo tit Jiwodlaksakov 2002 tit Jwodlaksakoy 20003 tit Jovqtaksakoy wo tit Jowoaksakoy wos tit ie Jwodlaksakoy 0006 tit Jovoqtaksakoy woo tit Jowoaksakoy one tit Jwodaksakov 0009 tit ial ee d M eld Files Sort Filetype ooo ooo Tiff Images Add Remove Numbers Up x pats lee fe Mest Cancel Fig 160 Select the files you want to import and add them to the list Click Add to open a file selection dialog Select one or several files and click Open The list with the selected files will then be displayed in the Import tool window To add more files to the list click again Add and repeat the procedure To remove files from the list select one or several files and click Remove You may also drag the selected files on the remove button to delete them from the list The files will only be removed from the list and will not be deleted from the hard disk or other data source 162 VGStudio 1 1 User s Manual 5 1 Importing Data Step 3 File order Cov Stutiostuntstuo222 bmp CouyvitGstutiostuntstu0208 bmp Cov Stutiostuntstul 7 0 mp C Ww Stutiostuntstule7 2 bmp Coyvtstutiostuntstuo1 4 bmp C Ww Stutiostuntstul 1 6 mp C Ww Stutiostuntstul 1 8 mp Cov S
76. e slice im ages Fit to scene Fit to primitive Actual Preels The slice window may be zoomed in enlarged or zoomed out reduced These functions may also be applied by using the zoom buttons in the lower right corner of the slice win dows The images will then be enlarged or reduced by a preset zoom factor The Fit to scene option will zoom the slice window so that all objects included in the scene may be seen The Fit to object option allows to zoom the active object so that it is displayed with maximum zoom factor The Actual Pixels option applies a zoom factor so that one pixel in the image of the slice window will be one pixel on your screen Use original color Select this command to display the slice images in its original color brightness and contrast settings Use classification color Select this command to apply the color brightness and contrast settings of the classification tool to the slice images VGStudio 1 1 User s Manual 4 5 The Workspace e Object relative mode Select this command to switch the three orthogonal slice windows into Object relative mode The object will be sliced along the axes of the object coordinate system The originally scanned slice data will be displayed in this case _ Scene coordinate system Fig 77 MRI scan sliced in object relative VGStudio 1 1 User s Manual 97 98 4 VGStudio Interface amp Tools Scene relative mode Select this command to switch
77. e while the middle mouse button or the Alt key and the left mouse button is pressed The whole bound ing box may be used as active area to apply the appropriate action Using the Shift modifier in Move mode allows you to pan the object along either the vertical or horizontal direction of the 3D window image plane For more information on the Move mode please refer to Chap ter 4 6 7 Object Properties VGStudio 1 1 User s Manual 101 4 VGStudio Interface amp Tools Rotate Select this command to rotate the selected object or object group The Rotate mode is characterized by the red bounding box around the selected object or group of ob jects When moving the cursor into the bounding box it will take the shape of one vertical and one horizontal circular arrow see the table in Chapter 3 1 2 Mouse Usage The object may be rotated around the x or y axes of the image plane by clicking into the bounding box and dragging the mouse while the left mouse button is pressed The object may be rotated around the viewing direction by clicking into the bounding box and dragging the mouse while the middle mouse button or the Alt key and the left mouse button is pressed The whole bounding box may be used as active area to apply the appropriate action Using the Shift modifier in Rotate mode allows you to rotate the object in either around the vertical or horizontal axes of the 3D window image plane For more information on the Rotate mode please refer
78. e will be rotated in any arbitrary direction 46 VGStudio 1 1 User s Manual 3 2 First Steps with VGStudio You may save your current work at any time by using the Save or Save as option in the File menu As an example use the Save as option and name the scene jawl the original file will then not be overwritten The file extension vgi Volume Graphics Info file will be added automatically and therefore has not to be added by you To reload the current scene you may use the Open option in the File menu A single image such as the rendered 3D image or one of the slice images may be saved by select ing the appropriate image window and using the Save image option in the File menu 3 2 1 Voxel Objects Polygon Objects and Scenes All objects loaded into VGStudio will be placed into the Scene The scene is the virtual space displayed in VGStudio s 3D window By default the scene coordinate axes will be displayed on your screen as shown in the following figure Fig 30 The VGStudio scene coordinate system The default coordinate system used by VGStudio is right handed with the coordinate origin in the lower left corner The coordinate origin is on the left side of a body x at the front y and at the feet z By default the positive x direction in the scene runs from left to right The posi tive y direction in the scene runs from the front to the back of the screen plane The positive z direction in the scene runs
79. ects are selected only isotropic scaling is supported Group the objects first if you need to perform uni sotropic scaling for several objects at a time For more information on the Scale mode please refer to Chapter 4 6 7 Object Properties Fig 62 The 3D window in Scale mode indicated by the blue bounding box and the perspective box dis played next to the cursor when moving it into an ac tive area 84 VGStudio 1 1 User s Manual 4 4 Icon Bar Clipbox att Click this icon to box clip the selected object or object group along the axes of its bounding box The Clipbox mode is characterized by the cyan bounding box with squared handles 1 e active areas on each side of the selected object or group of objects When moving the cursor into the active area a scissors will appear next to the cursor see the table in Chapter 3 1 2 Mouse Us age The object may be clipped by clicking one of the handles of the bounding box and drag ging the mouse along the desired clip direction while the left mouse button is pressed The box clipping will be disabled if several objects where selected Group the objects first if you want to clip several objects at a time For more information on the Clipbox mode please refer to Chap ter 4 6 7 Object Properties Fig 63 The 3D window in Clipbox mode indicated by the cyan bounding box and the scissors displayed next to the cursor when moving it into an active area Clipplane i Click this icon
80. ed The following image shows the slice images with the camera tool activated The look at handle is the active handle and the slices show the sections with the look at handle as center All camera parameters described here may be adjusted exactly by typing in numerical values in the Camera view tool For more information on this tool please refer to Chapter 4 6 9 Camera View T a Veinddow jcamera we Mi C Franial fer slices pa abe sal _ _ Ct lt BA ea Fig 89 The 3D window and the slice images while the Camera view mode is selected Reminder The camera and look at position are defined in scene coordinates while most of the other tools are displayed in object coordinates Also the color coding in the slice tools may not correspond to the color coding of the camera tool in case of a rotated object 106 VGStudio 1 1 User s Manual 4 6 Tool Box 4 6 Tool Box The tool box is located on the right hand side of the VGStudio user interface The activated tools will all be located in the tool box You may scroll through the tool box by means of the scroll bar located on the right hand side of the tool box vns ihabriias nr nterne Pij E Re Oe O DATEMA TEA AT TTEA m e Pekr 2D pebetet lg SLE Sa el lt lt y ho 1 E T g Fig 90 The tool box of VGStudio Tools can be enabled or disabled To do so click the corresponding menu item in the Tools menu A check mark next to the
81. ed object polygon mode C wireframe Zolid flat fill flat shading cy i solid smooth fill Ls r C smooth shading Fig 144 The Polygon properties dialog Choose between a shading mode or wireframe mode If no polygon object is selected the Poly gon properties tool will be disabled 142 VGStudio 1 1 User s Manual 4 6 Tool Box 4 6 7 Object Properties The Object properties tool provides four index cards for the different kinds of actions which may be applied to an object 1 e translation rotation scaling and clipping Each index card allows you to reset the properties to their default values by simply pressing the Reset button The entered values may be applied by pressing the Apply button The appropriate action will also be applied when moving the mouse cursor away from the Object properties tool into the 3D window Position Translation Object properties Pos Rotate Scale Clip Postion a 0 000 i Jo 000 E o on0 Fig 145 The Object properties dialog with the index card Position selected When the Pos index card i e the position translation index card is selected the bounding box of the selected object will be displayed in green the color of the Position Translation mode All positions in the Position index card refer to scene coordinates On the position translation index card the current position of an object is displayed in scene coordinates The position translation d
82. eeeeees 94 ASD De WAMGOW s tos unt paswohes dasanastaseahes taacenancnanetes aeseuatasoaet a Uaasenactucconeh S 100 Ao Wordand Camera N 16 Werra re aana bensduatseausbel Peomanai a a a a a a a seowshkLancuentad 103 4 6 AK R ON a EE E E I E E EEIE E IET I E RIE E T E A EERTE 107 Wok aseo TOO kiraan a a A EEA S 109 AOD DENO ECC Ea R E 133 LOD WREMCED PODOI S aaa a RA E 138 dod ETON PIO Dene S iroa E N A a capestesitves 140 WOS Sere POPEO S aa a E E a N A satascrtasitues 141 4O00 Poh CON Propere Sarreraren eaa a a E aa aeaa raa a n e 142 AOF OD eot PEO Me Mile S inenen oea a a a a a E 143 AOS WN ORIGIN 1G Wy iaraa a a a a aa a nate chanel 150 AO CaTa NVON i E a E E SS 152 4 7 EAUUS BAR cssiessicdecdestecsescabecsotececeuetcbctcucacetcouccesteduouctuceuetcdce duce dete cubadatadswnccucanstcbec deca E E E E 155 5 AMportine amp Expor ne Data siiieidecssdcsisessccecscssssuesedisassesdstarisessctecscasssvaswticesdeotstasiiessstenseds 157 5 1 Dr POPEING Datlaesa n E E T E E E 158 SEL PHEVOr Volume Grap mics Tno lessi na a T 158 S2 Tmporins Stacks ofImase SCS chitin a a O ehtes a uaaae ohana tleeenats 161 SES Ampon RIV Voume Dalasi a ai a ehok aid oh anal ec made a ase onanaitenn et 173 SLA Importing HDF Data ssicecanccic n E cadets ceca onan a a a a 183 SLS Importing ANALYZE M M Dalasa e a cade oc a a e O 184 SLG Tmportins DICOM Data erae a Bas eed Shedd ois 184 VGStudio 1 1 User s Manual 5 VGStudio 1 1 SA7 Jmporine Po
83. erties 102 VGStudio 1 1 User s Manual 4 5 The Workspace e Reset Select this command to reset actions of all categories applied to the selected object such as translation rotation clipping and scaling to their default values Reset single catego ries of actions in the Object properties tool For more information see also Chapter 4 6 7 Object Properties e Camera mode World view mode Select this command to switch between Camera mode and World view mode These options are toggles 1 e only visible one at a time depending on the mode you are currently working in If you are working in World view mode indi cated in the 3D view window with the text scene view you may switch to Camera mode and vice versa 4 5 3 World and Camera View VGStudio provides two different modes to view your data World view mode and Camera view mode By default VGStudio will start in world view mode You may switch between World view mode and Camera view mode by clicking the icons in the icon bar or by using the Camera view or World view option in the Scene menu In World view mode you can view your data from outside By using the World view tool you may rotate and move the whole scene or change the viewing angle without affecting the scene itself For more information see Chapter 4 6 8 In Camera view mode you can view your data from inside This means that you can place a camera into the scene and adjust all camera parameters such as
84. f coordinate system reset zoom 134 optional preview zoom in 134 region of interest zoom out 134 ROI and Skip selection icon bar 28 81 scan file object manipulaton section 81 skip function scene utilities section 81 insert handle 27 standard icon section 81 installation view selection section 81 instrument what s this section 81 position window layout tools section 81 instrument properties VGStudio 1 1 User s Manual 173 177 182 178 180 196 176 182 175 170 175 179 176 171 178 169 170 165 183 184 183 183 186 186 186 189 193 192 187 187 191 188 138 19 v2 163 73 197 interface layout interval apply color interval color set isotropic scaling keyboard shortcuts usage launching the program command line option VGStudio icon layout Level Window license update light properties front light source overall intensity light source apply color disable enable front shadow look at point maximize maximum projection algorithm MDI menu bar merge object minimize motion smooting mouse Magellan Space Mouse usage move MPR Multi Planar Reconstruction Multiple Document Interface multiprocessor new scene object center change name create reference delete deselection disable duplicate enable group 198 7 Index 55 96 136 139 154 30 29 28 28 28 96 134 24 24 80 50 77 147 148 148 148 148 148 50 148 50 148 108 109 161 98 145 78 96 28 6
85. f the Opacity manipulation area The resulting 3D image should look like it is shown in the following figure Only the bone struc ture the teeth and the braces are visible the noise air and the soft tissue are invisible 38 Classification one selection MOME Object overview Opacity manipulation area Pal Drag handle right a Gray wales i manipulation area Fig 14 Drag the new handle to the right to make soft tissue invisible in the 3D image VGStudio 1 1 User s Manual 3 2 First Steps with VGStudio oe ik io F Jemo P a d 2 hn jaje Fig 15 The 3D image after noise air and soft tissue have been removed Only the bone struc tures the teeth and metal parts are now visible The reason for this is explained in the following picture noe ea Leal I l Hone Fig 16 From left to right the grayvalues of the different structures are displayed i e noise air fat muscle and bone structures Noise and air will appear on the left hand side of the Opacity manipulation area The next tis sues which appear towards brighter grayvalues are fat and muscles The brightest tissue is the bone structure teeth and metal braces which appear on the right hand side of the Opacity ma nipulation area If all the grayvalues of tissues such as air noise fat and muscle are set to zero opacity o
86. ft click into the opacity manipulation area and keep the left mouse button pressed Fig 128 The Opacity manipulation area while moving the cursor up and down will change the Center value while moving the cursor in the left and right direction will change the Width value ae Sh cation AOE Fiam ee eee eae 5 20m 40 Ah pias Fig 129 Moving the cursor horizontal changes the Width value while moving the cursor vertical changes the Center value VGStudio 1 1 User s Manual 129 4 VGStudio Interface amp Tools Color manipulation area The Color manipulation area is used to apply and modify the color mapping of an object The default color of a voxel object is white Color manipulation area Fig 130 The Color manipulation area of the Classification tool He Reminder No color mapping will be possible for RGBA color data aa A color may be applied to a color handle an interval between two handles or a whole segment The appropriate element will be marked in the Color manipulation area To apply a color to a handle interval or segment double click the appropriate element with the left mouse button or open the context menu by clicking the element with the right mouse butto
87. gellan SPACE MOUSE To use VGStudio 1 1 in combination with a LogiCad Spacemouse start the Space Mouse driver before starting VGStudio 1 1 Fig 9 The Space Mouse The Space Mouse may be used to steer the six degrees of freedom of the currently selected ob ject The Magellan SPACE MOUSE allows you to control flying objects spatially without strain In a similar way you may also fly through virtual voxel worlds Information on the LogiCad Inc GmbH Magellan SPACE MOUSE can be found under the internet address http www spacemouse com VGStudio 1 1 User s Manual 33 3 Getting Started 3 2 First Steps with VGStudio This section will explain your first steps when using VGStudio and will guide you through the most important steps of the program A data set of a human jaw which was scanned with a CT scanner 1s used to show some of the basic functions of VGStudio This chapter will not go into detail 1 e describe all the options and alternatives available Each tool introduced in this chapter will be described in more detail in the following chapters He Reminder Some of the settings discussed here will only be valid for CT data ci Start the VGStudio application An empty scene will be displayed 1 e the slice windows and the 3D window will be empty Select the Open command in the File menu In the Open info file dialog select the file Jaw vgi by clicking it and pressing Open or by simply double clicking the f
88. h involving one or more subjects to determine the safety or effectiveness of a device Cf 21 CFR 812 3 h The FDA definition of a Subject is a human who participates in an investigation either as an individual on whom an investigational device is used or as a control A subject may be in normal health or may have a medical condition or disease Cf 21CFR 812 3 p Within this regulatory framework then a clinical investigation can be ar gued to be a more restrictive form of research in which the data and in formation collected are intended to be used to support the claims of a device s safety or effectiveness the FDA regards software used in medi cal applications to be a medical device At the present time Volume Graphics makes no representation that the VGStudio product is either safe or effective for any intended use for which research may currently be performed If you are conducting research or clinical investigations by law you are required to obtain prior Investigational Review Board IRB approval of VGStudio 1 1 User s Manual VGStudio 1 1 the clinical study protocol and of the patient informed consent docu ments and to provide each patient subject with a copy of the completed informed consent document Similarly if you are conducting research or clinical investigations using animal subjects you are obligated to follow Good Laboratory Practices and to observe the ethical treatment of the
89. he middle mouse button The classification tool should now look like the following figure Classification MOME Object overview oe selection Opacity manipulation area Segment Segment 2 Gray values Color manipulation area Sh rr l fo Fig 22 Reduce the noise by inserting a new handle and dragging it down to zero posi tion 42 VGStudio 1 1 User s Manual 3 2 First Steps with VGStudio Click with the right mouse button into the left segment s section of the Color manipulation area The following menu will pop up Insert point Dears pam serpant caa Set interval color Set segment color Custom color Copy segment color white Paste segment colar m black Import segment color B red Export segment color a green ai blue o cyan D magenta w yellow Fig 23 Select a color for the different segments Click Set segment color and select a color for the left segment the soft tissue by clicking one of the default colors or using the Custom color option to select a user defined color After you have done so the Classification tool will look as follows Classification Current preset pe o l e o y l Object overview Segment 2 a Ea Gray values E areg Fig 24 The Classification tool after you have selected a color for the segments The jaw in the 3D image will then look like in the figure below
90. he mouse while the left mouse button is pressed The jaw can be rotated in any direction VGStudio 1 1 User s Manual 35 3 Getting Started Col ee eee eT Lae area rea ie E Fig 11 The red bounding box indicates that the Rotate mode is active Rotate the image by clicking into the bounding box and dragging the mouse while the left mouse button is pressed One of the most powerful tools of volume graphics is the possibility to map any grayvalue of the original data to any arbitrary opacity This functionality is handled by the Classification tool In the main part of the Classification tool you find the Opacity manipulation area It shows a function which maps any grayvalue abscissa to any opacity value ordinate It also shows a histogram of the frequency of occurrence of the different grayvalues in the background The grayvalues are applied to the abscissa of the plot the opacity values are applied to the ordinate The line running from the lower left corner to the upper right corner is the default opacity func tion running from dark transparent voxels to bright opaque voxels An arbitrary function may be applied to the data by inserting new handles to the function and moving these handles 36 VGStudio 1 1 User s Manual 3 2 First Steps with VGStudio Object overview Opacity manipulation area Opacity manipulation ares middle mouse key to insert new handle Gray values Gray va
91. he object will be removed from the scene when you select this command You may also use the keyboard shortcut Ctrl Z to undo your last command You may undo the last 100 actions and commands Only one exception will de stroy the undo history 62 VGStudio 1 1 User s Manual 4 3 Menu Bar Reminder The undo history will be destroyed in case of deleting an object You have to select the undo command immediately after having deleted the object e Redo Select this command to redo your previous Undo action This menu item changes depending on the Undo action you last performed For instance if you have undone the past ing of an object the text reads redo paste object and the object will be pasted into the scene again when you select this command You may also use the keyboard shortcut Ctrl Y to redo your last Undo command e Cut Select this command to cut objects within a scene in VGStudio The cut objects will remain in the VGStudio clipboard When you cut objects you cut all related information such as opacity and color along with whatever you cut Note that VGStudio objects cannot be pasted into another program You may also use the keyboard shortcut Ctrl X to cut objects e Copy Select this command to copy selected objects into the VGStudio clipboard When you copy objects you copy all related information such as opacity and color along with whatever you copy Note that VGStudio objects cannot be copied into another program You m
92. he title bar These but tons can also be used to maximize minimize or close the slice windows In each slice window you will also find two scrollbars to pan large images as well as two zoom buttons and one slice selection box In the lower left corner of each slice window a small tripod colored in the VGStudio color scheme will be displayed which shows the orientation of the cor responding slice in the object coordinate system L 63 z Use the slice selection box in the lower left corner of the slice windows to scroll through the im age stack by clicking the up and down arrows or to select a specific slice by typing in the slice number and then clicking into another window The selected slice will then be displayed mo Use the zoom in and zoom out buttons in the lower right corner of the slice windows to zoom in on an image i e enlarge the image or to zoom out 1 e reduce the image The images will then be enlarged or reduced by a preset zoom factor p VGStudio 1 1 User s Manual 95 4 VGStudio Interface amp Tools When clicking into a slice window with the right mouse button a context menu will be opened 96 ZOOM ZOD b Use original color Use classification color cene relative mode Object relative mode Fig 75 A context menu will be opened when clicking into one of the slice windows with the right mouse button Zoom Select this command to open the Zoom menu Fig 76 The Zoom menu of th
93. i a Fig 72 Default layout screen after VGStudio has been started The VGStudio workspace includes four elements 1 e the 3D window and the three slice win dows The 3D window and the slice windows may be activated or deactivated by simply clicking into the title bar or into the windows The three slice windows form one entity which means that they can only be opened or closed all together and not separately To close one of the two parts click the Close I button in the upper right corner of the window To activate a disabled window again use the Window menu and select New slice windows or New 3D window For more in formation on how to work with the windows see also Chapter 4 3 7Window Menu The layout of the windows in the workspace can also be adjusted arbitrarily by simply clicking into the title bar with the left mouse button and dragging the window to the desired position Each window can be positioned or enlarged independently from the other windows You may use the Window menu or the window icons to enlarge minimize or close a window Use the Minimize button El to minimize a window within the workspace Use the Maximize button E to maximize a window within the workspace VGStudio 1 1 User s Manual 93 4 VGStudio Interface amp Tools 4 5 1 Slice Windows and Multiplanar Reformatting The slice windows provide the VGStudio user with full Multi Planar Reconstruction MPR functionality for voxel data sets In
94. ia log When several objects are selected the index card Scale will be disabled If you wish to manipu late several objects together you have to group the objects first For more information on the grouping and ungrouping of objects please refer to Chapter Fehler Verweisquelle konnte nicht gefunden werden Fehler Verweisquelle konnte nicht gefunden werden The index card Scale provides you with an interface which allows you to type in the scaling fac tors for the selected object You may also use the up and down arrows to increase or reduce the values Use the checkbox on the right hand side to lock the three values for isotropic scaling The three values will then be changed simultaneously and cannot be changed independently of each other Use the Reset button to set the scaling values to the default values of 1 0 On the index card Scale you may also enter the initial voxel resolution of the selected voxel ob ject The Resolution area will be disabled if an object group is selected Press the Reset button to reset the scaling of the selected object The index card Scale Reset leaves the resolution settings untouched Press the Apply button to activate the new scaling values entered in the rotation dialog Reminder You should not scale objects down to factors less than 0 1 Please take into account that scaling and resolution will end up in an effective object scaling Very low object scaling values will result in reduced imag
95. ialog allows you to type in the exact position values in x y and z coor dinates You may also use the up and down arrows to increase or reduce the values Press the Reset button to move the currently selected object back to the scene s origin Press the Apply button to accept the new values entered in the position dialog VGStudio 1 1 User s Manual 143 4 VGStudio Interface amp Tools Rotation When the Rotate index card is selected the bounding box of the selected object will be displayed in red the color of the Rotate mode The index card Rotate provides the VGStudio user with two different interfaces to rotate the selected object in the scene 1 e the Standard dialog and the Advanced dialog Use the Stan dard Advanced toggle button to switch between the two modes The Standard dialog looks like the following image Object properties Pos Rotate Scale Clip Rotation m o 000 ae Jo 000 2 o on0 Advanced Reset Apply Fig 146 The Standard dialog of the Rotate index card The Standard dialog provides you with an interface where you may enter incremental rotation values for each axis Type in the incremental rotation around the x y or z axis or use the up and down arrows to increase or reduce the rotation values 144 VGStudio 1 1 User s Manual 4 6 Tool Box The Advanced dialog looks like the following image Object properties Pos Rotate Scale Clip Rotation Axes m 0 0
96. ick Reset to reset the zoom factor to its default value In the context menu click Move or Rotate to access the Move or Rotate mode Select Reset to reset the World view settings to its default values For more detailed information on the World view mode please refer to Chapter 4 6 8 4 6 9 Camera View While the Camera mode is activated you may use the Camera View tool to adjust camera relevant settings The Camera View tool is activated by pressing the Camera mode button in the icon bar or by clicking Camera mode in the Scene Menu 152 VGStudio 1 1 User s Manual 4 6 Tool Box Camera views Camera position Loak at A 14 00 HM 26 00 ve 64 00 ie 64 00 oon Z oon Up vector _ K ie dy l Jo 000 Jo 000 fi ooo Viewing ange HH Fig 155 The Camera view tool of VGStudio You may either type in the exact values for the Camera position and for the Look at point or use the up and down arrows to increase or reduce the x y and z position values Up vector Camera position Result imag Fig 156 The Camera view mode allows you to view your data from inside You may adjust all camera parameters shown here accord ing to your needs Use the Up vector section to type in the exact value for the up vector relative to scene coordi nates VGStudio 1 1 User s Manual 153 4 VGStudio Interface amp Tools Reminder The camera and look at po
97. ile The file extension vgi stands for Volume Graphics Info file The data is loaded into VGStudio and images will appear in the four windows of the workspace as shown below 34 VGStudio 1 1 User s Manual 3 2 First Steps with VGStudio a FE ml Oa ae oe 1d OE eee Oey iio oll Ea F J a J m om P a EE ei Bun x Fig 10 The VGStudio screen after a file has been loaded Here the Move mode is activated which is indicated by the green bounding box The jaw data set is loaded into the scene Around the jaw a green bounding box will appear The green box indicates that the object is the currently selected object and that the Move mode indi cated by the green box around the jaw data set is activated An action can be applied to the se lected object only Click with the left mouse button into the 3D view window outside the green bounding box to deselect the object The bounding box will disappear Click the jaw again to select the object The green bounding box will reappear Now move the object by clicking into the green bounding box with the left mouse button and dragging the mouse while the left mouse button is pressed To activate the Rotate mode press the Rotate icon in the icon bar The bounding box around the jaw will appear now in red color which indicates that the Rotate mode is active Rotate the jaw by clicking into the red bounding box with the left mouse button and dragging t
98. ily arranged windows You may also arrange the windows by using the options of the Window menu see Chapter 4 3 7 VGStudio 1 1 User s Manual 91 4 VGStudio Interface amp Tools 4 4 6 What s this Section ih Click this icon to change into What s this mode A question mark will then be displayed next to the cursor If you need help or information on a certain function simply click into a window or on a component of the user interface a popup window containing online help topics about the selected component will then appear There you will find short information on the functions and also on where to find the information in the User s Manual lent ihia C a a wel Pial EF Me Gi phei pome fh e tj Ose hao Hondy E eee DEED lg T Asa inn lol i cl E weer err fore o os s Pf I EF E T A E k 1i Ei S Uria rin 0 rF ra 30 eee Ge E ee Oe Ng i r ae et Lt O r e r ee al n a E Po mya era pba jo E Se 20 ra Hn fee Foes rr pee a2 n J EJ ig A e gee ree come H i me os o marae Fig 71 VGStudio s online help 92 VGStudio 1 1 User s Manual 4 5 The Workspace 4 5 The Workspace ri e e 1 e E aj E 5 a _ i PE cel UJ AS LDL es SS E tle Tr 2 oa St oa Gel F aT a AO eeN T Dewi E a eaa i i OOO e O i nne LE ee ad SSS SSS q1 ES oI ES E 7 a _ E F ot e
99. ing as well as scene relevant information such as light settings rendering algorithm or background color VGStudio 1 1 User s Manual 159 5 Importing amp Exporting Data Hs in Fig 158 Import data into VGStudio and then save the scene by using the save or save as command in the File menu to generate a vgi file Data saved in VGStudio always consists of two elements 1 e the data file s and the Volume Graphics Info file A vgi file contains references to all data included in the scene so that a com plex scenario can be restored by loading a single vgi file The concept of VGStudio s data han dling is to leave the original data untouched All information on how data has to be processed during the import will be saved in a vgi file Example A voxel data set includes 32 bit floating point data but the dynamics of the data is very low so that it will fit into a 8 bit integer 256 grayvalue representation During the import procedure the user may specify that data should be converted into a 8 bit data representation This will re duce the amount of RAM needed on your PC or workstation by a factor of 4 This conversion will be done automatically while loading the data into VGStudio The original data set on your hard disk will remain untouched and no second 8 bit data set which would increase your disk capacity requirements has to be generated However VGStudio allows its users to export the data in the internal data
100. ing box and dragging the mouse while the left mouse button is pressed The whole bounding box may be used as active area to apply the appropriate action The object may be moved forwards or backwards and thus will be enlarged or reduced by clicking into the bound ing box and dragging the mouse while the middle mouse button or the Alt key and the left mouse button is pressed The whole bounding box may be used as active area to apply the ap propriate action Using the Shift modifier in Move mode allows you to move the object along either the vertical or horizontal direction of the 3D window image plane For more information on the Move mode please refer to Chapter 4 6 7 Object Properties a Fig 60 The 3D window in Move mode indicated by the green bounding box and the tripod displayed next to the cursor when moving it into an active area 82 VGStudio 1 1 User s Manual 4 4 Icon Bar Rotation m Click this icon to rotate the selected object or object group The Rotate mode is characterized by the red bounding box around the selected object or group of objects When moving the cursor into the bounding box it will take the shape of one vertical and one horizontal circular arrow see the table in Chapter 3 1 2 Mouse Usage The object may be rotated around the x or y axes of the image plane by clicking into the bounding box and dragging the mouse while the left mouse button is pressed The object may be rotated around the viewing
101. ing the rendering process Higher values normally lead to higher image quality Images may appear darker with higher oversam pling factors due to higher light absorption during the rendering process To adjust the values simply type in the appropriate values or use the up and down arrows to e1 ther increase or reduce the oversampling value Motion smoothing Motion smoothing allows to apply and adjust a reduction factor by which the image size is re duced in x and y direction while manipulating a scene Higher reduction factors will lead to more smooth interaction This is a helpful function especially on computers with a lower per formance Type in the appropriate value or use the arrows or the scroll function to enlarge or reduce the motion smoothing value Perspective rendering This switch allows to disable enable perspective rendering 4 6 4 Light Properties VGStudio supports the illumination of the scene by two light sources with parallel light You may adjust the light settings in the Light properties dialog Light properties Overall intensity _k _ _J _ 50 0 Front light source ambient ja a diffuse E a Shadow light source ambient ja W diffuse E Fig 141 The Light properties dialog 140 VGStudio 1 1 User s Manual 4 6 Tool Box The Overall intensity determines the total brightness of the scene s illumination To adjust this value simply drag the slider t
102. io 1 1 User s Manual 117 4 VGStudio Interface amp Tools Opacity manipulation area Segment 1 ao a aT rou oe a Gray values Fig 110 Insert a new handle by clicking the desired position with the middle mouse but ton The handle may be moved by clicking it with the left mouse button and then dragging it to the desired position while keeping the left mouse button pressed Opacity handles may be removed by clicking them with the middle mouse button or with the left mouse button while keeping the Alt key pressed You may also remove a handle by using the context menu which you open by clicking into the Opacity manipulation area with the right mouse button Click the handle you wish to remove with the right mouse button and then select Remove handle in the context menu Please note that the two outer handles can neither be moved nor removed Opacity manipulation area Segment 1 Gray values Fig 111 The new handle is displayed Any element of the opacity function 1 e opacity handles or line segments may be moved within the opacity manipulation area by clicking the element and dragging it around while the left mouse button is pressed The cursor s shape will change when moving it on a handle or the opac ity function line to indicate that the appropriate element may be moved The cursor s shape also indicates into which direction the element may be moved generally in horizontal and vertical directi
103. io functions that are accessed via the menu may also be activated by using key board shortcuts If keyboard shortcuts exist they are displayed next to the entries in the pulldown menus This can be seen in the following image where the Edit menu is shown as an example VGStudio 1 1 User s Manual 29 3 Getting Started Edit EY undo group object Ctri zZ hal hedoy Won paSSiHIE db Cut Copy fA Paste Delete Duplicate select All Deselect Select Inverse Preferences List of Keyboard Shortcuts Command File Menu New Open Save Save As Quit Object Menu Move Rotate Scale Clipbox Clipplane Group Ungroup Edit Menu Undo Redo Cut Copy Paste Delete Duplicate Select All Deselect Select Inverse 30 Keyboard Shortcut Ctrl N Ctrl O Ctrl S F12 Alt F4 Shift Ctrl M Shift Ctrl R Shift Ctrl S Shift Ctrl B Shift Ctrl C Ctrl G Ctrl U Ctrl Z Ctrl Y Ctrl X Ctrl C Ctrl V Del Ctrl D Ctrl A Alt D Alt trit Ctrl Ctrl C Ctr Ctri D Ctri 4 A Fig 5 The keyboard Shortcuts are dis played next to the menu entries VGStudio 1 1 User s Manual 3 1 Launching the Program 3 1 2 Mouse Usage VGStudio is designed to work with a mouse with either two or three buttons If you are using a two button mouse the third middle mouse button is emulated by simultaneously pressing the Alt key on your keyboard and the left mou
104. ion of interest or grab the frame itself by clicking it with the left mouse but ton You may now resize the region of interest by dragging the frame to the desired position while holding the left mouse button pressed Use the Auto scan checkbox to automatically scan the currently displayed slice for optimal erayvalue mapping The Auto scan function will modify any previously adjusted data range mapping performed in step 8 He Reminder The preview performance might be low when viewing ASCII or com pressed data files eS h 172 VGStudio 1 1 User s Manual 5 1 Importing Data Step 10 Manipulation of the object coordinate system E Import tool OF x Manipulation rs Select axes to be mirrored or swapped Mirror axes m KO i Wa aS T MMN AYZ normal Preview Finish Cancel Fig 171 Mirror or swap the x and y axes of the data set The coordinate system of the imported data may be manipulated arbitrarily The x and y axes of the data set may be mirrored To mirror the z axis change the sorting order in the file selection dialog step 1 The order of the axes may be swapped You may now start the import procedure by clicking Finish 5 1 3 Importing Raw Volume Data To import Raw volume data click File in the menu bar and select Import Select Raw Volume from the Import menu to open the Raw Volume Import Wizard The Raw Volume Import Wizard guides you step by step through
105. it float 32bit RGBA no mapping possible 32bit RGBA The voxel Resolution may be adjusted for data sets with non isotropic voxel dimensions el GStudio warning k Significant difference between pixel spacing and slice distance detected Do you want to resample dataset Fig 168 Resampling warning Pop up A Warning dialog may come up in case that you import data series with Significant difference in voxel Resolution Press Yes to resample the data The software will calculate additional slices by trilinear resampling This will result in a better 3D image quality However keep in mind that slice images will be generated out of your original data which are not generated by the scanning device The resampling will also result in an additional amount of memory needed by the VGStudio application This process may exceed the available memory installed in your computer depending on your initial image data Press No to skip the resampling process so that only the original image data is loaded However this may result to low 3D image quality The Data range may be mapped arbitrarily within a maximum data range for the different data types The maximum values will appear as default values when opening the dialog for the first time Pressing the Reset button will restore these default values 170 VGStudio 1 1 User s Manual 5 1 Importing Data The maximum data ranges for the different data types that can be handled by VGStudio are listed
106. itional system memory Therefore a reference is a memory saving possibility to copy objects You may also use the keyboard shortcut Ctrl R to create a reference In the Scene tree tool a small arrow will appear in the symbol displayed on the left hand side of the scene name EF and next to the scene name the text reference will appear Applying the Create reference command to a polygon object will result in a normal copy of the object Creating a refer ence includes a smart placement functionality An example select an object and click Create reference in the Object menu or press Ctrl R The new referenced object will appear as the currently selected object Move the reference to a new position in the scene Select Create VGStudio 1 1 User s Manual 69 4 VGStudio Interface amp Tools Reference in the Object menu or press Ctrl R once again The second referenced object will appear in the same relative position as in the first reference Reminder The new offsets of the smart create reference procedure will be reset to their default values as soon as you deselect the object 4 3 5 Scene Menu Click Scene to open a pulldown menu containing the following entries 70 Scene Camera mode Axis Grid Instrument Properties w Background color Fig 47 The scene menu Camera mode World view mode Select this command to switch between Camera mode and World view mode These options are toggles i e only visi
107. king it with the left mouse but ton You may now resize the region of interest by dragging the frame to the desired position while holding the left mouse button pressed Use the Auto scan checkbox to automatically scan the currently displayed slice for optimal erayvalue mapping The Auto scan function will modify any previously adjusted data range mapping performed in step 5 182 VGStudio 1 1 User s Manual 5 1 Importing Data Reminder The preview performance might be low when the viewed slice is flipped or when viewing ASCII or compressed data files Step 7 Manipulation of the object coordinate system E Import tool OF x Manipulation Select axes to be mirrored or swapped Mirror axes Ir x Poy MZ Swap axes AAA a2 normal rs Previewy Previous Finish Cancel Fig 182 Mirror or swap the x y and z axes of the data set The coordinate system of the imported object may be manipulated arbitrarily All three axes of the data set to be imported may be mirrored The order of the axes may be swapped You may now start the import procedure by clicking Finish 5 1 4 Importing HDF Data VGStudio is capable to import image and volume data stored in the Hierarchical Data Format HDF 4 x Select the Import HDF volume option in the File menu to load HDF volume data files into VGStudio More information on HDF data can be found under the following internet address http hdf ncsa uiuc edu VGStu
108. l in the 8 column 1 row and 2 image would then have the position 7 0 1 VGStudio 1 1 User s Manual 49 3 Getting Started Woe Fr Wome 0 0 0 Fig 34 A schematic Voxel data set 3 2 2 The Illumination Model VGStudio supports an illumination of the scene by two light sources with parallel light You may adjust the light settings in the Light properties dialog for more information on the Light prop erties dialog please refer to Chapter 4 6 4 Light Properties The Front light source is positioned in 0 i e in the eye of the observer the Shadow light source is positioned in 45 to the right of the observer The light sources are located at fixed positions relative to the observer Fig 35 Usage of the light sources in VGStudio will en hance the 3D perception of an image 50 VGStudio 1 1 User s Manual 3 2 First Steps with VGStudio Activating the shadow light source will considerably enhance the 3D perception of an image 3 2 3 VGStudio Clipboard VGStudio has its own clipboard and does NOT use the standard clipboards of your operating system since these clipboards are not capable to handle the different data used by VGStudio Due to this you will not be able to use the cut copy and paste commands to copy data or images into other applications or from other applications into VGStudio Use the Save Image command to export rendered 3D images or slice images in standard image files VGStudio 1 1 User s
109. l Panel from the Settings menu Step 3 Double click the System icon to display System Properties Step 4 On the Environment index card click any existing variable name in the list you want to add the variable to Step 5 Type in the name of the new variable in the Variable box Step 6 Type in the value in the Value box Step 7 Click Set Notes If you are not an administrator you may add variables only to the User Variables list Windows NT will save changes in the registry so that they will be available automatically the next time you start your computer Changes will not affect programs that are running and will only be effective once you have restarted your computer Adding environment variables on a Unix system Examples for utilization of 2 processors For tcsh users type setenv PROCESSORS 2 For bash users type export PROCESSORS 2 VGStudio 1 1 User s Manual 21 2 Installation Notes Ask your system administrator for help if you are not familiar with modifying system or envi ronment variables To modify your PATH variable type in one of the following commands de pending on what shell you use and where you have installed the software Include the corresponding line into your cshre or your bashrc file if you do not want to modify your envi ronment variables every time you log into your system 22 VGStudio 1 1 User s Manual 2 3 Installation Instructions 2 3 Installation Instructions Please refer t
110. l be displayed if a slice outside the actual volume data set is chosen VGStudio 1 1 User s Manual 99 4 VGStudio Interface amp Tools The object that was selected last will remain visible in the slice windows when it is deselected until a new object is selected This feature helps the user to navigate in Camera mode with no bounding box visible for more information on the Camera mode please refer to Chapter 4 6 9 Camera View 4 5 2 3D Window The 3D window shows the result image of the rendering process Two modes are supported in the 3D window Scene view i e World View mode and Camera view i e Camera mode In the title bar of the 3D window the currently selected mode World view mode or Camera view mode is displayed In the left corner of the title bar you find the Control icon which you use to access the Control menu Double clicking this icon will close the 3D window You can use the Control menu to maximize or minimize the 3D window or to close it The window but tons can be found in the right corner of the title bar These buttons can also be used to maximize minimize or close the 3D window In the 3D window you will also find two scrollbars to pan large images as well as two zoom but tons 9 3D Window scene view Fig 81 The 3D window in scene view mode When clicking into the 3D window with the right mouse button a context menu will be opened 100 VGStudio 1 1 User s Manual 4 5 The Workspace
111. l erage vie Oech soro tome yoo eee OBB e Pe ing eee JD Wilcke salen weap SS Fig 38 Tool tips will pop up when the mouse pointer rests on an icon VGStudio 1 1 User s Manual 57 4 VGStudio Interface amp Tools 4 2 Title Bar Elements Title bar In the title bar VGStudio and the filename of the current scene are displayed Control icon In the left corner of the title bar you find the Control icon which is used to access the Control menu see following section Double clicking the Control icon will close VGStudio Control menu You open the Control menu by clicking the Control icon with the left mouse button You can use the Control menu to position the main window or to exit VGStudio Window buttons The window buttons can be found in the right corner of the title bar You can use the buttons to position the main window or to exit VGStudio 58 VGStudio 1 1 User s Manual 4 3 Menu Bar 4 3 Menu Bar The Menu bar displays VGStudio s menu titles Each menu lists a group of entries and with each entry a specific action is performed Menus or menu items that are not available are disabled Using the menus 1 You open a menu by clicking it or by pressing lt Alt gt plus the letter that is underlined in the menu s title For example to open the File menu you press lt Alt gt lt F gt 2 Once you have opened a menu you choose a menu item by clicking it by pressing the un
112. lbox again AmA EL T E menr r l ae T E re i oie be be ie jji l i Ose ibe Sodee be ea OO Fig 91 The Classification tool is now inside the tool box Click into the title bar of the tool and drag it out of the tool box while the left mouse button is pressed You may then adjust the size of the tool 108 VGStudio 1 1 User s Manual 4 6 Tool Box rhe the tesa OE eee DODRR ee jr E agis Fe bo ee Epo Fig 92 The Classification tool is dragged out of the tool box where you may adjust its size to your needs You may use the Close button E to close a tool Use the Tools menu to enable a tool again by clicking it A check mark will then appear next to the menu item For further information on the Tools menu see also Chapter 4 3 6 Use the minimize button El to minimize the tool If you press the minimize button in a floating tool the tool will be placed back into the tool box as a minimized tool and will appear at the end of the tool box When you click the maximize button El of a tool it will be taken out of the tool box and will become a floating tool If you press the maximize button lB in a floating tool the tool will be placed back into the tool box as the last tool in the box 4 6 1 Classification Tool The Classification tool is one of the most important and most powerful tools of VGStudio 1 1 The main purpose of the Classification tool is used to apply user defined transfer
113. licking one of the han dles of the bounding box and dragging the mouse along the desired clip direction while the left mouse button is pressed Group the objects first if you want to clip several objects at a time For more information on the Clipbox mode please refer to Chapter 4 6 7 Object Prop erties Clipplane Select this command to clip the selected object or object group by an arbitrary clipplane The Clipplane mode is characterized by the cyan bounding box with a normal vector on one side of the active object When moving the cursor into the bounding box a scissors will appear next to the cursor see the table in Chapter 3 1 2 Mouse Usage The ob ject may be clipped along an arbitrary clipplane by moving the mouse up and down while the middle mouse button or the Alt key and the left mouse button is pressed To rotate the clip plane around the origin of the clipplane s normal vector click into the clipplane and drag the mouse while the left mouse button is pressed The origin of the clipplane s normal vector may be moved to any arbitrary position on the clipplane by clicking the clipplane s normal vector origin with the left mouse button and dragging the mouse while the left mouse button is pressed The clipplane will be disabled if several objects are selected Group the objects first if you want to clip several objects with one clipplane at a time For more information on the Clipbox mode please refer to Chapter 4 6 7 Object Prop
114. lipped object The clipplane s origin may be placed to any arbitrary position in order to be able to rotate the clipplane around the specified point 148 VGStudio 1 1 User s Manual 4 6 Tool Box The clipping of an object group will be reset if the object group is ungrouped Fig 151 The clipplane is defined by the clipplane s normal vector and the distance between the clipplane and the ori gin of the clipped object When several objects are selected the Clip index card will be disabled If you wish to manipu late several objects together you have to group the objects first For more information on the grouping and ungrouping of objects please refer to Chapter Fehler Verweisquelle konnte nicht gefunden werden Fehler Verweisquelle konnte nicht gefunden werden Press the Reset button to remove any clipplane from the selected object Press the Apply button to activate the new values Center When the Center index card is selected the center of an object or say the origin of the object coordinate system can be applied in voxel coordinates By default the center of an object is at the position Xmax 2 Ymax 2 Zmax 2 where Xmax Ymax and Zmax describe the objects dimen sion in voxels VGStudio 1 1 User s Manual 149 4 VGStudio Interface amp Tools Object properties Pos Rot Scale clip Center Center m 103 983 a ae 125 077 Z 137 683 Reset Apply Fig 152 The Clipplane index card of the
115. lor coding color handle move color interval move color manipulation area 196 7 Index 91 28 78 105 79 32 111 T2 73 75 31 104 72 108 160 161 162 161 162 161 162 108 161 109 77 95 105 108 160 108 108 109 108 110 109 108 108 134 67 67 77 114 114 116 116 119 116 122 51 70 89 107 155 155 157 70 89 107 155 156 156 156 114 136 57 137 137 116 136 copy segment color delete handle export segment color import segment color insert handle paste segment color set handle color set interval color set segment color color mapping color scheme color values command line option control icon control menu coordinate system manipulation mirror swap copy copy opacity curve create reference cross section axial frontal sagittal cut data files compressed data range data range mapping data representation data range reset resolution data type 32bit float 32bit RGBA 8 16 32bit signed 8 16 32bit unsigned data value mapping default view buttons delete handle segment deselect disable duplicate objects 139 138 139 139 138 139 139 139 139 136 57 163 28 59 100 105 59 100 105 193 182 193 182 193 182 193 64 83 127 71 178 177 189 191 178 191 190 172 172 172 172 133 159 162 65 127 138 128 65 144 VGStudio 1 1 User s Manual 7 Index edit menu 63 illumination model
116. lues i manipulation area Color manipulation area Fig 12 To insert a new handle or to remove an existing handle in the Opacity manipulation area Click the desired position with the middle mouse button To manipulate the opacity function place the mouse into the Classification tool s Opacity ma nipulation area as shown above Click the middle mouse button or the left mouse button while the Alt key is pressed to insert a new handle or remove an existing handle on the opacity func tion s line Click the new handle with the left mouse button and drag it down to zero opacity The opacity function should now look like the following example Classitication MOME Object overview fone selection Opacity manipulation area T Drag handle cion Gray values e 3 Fig 13 The opacity function after a new handle has been inserted i manipulation area VGStudio 1 1 User s Manual 37 The resulting 3D image will appear much clearer since all the noise included in the lowest the 3 Getting Started left side grayvalues is now set to zero opacity and is therefore invisible For another step grab the new handle by clicking it with the left mouse button and drag it to the right while the left mouse button is pressed Keep the handle on the base line zero opacity as shown in the following example Drag it to the right hand side of the gray peak displayed in the histogram o
117. ly sot Data siies a secs ti cee eters ea Laden E aaah ea eh Locanda 186 5 2 BX POEUING Dal ais iccese cosas vec asic R nates sucuccueuseeaseneescecev ens sadudeesesueaueenroeerseaee 187 IAL Exporting Raw VOUM S scs 4h scnss tes ia csitesaisa A E E a eee 187 0 APPENA ogre soo ca oes T N E E 191 6 1 VGStudio 1 1 and memory consumption sseeeseeccssssseecocossssececcossssccecosossssscecocossssscecossssssecesosssssseeesesssee 192 GRE Memory consumpto VOXEl Gala nprs a E a a hoe ee ead Sees 192 G2 Rendenne larse Moh Quality Mare Sissi e tun nda ous Bubumehcaeosaea ree 192 6 2 Limitations and Known Bugs ossaa ea a aeae eaae Eea aaeeea EESO aS ESE EEEE 193 A nde n E E 195 VGStudio 1 1 User s Manual VGStudio 1 1 WELCOME TO VGSTUDIO 1 1 USER S MANUAL VGStudio 1 1 is a highly sophisticated image analysis and visualization software and was devel oped to provide the user with a powerful but easy to use interface to process and visualize voxel volume data with high performance analyzing and volume rendering algorithms It uses an intuitive graphical user interface GUI with standard functions which are well known by most users from many other software packages Apart from volume data analysis VGStudio 1 1 may also be used for documentation and presentation purposes You may render high quality images of the data set under investigation We hope you enjoy working with VGStudio 1 1 All terms you might be unfamiliar with here will be ex
118. mouse button is pressed the clipplane will be rotated in any arbitrary direction 86 VGStudio 1 1 User s Manual 4 4 Icon Bar 4 4 3 Scene Utilities Three different utilities may be activated for data analysis and evaluation or better orientation in the scene Activate the utilities by clicking one of the three icons in the icon bar me L H or by using the Instrument Axis and Grid options in the Scene menu 3D instrument hs Click this icon to activate or deactivate the 3D instrument in the scene A small cross will appear in each slice window as well as in the 3D Window The 3D instrument can be positioned any where in the scene or an object within the three slice windows The scene coordinates and the gray and color values of the 3D instrument will be displayed in the status bar f _ Slice 57 7 J _ A i ro F Fa a G E 1 Fig 65 The 3D instrument is displayed as a small cross in the slice windows and the 3D window VGStudio 1 1 User s Manual 87 4 VGStudio Interface amp Tools When moving the cursor in the slice windows the three cross sections through the volume data will be displayed with the 3D instrument in the center of the three sections You may use the 3D instrument to scroll through the volume data set in the slice windows in two directions simulta neously by clicking it with the left mouse button and then dragging the mouse while the left mouse button is pressed re Axia li
119. n 130 VGStudio 1 1 User s Manual 4 6 Tool Box Color manipulation area Hande A E Color manipulation area Interval f Il Color manipulation area Segment M Fig 131 Different colors may be applied to handles intervals and segments The two handles at an interval or segment border will receive the identical color when applying a color to an interval or a segment Colors between two handles will be interpolated This allows the VGStudio user to easily define color transitions To create a sharp color transition either cre ate grayvalue segments or insert two color handles with the appropriate color and place the han dles directly side by side A single color handle or an interval not adjoined to a segment border may be moved The mouse cursor will change to a two sided arrow as soon as your cursor is placed on a movable element of the color mapping area Click a single color handle with the left mouse button or click into the appropriate interval and drag the mouse to the left or right to move the color mapping The gray values of the appropriate color handles will be displayed while moving the color handles or in tervals manipulation area a 3 Y N E manipulation area mo Fig 132 Color handles or intervals that are not adjoined to a segment border may be moved by clicking them and then dragging the mouse while the left mouse button is pressed The color mapping will be shifted during
120. n area 132 VGStudio 1 1 User s Manual 4 6 Tool Box e Set handle color Select this command to apply a color to a single color handle in the Color manipulation area Use the following menu to choose a color or to open the color se lection tool to define a custom color Custom color white E slack H red E green a blue cyan a magenta yellow Fig 135 Select a color for handles intervals and segments e Set interval color Select this command to apply a color to an interval between two color handles in the Color manipulation area e Set segment color Select this command to apply a color to a whole segment in the Color manipulation area e Copy segment color Select this command to copy the current segment s color mapping to the clipboard Use Paste segment color to apply the copied color mapping to another object or segment e Paste segment color Select this command to apply a previously copied segment color mapping to the currently selected object or segment e Import segment color Select this command to import a previously saved segment color map file e Export segment color Select this command to save the color mapping of the currently selected segment to a human readable colormap file on your disk e Save Delete preset Select this command to save or delete Window Level Opacity and color presets from the Preset selection list See Preset selection within this chapter e Change to
121. n info file window You may also use the keyboard shortcut Ctrl O to open an existing scene Save Select this command to save your work You should save your work frequently throughout the scene creation process Saving a scene with Save or Save as will generate a Volume Graphics Info file vgi extension The vgi file includes data relevant information such as the file name and path data type file type file size and data mapping as well as scene relevant information such as light settings rendering algorithm or background color You may also use the keyboard shortcut Ctrl S to save a scene Save As Select this command to save the current scene under a different name You could use this for example to save the current scene to a different drive or to save the changes un der a different name thereby keeping the original scene intact You may also use the F12 key on your keyboard to save a scene under a different name Merge Object Select this command to load additional objects into the active scene To merge objects select a vgi file and click Open If the vgi file includes more than one ob ject a dialog box will open where you may select one or several of the included objects that are to be loaded into the active scene All object properties of the merged object such as posi tion and rotation will remain unchanged during a merge process The scene properties of the active scene e g background color or illumination will also
122. nd drag the line to the desired position in the Opacity ma nipulation area The segment ranges will be displayed while dragging the line Opacity manipulation area we i Fan i Graw walues ita Fig 115 While dragging the line the seg ment ranges will be displayed A new segment may be generated by dragging either the left or the right border of the Opacity manipulation area or the blue segment border line When placing the cursor on one of the seg ment border lines it will assume different shapes Each shape indicates the action that can be applied when clicking the line with the left mouse button and then dragging the line see Fig 116 for the different shapes the cursor may assume VGStudio 1 1 User s Manual 119 4 VGStudio Interface amp Tools Opacity manipulation area Opacity manipulation area Opacity manipulation area Pal Gray values Gray values Gray values Fig 116 The cursor shown in the left image indicates that you may generate a new segment to the left of the current segment s border The middle image indicates that the segment border may be moved to the left or right The right image indicates that you may generate a new segment to the right of the current segment s border VGStudio allows the user to generate the maximum number of one segment per grayvalue This provides a maximum degree of freedom when applying arbitrary opacity and color values The segment names displ
123. nder properties tered properties v Scene tree Light properties z D a I wf Camera view w Polygon properties BIRT W Object properties Fig 53 The Tools menu Use the Tools menu to activate or deactivate the various tools of VGStudio A check mark in VGStudio 1 1 User s Manual 73 4 VGStudio Interface amp Tools front of each entry indicates that a tool 1s activated 74 Classification Select this command to activate or deactivate the Classification tool For more information on the Classification tool please refer to Chapter 4 6 1 Render properties Select this command to activate or deactivate the Render properties tool For more information on the Render properties tool please refer to Chapter 4 6 3 Stereo properties Select this command to activate or deactivate the Stereo properties tool For more information on the Stereo properties tool please refer to Chapter 4 6 5 Scene tree Select this command to activate or deactivate the Scene tree tool For more information on the Scene tree tool please refer to Chapter 4 6 2 Light properties Select this command to activate or deactivate the Light properties tool For more information on the Light properties tool please refer to Chapter 4 6 4 World view Select this command to activate or deactivate the World view tool For more information on the World view tool please refer to Chapter 4 6 8 Camera view Select this command
124. ne CT Tissue CT Lung CT Liver CT Abdomen CT Bone Tissue CT Color and MR Head You may add your own or overwrite existing settings in the preset list by saving the actual set tings defined in the classification tool Press the right mouse key within the classification tool to bring up the context menu Select the Save preset option to save the actual settings Reset Rol Delete all segments nave preset Delete preset Change to levelsyvindoy mode Fig 96 The context menu with theSsave Delete preset options A dialog will come up to where you have to either select an existing preset to overwrite or to enter an name to create a new preset lel Save preset Save preset please chose preset to Update or enter new name then click button my Preset E Absolute Preset oron Fig 97 The Save preset dialog A Preset will be applied relative to the existing data range of your data This means that the color and opacity window level settings for a certain gray value may vary in case that the data range minimum to maximum gray value in your data changes You may save absolute Presets to pre vent this behavior Activate the Absolute Preset check box in case that the Presets should be applied according to absolute gray values You may delete a preset from the preset list To do so press the right mouse key within the clas sification tool to bring up the context menu Select the Delete preset option to
125. nly the bone structure teeth and metal will remain visible VGStudio 1 1 User s Manual 39 3 Getting Started To enhance the 3D perception of the image activate the Shadow light source Light properties Overall intensity I229 Front light source ambient E Jw diffuse E Shadow light source ambient E M diffuse 33 Fig 17 The Light properties dialog To activate the shadow light source click the checkbox in the Shadow light source section of the Light properties dialog Fig 18 The 3D image after having ac tivated the Shadow light source The jaw will now appear with realistic shadowing Another very powerful function of the Classification tool is the grayvalue segmentation To demonstrate this feature we will first reset the Classification tool To do so click into the Object overview section with the right mouse button and click Delete all segments as shown in the fol lowing figure 40 VGStudio 1 1 User s Manual 3 2 First Steps with VGStudio Classification Urrent preset pe Object overview K Reset Rol Delete all segments Opacity Manipulation area Segment 1 Gray values Color manipulation area H ant i Fig 19 Click Delete all segments to reset the Classification tool to its default values Then move the mouse cursor to the right border of the Opacity manipulation are
126. o the Installation amp Information Card which is supplied with your VGStudio 1 1 software package for up to date and detailed information on the installation procedure for your operating system It also provides you with the latest information on the current VGStudio 1 1 release VGStudio 1 1 User s Manual 23 2 Installation 2 4 VGStudio 1 1 License The VGStudio 1 1 License update window will pop up when you start VGStudio 1 1 for the first time or when no valid license was found on your system Enter your name or the name of your company and the license key which is included in your VGStudio 1 1 software package and click OK You may also ask the Volume Graphics support for a trial license at vgstu dio volumegraphics com To do so press the Create registration form button fill in the re quired information and send the registration form to Volume Graphics See Chapter 1 6 Feedback for more information on how to contact Volume Graphics directly lee Update node locked license License eee To order full or trial license please create registration farm Till out form and send the fully tilled out form to Yolume Graphics Create registration form Licensed to Dr GUENNE Hardware ID O CIEE DSF AHASS 28DAFOCBEOS27 1436 License key E E 5 E ee E E 5 p ee B Expiry Data rmm dd yyyy 7 Hi S Fig 3 The License update window where you enter your name and license key 24 VGStudio 1 1 User s
127. o the left or the right or type in the desired value and press Enter The Front light source is positioned in 0 i e in the eye of the observer the Shadow light source is positioned in 45 to the right of the observer The light sources are located at fixed positions relative to the observer Fs set m e l e T aa a at a a a ee ae as _ i ee S E oe Sias a A aie a m en O Te T T e a a T e m OTs en T a en Fa et en re Te te ae Pe i oe ee B a re T E e ort ane i L F lt a F Pam F a a a a Fa Ao gt oe yE fm Fig 142 The front light source and the shadow light source are located at fixed positions relative to the observer The two light sources Front light and Shadow light consist of two parts each 1 e an Ambient part and a Diffuse part Each part s intensity can be adjusted independently by typing in the de sired values or using the up and down arrows Deactivating the shadow light source will result in an increased rendering speed when working with the Scatter or Scatter HQ algorithms the speed will be increased by a factor of two Click the white push buttons to apply a color to the appropriate light source Use the checkbox on the right hand side to enable or disable the light sources 4 6 5 Stereo Properties VGStudio supports several stereo image rendering modes Stereo properties Stereo p
128. oft Windows 9x Windows NT 4 0 or Windows 2000 operating system Pentium III or higher or equivalent CPU 64 MB RAM 128 MB or more recommended Super VGA display 17 or larger recommended with 800x600 resolution and 256 colors 1280x1024 at High Color recommended CD ROM drive Unix Linux 2 0 other Unix OS on request operating system 64 MB available RAM 128 MB or more recommended Super VGA display 17 or larger recommended with 800x600 resolution and 256 colors 1280x1024 at High Color recommended CD ROM drive 20 VGStudio 1 1 User s Manual 2 2 VGStudio 1 1 on Multiprocessor Hardware 2 2 VGStudio 1 1 on Multiprocessor Hardware Almost all features included in VGStudio 1 1 are implemented multithreaded so that VGStudio 1 1 takes full advantage of modern processor technologies Especially on multiprocessor SMP hardware VGStudio 1 1 delivers an almost linear speedup proportional to the number of proces sors in use VGStudio 1 1 utilizes the full memory bandwidth of today s and upcoming system designs to provide its users with an optimal performance By default VGStudio 1 1 utilizes all processors available in a system The user may limit the number of processors used by VGStudio 1 1 by applying the environment variable PROCES SORS with the appropriate number of processors Adding environment variables on a Windows NT 4 0 2000 System Step 1 Choose Settings in the Program Manager Start menu Step 2 Choose Contro
129. omputational power and memory re quired for real time volume rendering In contrast to classical or advanced 2D image processing volume visualization and analysis produces huge amounts of data so that memory processor performances and algorithms are critical Due to the highly sophisticated algorithms used in VGStudio 1 1 and the increase in PC computing power volume graphics and volume analysis became accessible to everybody as the program runs on a standard PC The adoption of efficient solutions in VGStudio 1 1 e g the multiprocessor SMP capable implementation of nearly every VGStudio 1 1 feature allows the user to apply a trial and error approach to the analysis of 3D data the user can apply an operation or a transformation to the data and control the result in an interactive and real time environment and may thus select the best suited operation for his her needs By using VGStudio 1 1 everybody can take advantage of volume graphics tech nology which has inherent advantages for applications that need visualization of irregular ob jects or where the interior structure and a high quality detail representation are essential e g representations of the human body 12 VGStudio 1 1 User s Manual 1 2 Example Images Rendered by VGStudio 1 1 Users 1 2 Example Images Rendered by VGStudio 1 1 Users Fig 2 Here are example images rendered by VGStudio users VGStudio 1 1 User s Manual 13 1 Introduction to VGStudio 1 1 1 3 Abo
130. on which is indicated by one vertical and one horizontal arrow Please note that the two outer handles may only be moved in vertical direction Opacity manipulation area Opacity manipulation area Segment 1 T Segment 1 152 1 6135 h 1680 p 2725 Erral ee 2024 ort Pa d a Grayvalues Fig 112 You may drag the line and the handles to new positions with the left mouse button pressed VGStudio allows the user to generate the maximum number of one opacity handle per grayvalue This provides a maximum degree of freedom when applying an arbitrary opacity mapping 118 VGStudio 1 1 User s Manual 4 6 Tool Box Opacity manipulation area segment 1 Fig 113 The Opacity manipu lation with four new handles VGStudio 1 1 provides the user with a powerful tool to separate structures within a volume data set by their grayvalue range This process is called grayvalue segmentation A segment is defined by a grayvalue range within a data set A segment may include a range from one single gray value up to the full grayvalue range of the volume data set To define a grayvalue segment place the cursor on the borders of the Opacity manipulation area so that the cursor s shape changes as shown in the following figure Opacity manipulation area ra Gray values Fig 114 To define a segment drag the line to the desired position Keep the left mouse button pressed a
131. option The Enable and Disable options will toggle in the context menu i e will only be visible one at a time Enable Select this command to enable a previously disabled object or object group To do so select a disabled object in the Scene Tree window by clicking it with the left mouse but ton then click with the right mouse button into the Scene tree window to open the context menu and select the Enable option The Enable and Disable options will toggle in the con 135 a a ae 4 VGStudio Interface amp Tools text menu 1 e will only be visible one at a time Reset Select this command to reset actions of all categories applied to the selected object such as translation rotation clipping and scaling to the default values Reset single catego ries of actions in the Object properties tool See also Chapter 4 6 7 Object Properties Group Select this command to combine the current selection of objects or groups to a sin gle group A group of objects can be handled like a single object The Group command re mains disabled until more than one object is selected Several objects can be selected by dragging a frame over the objects in the 3D view window by clicking the objects with the left mouse button while the Ctrl key is pressed or by clicking the object s name with the left mouse button while the Ctrl key or Shift key is pressed in the scene tree tool The bounding box of each selected object will be visible when sever
132. orithms e Scatter e Scatter HQ e Scatter gradients e Maximum projection MIP e Sum along ray e X ray The following examples show one image in the six different rendering algorithms 138 VGStudio 1 1 User s Manual 4 6 Tool Box Examples Scatter Scatter gradients Maximum projection MIP Sum along ray X ray Fig 140 One image is shown in the six rendering algorithms available in VGStudio Reminder In most cases the opacity settings have to be adjusted in the Classifica tion tool to achieve optimal results with Maximum Projection MIP Sum along ray or X ray algorithms e g reduce the opacity and at the same time increase the illumination intensity to achieve best results when working with the X ray algo rithm Result image size Use the Result image size in the Render properties dialog to set the size in which the image should be rendered by VGStudio In addition the image on the screen may be enlarged or re duced by applying a zoom factor to the 3D View window Set the image size by simply typing in the desired values or by using the up and down arrows to either enlarge or reduce the width or height of the image VGStudio 1 1 User s Manual 139 4 VGStudio Interface amp Tools Rendering quality Images may be rendered in true color or in monochrome Rendering in monochrome will in crease the rendering speed by a factor of two Oversampling allows to adjust the resampling step width dur
133. oving the mouse up and down while the middle mouse button or the Alt key and the left mouse button is pressed To rotate the clipplane around the origin of the clipplane s normal vector click into the clip plane and drag the mouse while the left mouse button is pressed The origin of the clipplane s normal vector may be moved to any arbitrary position on the clipplane by clicking the clip plane s normal vector origin with the left mouse button and dragging the mouse while the left mouse button is pressed The clipplane will be disabled if several objects are selected Group the objects first if you want to clip several objects with one clipplane at a time For more in formation on the Clipplane mode see also Chapter 4 6 7 Object Properties Reset Select this command to reset actions of all categories applied to the selected object such as translation rotation clipping and scaling to their default values Reset single catego ries of actions in the Object properties tool For more information see also Chapter 4 6 7 Object Properties Group Select this command to combine the current selection of objects or groups to a sin gle group A group of objects can be handled like a single object The Group command re mains disabled until more than one object is selected Several objects can be selected by dragging a frame over the objects in the 3D view window by clicking the objects with the VGStudio 1 1 User s Manual 4 3 Menu Bar
134. p the Ctrl key pressed while clicking the objects to be selected A bounding box will appear around the selected active ob jects To deselect an object press the Ctrl key and click the selected object The bounding box will then disappear For different actions such as positioning rotating clipping or scaling the bounding boxes around the objects will be displayed in different colors see table below These bounding boxes also include active areas The mouse cursor has to be moved into an active area before an action can be applied to the object In positioning rotation and clipplane mode the whole bounding box is the active area In clipbox mode see figure below or scale mode squared handles on each side of the bounding box indicate the active areas Acive area Mowe cursor into active area Fig 8 Move the cursor into the active area to perform an action 32 VGStudio 1 1 User s Manual 3 1 Launching the Program The mouse cursor will change as soon as the mouse is moved into an active area which indicates that an action can now be performed The following table shows the colors of the bounding boxes and the shape of the cursor when a certain mode is selected Action Color of Default cursor Cursor on ac bounding box tive area Positioning green hag Clipbox cyan be be y Clipplane eo l e i a l e VGStudio 1 1 Magellan SPACE MOUSE support VGStudio 1 1 is designed to work with the LogiCad Inc GmbH Ma
135. piperi nani Hie fic id Che aca ta fpo y joa Jz foa Fig 50 The Instrument index card in the Grid Axes amp Instrument properties dia log Use the dialog shown in Fig 50 to adjust the instrument position in scene coordinates The size of the instrument can also be adjusted Click Apply to accept the new settings To reset the val ues to their default simply click Reset If you want to quit the dialog without accepting the new settings click Cancel All labels related to axes or planes orthogonal to the appropriate axis are colored according to the VGStudio color scheme 1 e all labels related to the x axis are displayed in red all labels related to the y axis in green and all labels related to the z axis in blue e Background color Select this command to choose a background color for the current scene Select one of the default colors from the menu shown in the figure below tue Fig 51 Choose one of E yen the default colors as background color for the current scene 72 VGStudio 1 1 User s Manual 4 3 Menu Bar You may also select Custom color to activate a color selection tool shown in Fig 52 background color Color selection Red re Green hss Blue 255 Fig 52 In the background color window you may define a background color for the active scene 4 3 6 Tools Menu Click Tool to open a pulldown menu containing the following entries Tools v Classification v Re
136. plained throughout this manual VGStudio 1 1 User s Manual 7 VGStudio 1 1 Medical Use Restrictions We wish to thank you for your past Support and continued usage of the VGStudio voxel data visualization and analysis program We have many future plans for the product and we will advise you through the appropri ate channels as these enhancements become available At the same time however we wish to remind you that the VGStudio products are for research use only or for investigational use only The Department of Health and Human Services DHHS National Institute of Health NIH defines research as a systematic investigation including research development testing and evaluation designed to develop or contribute to generalizable knowledge Cf 45 CFR 46 102 d The human subject in research is a living individual about whom an investigator conducting research obtains 1 data through intervention or interaction with the individual or 2 identifiable private information Intervention includes both physical procedures by which data are gathered and manipulations of the subject or the subject s environment that are performed for research purposes Interaction includes communication or interpersonal contact between the investigator and subject Cf 45 CFR 46 102 f Similarly the DHHS Food and Drug Administration FDA defines an in vestigation as a clinical investigation or researc
137. r VGStudio is capable to import GNU zip compressed data files Mark the GNU zip checkbox to import compressed data He Reminder Compression will not work in conjunction with ASCII data zgr F 164 VGStudio 1 1 User s Manual 5 1 Importing Data Step 5 Image size selection for RAW data only lee Import tool OF Xx Size Please specify the size of your data set The header size defines the number of bytes which eventually have to be skipped trom the start of the file due to file headers Se c I I I II I OS AAAA 256 y ae eee eee 256 Header _ i GUESS Previous Pest Cancel Fig 163 Select the image and header size for RAW data by dragging the sliders or typing in the desired values The image size and header size in bytes has to be specified 1f the file type RAW was selected Use the sliders or type in the x y and z size of the volume data If the volume data set includes a header enter the header size in bytes The header has to be located at the beginning of the data file and will be skipped while loading You can use the Guess button after having entered the size to compute the header size automatically VGStudio 1 1 User s Manual 165 5 Importing amp Exporting Data Step 6 Data type selection for TIFF JPEG BMP and PPM images only Biel Es lel Import tool Data type Chose the colorsceme of data stored in your files Color i Gre
138. r of the corresponding window with the left mouse button and dragging the window to the desired position The arbitrarily arranged windows may be rearranged by one of the Arrange modes or by the Cascade option VGStudio 1 1 User s Manual 75 4 VGStudio Interface amp Tools 4 3 8 Help Menu Click Help to open a pulldown menu containing the following entries Abot License update Manual Fig 55 The Help menu e About Select this command to open a window with information on your VGStudio release me VGS 1 bude TIT hac ET 14077 Pot credits pam et toh raul Fig 56 In this window you will find information on your VGStudio release 716 VGStudio 1 1 User s Manual 4 3 Menu Bar e License update Select this command to open VGStudio s License update window Update node locked license _ _ Fig 57 VGStudio s License update window e Manual Select this command to open VGStudio s Manual Please keep in mind that the Adobe Acrobat Reader has to be installed on your computer to be able to open up the man ual VGStudio 1 1 User s Manual 71 4 VGStudio Interface amp Tools 4 4 Icon Bar JO sR S BOO gt i D ek eo Be B r Fig 58 The VGStudio icon bar The tools in the icon bar provide quick access to many common VGStudio functions When placing the cursor on an icon a tooltip will appear which shows the function of the icon The tools ar
139. s Disable histogram Select this command to disable the histogram within the Opacity manipulation area Zoom in Select this command to zoom in the histogram within the Opacity manipula tion area Zoom out Select this command to zoom out the histogram within the Opacity ma nipulation area Zoom reset Select this command to reset the zoom factor of the histogram within the Opacity manipulation area to its default value e Change to Level Window mode Select this command to switch the classification tool into Level Window mode e Save Delete preset Select this command to save or delete Window Level Opacity and color presets from the Preset selection list See Preset selection within this chapter Level Window area Level Window mode The user may apply a value for Center also known as Level value and Width also known as Window value of a ramp in Level Window mode To adjust the values simply type in the ap propriate values or use the up and down arrows to either increase or reduce the Center or Width value The resulting opacity ramp can be seen immediately in the Opacity manipulation area Level Window area Center 538 0 idth S66 Oe Level Window area Fig 127 The Opacity manipulation area 128 VGStudio 1 1 User s Manual 4 6 Tool Box Opacity manipulation area Level Window mode The opacity manipulation area can be used as an convenient tool to adjust the Level and Window values Le
140. se button In conjunction with certain window manag ers the Alt left mouse button combination is already in use A second alternative to emulate the middle mouse button when using a two button mouse is to use the combination Shift Ctrl left mouse button Throughout the manual you will find the following icons The icons indicate which mouse but ton you should press to perform the appropriate action Press left mouse button Press middle mouse button Press right mouse button select object by clicking on tt Fig 6 When clicking an object with the left mouse button you select or activate it This is indicated by a bounding box around the object By clicking an object with the left mouse button you select or activate an object You may also select several objects at once by clicking into a window with the left mouse button and then dragging a frame over the objects while the left mouse button is pressed or by using the shortcut Ctrl A when using this shortcut all objects currently displayed in the scene will be selected You may deselect one ore several objects by clicking outside the bounding box of any object The box around any object will disappear VGStudio 1 1 User s Manual 31 3 Getting Started _ z a A A Scere Fig 7 Select several objects by dragging a frame over the objects while the left mouse button is pressed To select more than one object but not all objects of the scene kee
141. select all objects e Deselect Select this command to deselect all selected objects in the scene You may also VGStudio 1 1 User s Manual 63 4 VGStudio Interface amp Tools use the keyboard shortcut Alt D to deselect all objects e Select Inverse Select this command to invert the active objects in the scene You may also use the keyboard shortcut Alt I to generate an inverse selection e Preferences Select this command to access the Preferences dialog box where you can set VGStudio preferences For more information on this dialog please refer to Chapter 4 3 3 Setting Preferences 4 3 3 Setting Preferences Numerous program settings are stored in the preferences file vgstudio cfg located in the VGStudio application folder The settings stored in this file include general appearance options directory information tool options and options such as time periods for auto saving the scenes you are currently working on In the Preferences dialog you may adjust the settings for Direc tory information and other Options such as auto saving Preference settings are saved each time you exit VGStudio To open the Preferences dialog box select Preferences in the Edit menu Then choose the de sired preference index card by clicking it The index card Directories is used to set up where VGStudio should look up or save different kinds of files Enter the appropriate path or click the Browse button to select a directory in the Find Direc
142. sition are defined in scene coordinates while aF most other tools work in object coordinates The color coding in the slice tools may J liy f kia not fit to the color coding of the camera tool in case of an rotated object Click one of the six Default view buttons to view the scene either from the front back left right top or bottom pal il ad at gh The distance between the observer and the scene s center which can be adjusted in Move mode will remain unchanged when one of the Default view buttons is pressed Drag the Viewing angle slider to the left or right or type in the desired value to adjust the view ing angle For more detailed information on the Camera view mode please refer to Chapter 4 5 3 154 VGStudio 1 1 User s Manual 4 7 Status Bar 4 7 Status Bar instrument position 54 060 62 4354 126 219 value 26574 idle U The status bar is displayed at the bottom of the main window In the status bar you will find in formation on the current process performed in VGStudio and the progress of the different proc esses as well as the instrument position and the appropriate gray or color values at the instrument s position when the instrument is activated VGStudio 1 1 User s Manual 155 5 Importing amp Exporting Data This chapter provides information on the data I O capabilities of VGStudio Detailed information on e importing data and e exporting data will be given in this chap
143. ssssscssssesscees 56 Al 2D slices and 31 Mates aa e can era tdanetss wcamare nucle a omaains hab tuaabetecchonmats ibaa lay 56 AM WAG SUG COLOR COGN Ss ssh Sie el ee Ss eet Somat ah tl Secale Sead A 56 Al Tool Doosan area Sansa se actin cetera unscee tae sth uan sitet A 57 4 2 Title Bar Elements scecssisvascssececeasasewsscasaassuataciwssstewardvataacwsssisaarinatsiewssstanardvadaacvsssisaadinedsievisstaaardvedsacncsbanaenieets 58 4 3 Men Baionari nEn EA E A TA A E a 59 do E Me n E E A E E E 59 ee Ee MGE a a A E a a EA 62 For De Pr EC S e EE EN E E a 64 Pe MOD FSC E a e a E S 67 Poo o EN a ate aea a a aguas at cece nenteanseieue ss 70 Ee Too EN Aa aea a a a sete dear ueteacasenenteacensesouos 73 Boe W dOn Me Piee ee evesannean tacsabacaasedeas uetannaneneuneacen oguenats 75 Wa HPN Ia A E EO 76 4 4 lon Baise E ENE ENEE E E R EE E EE 78 JA Standard COn Secon ene a aia Olona cteeth dat acans Ghauesaeuade 78 AA ObjectNianipulatOn SECOs hiss senctucuastiadtadianisn sda tie aan nell ouaue eietndalareag td eens 81 AAS SCCM OOS sreistetncs Sea cata a R Gdewnaiie 87 Ah VIEW SClECUON cht etiosboncsiaushectes sda Geaian A naa Cdeehaiies 90 AAS Window Layout Section s inre facia a a ke td a octuea a ewe ade rct EA 91 AAG Wihat s his Section e E AE 92 4 5 THEW orks pa Cna E E N see ca sdaveevecteseress 93 4 5 1 Slice Windows and Multiplanar Reformatting cccccscesssseeeceeceeeeeeeeeeaeeaeseeseeeeeeeeeeeeeeeeeeeeeeeaaaae
144. step and change the settings and then check the results again in the Preview window Use the slice selection slider to select the slice to be displayed VGStudio 1 1 User s Manual 185 5 Importing amp Exporting Data Fig 186 The Import Dicom files window A region of interest ROI may also be defined To do so grab one of the corners of the blue frame around the region of interest or grab the frame itself by clicking it with the left mouse but ton You may now resize the region of interest by dragging the frame to the desired position while holding the left mouse button pressed Use the Auto scan checkbox to automatically scan the currently displayed slice for optimal grayvalue mapping 5 1 7 Importing Polygon Data VGStudio is capable to import polygonal data stored in Off file format More information on the off file format can be found in the Geomview Manual which can be accessed via the following internet address http www geom umn edu software geomview geomview_toc html The man ual is provided by the Geometry Center of the University of Minnesota 186 VGStudio 1 1 User s Manual 5 2 Exporting Data 5 2 Exporting Data 5 2 1 Exporting Raw Volumes A single volume object can be exported as a Raw volume data file To do so select Export and Raw Volume in the File menu cy Eyy Ctri h en Ctrl a av Ctr S T ai AE ER is SAVE GS Merge object save object Import H
145. sue object was clipped half by means of the clipbox mode so that half of the bone structure can be seen Please note that you have to enable both the CT scan of the jaw and the extracted soft tissue otherwise the bone structure will not be visible when clipping the object Fig 123 The CT scan of a human jaw after the soft tissue has been removed from half of the jaw The extracted segment in the original volume data object will not be destroyed The extracted segment will only be disabled in the original object VGStudio 1 1 User s Manual 125 4 VGStudio Interface amp Tools Classification Preset selection rove Object overview Opacity Mo area EE noise f air bone matal Gray values r manipulation area Te Fig 124 The soft tissue segment will be disabled after the extraction process The extracted and disabled segment may be enabled again by using the Enable segment option in the context menu of the Opacity manipulation area This allows the VGStudio user to ex tract a segment several times to apply different clippings or opacities as shown in the following example Fig 125 Different clippings or opaci ties may be applied to an object Data extracted from an object may be saved to disk as a separate data file If data from an ex tracted segment is saved with the Export raw option of the File menu only the grayvalue range of the extracted segment will be saved All other vo
146. t or group of objects When moving the cursor into the bounding box it will take the shape of one vertical and one horizontal circular arrow see the table in Chapter 3 1 2 Mouse Usage The object may be rotated around the x or y axes of the image plane by clicking into the bounding box and dragging the mouse while the left mouse button is pressed The object may be rotated around VGStudio 1 1 User s Manual 67 68 4 VGStudio Interface amp Tools the viewing direction by clicking into the bounding box and dragging the mouse while the middle mouse button or the Alt key and the left mouse button is pressed The whole bound ing box may be used as active area to apply the appropriate action For more information on the Rotate mode see also Chapter 4 6 7 Object Properties Scale Select this command to scale the selected object or object group The Scale mode is characterized by the dark blue bounding box with squared handles 1 e active areas on each side of the selected object or group of objects A rectangular shape will appear next to the cursor when moving it into the active area see the table in Chapter 3 1 2 Mouse Usage The object may be scaled along the x y or z axes by clicking the handle 1 e the active area on one side of the bounding box and dragging the mouse while the left mouse button is pressed Isotropic scaling may be performed by clicking into the bounding box and moving the mouse up or down while the middle mouse
147. tain several sections in case that the users loads a data set which was segmented with VGStudio MAX segmentation capabilities Each segment will result in an own section in the scene tree VGStudio is not capable to generate sections however VGStudio is capable to handle data sets prepared by VGStudio MAX 134 VGStudio 1 1 User s Manual 4 6 Tool Box You may change the name of the object or object group Simply double click the object with the left mouse button and then type in the new name Scene tree cene tree El ES groug 1 fan a jaw CT scan reterence a EF jaw CT scan reterence Fig 137 The name of the object may be changed by double clicking it and then typ ing in the new name Disable Enable Group Ungroup Delete Duplicate Create Reference Select All Select Mone Select Inverse Fig 138 The context menu of the Scene tree tool Click into the Scene tree tool with the right mouse button to open the following context menu VGStudio 1 1 User s Manual Disable Select this command to disable an object or object group A disabled object will no longer be displayed in the scene No action can be applied to a disabled object You first have to enable it again To do so click the object in the Scene tree window with the left mouse button then click with the right mouse button into the Scene tree window to open the con text menu and select the Enable
148. te Siceh re Axia lite Sbieh Fig 66 The 3D instrument will be displayed in red when the cursor is located in the currently selected slice In a slice image the cursor will appear in red when the cursor is located in the slice that is cur rently selected It will appear in white as soon as the displayed slice is another one than the one in which the cursor is positioned at the moment In the example shown in Fig 66 the cursor is located in slice 54 and the cursor in the left image slice 54 is displayed in red In the right image slice 55 is shown and the cursor is displayed in white If the cursor is placed outside the selected voxel data set or if the active object is a polygon ob ject only a red bounding box will appear in the slice windows see figure below Fig 67 A red bounding box will be displayed when the cursor is placed outside the selected voxel data set 88 VGStudio 1 1 User s Manual 4 4 Icon Bar Scene Axes Click this icon to activate the scene coordinate axes The display of the axes can be customized in the Properties dialog which you open via the Scene menu Fig 68 The coordinate axes are displayed Scene Grid E Click this icon to activate a grid in the scene The display of the grid can be customized in the Properties dialog in the Scene menu VGStudio 1 1 User s Manual 89 4 VGStudio Interface amp Tools ENERET PETTY PEER i ae ae ae eas Py BEEP 3
149. ter 5 Importing amp Exporting Data 5 1 Importing Data 5 1 1 The VGI Volume Graphics Info file VGStudio allows its users to import a wide variety of different data files and data types The voxel or volume data my be provided as a single data file or as a stack of several image data files Stack of Image Slices PPM See Appendix RAW signed unsigned 8 bit integer RAW signed unsigned 16 bit integer RAW signed unsigned 32 bit integer 20 bit effective range 32 bit float 32 bit RGBA E Volumes o meon o r Anaye RAW szbitffo o 32 bit float RAW 32 bit RGBA Select the Import option in the File menu and choose the appropriate option to import the dif ferent data types and files 158 VGStudio 1 1 User s Manual 5 1 Importing Data a rrr a EnA tS LaF ELL Sare Maden r ai B ratini Fig 157 Select Import in the File menu and choose the appro priate option to import the different data types After having imported the data you may save your scene Saving a scene with the Save or Save as option in the File menu will generate a Volume Graphics Info file vgi extension The vgi file contains all information needed by VGStudio 1 1 to load data again by using the Open command in the File menu You do not have to use the import procedure again The vgi file con tains data relevant information such as data file names and the path to the data files data type file type file size and data mapp
150. the slice windows three perpendicularly oriented cross sec tions axial sagittal and frontal of the currently selected object are displayed The projection of the data sets origin is always displayed as a colored tripod in the lower left corner of the window The coordinate system used in the slice images is either the object coordinate system object relative mode of the currently selected object or the scene coordinate system scene coordinate system The slice images show in both modes perpendicular cross sections through the selected data set In object coordinate system Axial slices are perpendicular to the z axis frontal slices are perpendicular to the y axis and sagittal slices are perpendicular to the x axis Fig 73 In the three slice windows of VGStudio the cross sections axial frontal and sagittal are displayed 94 VGStudio 1 1 User s Manual 4 5 The Workspace Frontal xz slice Iof x al a 63 r 4 H 2 Fig 74 VGStudio s frontal view window In the title bar of the slice windows the orientation 1 e axial sagittal or frontal and the image planes i e the xy yz and xz planes are displayed In the left corner of the title bar you find the Control icon which you use to access the Control menu Double clicking this icon will close all three slice windows You can use the Control menu to maximize or minimize the slice windows or to close them The window buttons can be found in the right corner of t
151. the three orthogonal slice windows into Scene relative mode The object will be sliced along the axes of the scene coordinate system This mode allows the user to slice the object along any arbitrary axis To define the slicing orientation rotate the object against the scene coordinate system Select the rotate mode in the 3D window and rotate the object against the scene coordinate system The scene coordinate system can be seen when activating the Axis in the 3D window Scene coordinate system Fig 78 MRI scan sliced in scene relative mode VGStudio 1 1 User s Manual 4 5 The Workspace Cross Sections Displayed in the Slice Images If several objects are loaded into the scene only one of the objects will be displayed as slice im ages All other objects or groups of objects will appear as a cross section through their bounding box if the box is crossed by the slice plane of the currently selected object Only the bounding boxes will be displayed in the slice windows if several objects a group of objects or a polygon object are selected Fig 79 If several objects are loaded into the scene one of the objects will be displayed as a slice image for the other objects only the bounding boxes will be shown If a slice outside the active volume data set is chosen only a red bounding box will be displayed in the slice windows to display the currently selected object offs 5 Le P E Se er aif A Fig 80 A red bounding box wil
152. the whole import process Click the Next or Previous buttons to go through the different steps of the import process The different steps will be explained in the following VGStudio 1 1 User s Manual 173 5 Importing amp Exporting Data Step 1 File selection E Import tool Jovg4icds data yolwrist dat Fig 172 Select the file you want to import Click Browse to open a file selection dialog Select one file and click Open The selected path and filename will appear in the File name section of the Import Wizard Then click Next to continue 174 VGStudio 1 1 User s Manual 5 1 Importing Data Step 2 Data type selection fe Import tool Pile Es Data type Choose the type of data stored in your file Signed means that there may be negative numbers unsigned means all the numbers are postive or Zero unsigned 16bit f binary fC ASCH Endian fe little C big Ompression e r GNU zip Previous Mest Cancel Fig 173 Specify the data type for Raw images The data type has to be specified Select the data type of the chosen file from the pulldown menu Possible data types are e signed or unsigned 8bit 16bit or 32bit e 32bit float e 32bit RGBA Decide whether the data is to be stored in binary or in ASCII format and select the byte order VGStudio is capable to import GNU zip compressed data files Mark the GNU zip checkbox to import compressed data Reminder Compression
153. to clip the selected object or object group by an arbitrary clipplane The Clip plane mode is characterized by the cyan bounding box with a normal vector on one side of the active object When moving the cursor into the bounding box a scissors will appear next to the cursor see the table in Chapter 3 1 2 Mouse Usage The object may be clipped along an arbi trary clipplane by moving the mouse up and down while the middle mouse button or the Alt key and the left mouse button is pressed To rotate the clipplane around the origin of the clipplane s VGStudio 1 1 User s Manual 85 4 VGStudio Interface amp Tools normal vector click into the clipplane and drag the mouse while the left mouse button is pressed The origin of the clipplane s normal vector may be moved to any arbitrary position on the clip plane by clicking the clipplane s normal vector origin with the left mouse button and dragging the mouse while the left mouse button is pressed The clipplane will be disabled if several ob jects are selected Group the objects first if you want to clip several objects with one clipplane at a time For more information on the Clipplane mode please refer to Chapter 4 6 7 Object Prop erties Liven mouss chosen while J 5 Toole TOUS eS i oe A ie Fig 64 Clip the object along an arbitrary clipplane by dragging the mouse up or down while the middle mouse button is pressed By dragging the mouse inside the active area while the left
154. tory dialog box im elerne Sanes ribal Berara Pwe p o O Tejacis fia s Broese Raw marte ite n HOP hrpta a Drowse Browns Seow Browse Browns Dicom imporre oa re hee isn Enem Fig 42 The Preferences dialog box with the Directories index card selected e The Scenes path is the default directory where the Open file dialog looks up scene files saved as Volume Graphics Info files vgi 64 VGStudio 1 1 User s Manual 4 3 Menu Bar e The Polygons path is the default directory where the Import Polygon file dialog looks up polygonal data files off e The Objects path is the default directory where the Merge object file dialog looks up Vol ume Graphics Info files vgi e The Raw Imports path is the default directory where the Import Raw volume import wiz ard looks up raw data files e The HDF Imports path is the default directory where the Import HDF volume file dialog looks up Hierarchical Data Format files hdf e The Dicom Imports path is the default directory where the Import DICOM image series file dialog looks up Dicom and Papyrus files e The Images path is the default directory where the Save image file dialog saves image files e The Exports path is the default directory where the Save data file dialog saves data files e The Presets path defines where the VGStudio Classification tool presets where located Re fer to Chapter 4 6 1 Classification Tool The index card
155. ts offset to the original object is used as offset for every new duplication process This procedure is called smart duplicate Reminder The offset adjusted during a smart duplicate will be set to its default value zero as soon as the duplicated object is deselected or another object is se lected VGStudio 1 1 User s Manual 4 6 Tool Box Create Reference Select this command to create a reference of an object A reference is a copy of an object which uses the same classification tool settings color and opacity settings as the original object Due to this special property a reference needs hardly any additional system memory Therefore a reference is a memory saving possibility to copy objects You may also use the keyboard shortcut Ctrl R to create a reference In the Scene tree tool a small arrow will appear in the symbol displayed on the left hand side of the scene name and after the scene name the text reference will appear Applying the Create Refer ence command to a polygon object will result in a normal copy of the object Creating a reference includes a smart placement functionality An example select an object and click Create Reference in the context menu or press Ctrl R The new referenced object will ap pear as the currently selected object Move the reference to a new position in the scene Se lect Create Reference in the context menu or press Ctrl R once again The second referenced object will appear in
156. tutiostuntstuo220 bmp Cov Stutiostuntstu0206 bmp Cov Stutiostunt stu 34 bmp Cov Stutiostuntstul226 mp e r ee oe ee Lee Unsorted Alphabetic Up Alphabetic Down Canonic Up Canonic Down Numbers Up Numbers Down Reverse Up Reverse Down Fig 161 Sort the files by using the Sort function of the Import tool window To sort the files you may use the Sort function of the Import tool window there you may choose the order in which you wish to sort the files e g alphabetical order You may also use drag and drop to bring the files into the correct order Click Next to continue with the import process VGStudio 1 1 User s Manual 163 5 Importing amp Exporting Data Step 4 Data type selection for RAW data only lee Import tool Biel Es Data type Choose the type of data stored in your files Signed means that there may be negative numbers unsigned means all the numbers are positive or Zero unsigned 16bit f binary i ASC Endian i little c hig OMmpression ee r GNU zip Previous Mest Cancel Fig 162 Specify the data type for RAW images The data type has to be specified if the file type RAW was selected Select the data type of the chosen file from the pulldown menu Possible data types are e signed or unsigned 8bit 16bit or 32bit e 32bit float e 32bit RGBA Decide whether the data is to be stored in binary or in ASCII format and select the byte orde
157. uality However keep in mind that 184 VGStudio 1 1 User s Manual 5 1 Importing Data slice images will be generated out of your original data which are not generated by the scanning device The resampling will also result in an additional amount of memory needed by the VGStudio application This process may exceed the available memory installed in your computer depending on your initial image data Press No to skip the resampling process so that only the original image data is loaded However this may result to low 3D image quality Press the Details button to get an detailed overview of the selected DICOM acquisitions which will be displayed in the Import Dicom files window along with other information included in the files such as patient name date of birth etc You may again select or deselect one or several files to setup a correct lists of files to be im ported into VGStudio Only selected files which are highlighted by a blue background will be imported E mpat COCO thes h ak k ck ak ck ck cm oe ch ch ch Ra all mi F 5A Fig 185 The Import Dicom files window EEEH TE 23 rE NA EEA tS TEEN tS Pria ee rier 203 EPLE pees 23 pees 23 E e HG F b The Preview window may be used to view your data as slices before starting the import process This may help you to choose the right parameters If you are not satisfied with the results you may always go back to any previous
158. ut this Manual VGStudio has been designed to be as intuitive as possible but as it is a sophisticated program you might need help from time to time In this case you should refer to this manual which in cludes a comprehensive table of contents and an index to help you find the information you need This manual assumes that you are familiar with the Unix or Windows operating systems If you need help with features specific to either system please refer to the documentation supplied with your computer 14 VGStudio 1 1 User s Manual 1 4 Conventions Used in this Manual 1 4 Conventions Used in this Manual This manual uses the following conventions to identify information e Whenever you must execute a command by clicking the mouse the command will be dis played in bold text for example click OK to continue e Menu items and buttons also appear in bold text for easy identification for example the File menu or the Save button e You will find the following icons throughout the manual The icons indicate which mouse button you should press to execute the appropriate action Press left mouse button Press middle mouse button Press right mouse button e Throughout the manual you will find Reminder icons They indicate important facts and exceptions e Chapter cross references are displayed in italics for example Chapter 1 Introduction e This manual combines Windows and Unix instructions In most cases they overlap
159. will not work in conjunction with ASCII data VGStudio 1 1 User s Manual 175 5 Importing amp Exporting Data Step 3 Image size E Import tool Fig 174 Select the image and header size by dragging the sliders or typing in the desired values Use the sliders or type in the x y and z size of the volume data If the volume data set includes a header enter the header size in bytes The header has to be located at the beginning of the data file and will be skipped while loading You can use the Guess button after having entered the size to compute the header size automatically 176 VGStudio 1 1 User s Manual 5 1 Importing Data Step 4 ROI and Skip selection E Import tool Fig 175 Define Regions of Interest and choose the skip rate Use this dialog of the import wizard to define a region of interest within the imported stack of images or to define the number of voxels to be skipped in each direction of the image planes by dragging the sliders or typing in the desired values These functions may be of special interest for very large data volumes to reduce the amount of data loaded in VGStudio Use the six Region of Interest sliders to define a sub cube within the data set which should be loaded into VGStudio VGStudio 1 1 User s Manual 177 5 Importing amp Exporting Data e voxel data set Fig 176 Define a Region of Interest that is to be loaded into VGStudio Use the three Skip sliders to specif
160. with the three orthogonal cross sections axial frontal and sagittal Fig 36 In addition to the 3D view window VGStudio also displays 2D image viewing windows with the three orthogonal cross sections axial frontal and sag ittal 4 1 2 VGStudio Color Coding The x y and z axes and the planes orthogonal to these axes are coded by a color scheme throughout the whole VGStudio user interface The x axis and image planes orthogonal to the X axis are displayed in red the y axis and image planes orthogonal to the y axis in green and the 56 VGStudio 1 1 User s Manual 4 1 Basic Concepts of the VGStudio User Interface Z axis and image planes orthogonal to the z axis in blue In the three slice windows a small col ored tripod is displayed in the lower left corner which shows the orientation of the respective image in the 3D data set Labels in tools as well as scene axes or grids are displayed in the same colors The bounding box of an object includes a colored tripod at voxel position 0 0 0 The axes are colored in the same scheme 1 e the x axis is red the y axis is green and the z axis is blue Fig 37 A tripod colored according to the VGStudio color scheme is displayed at voxel position 0 0 0 4 1 3 Tooltips A tool tip will pop up and display the function of an element of the VGStudio user interface when the mouse pointer is placed on an element e g buttons or tools VG StudioM aa Eie dueg budio Vals indies ia
161. xels with grayvalues below the data range of the extracted segment will be mapped to the minimum value of the appropriate data representa tion all values above the data range will be mapped to the maximum value of the appropriate data representation 126 VGStudio 1 1 User s Manual 4 6 Tool Box Grayvalue segmentaton 127 Data value mapping Mapped to min value Mapped to Max value Extracted segment WIth ongina mapping Fig 126 After the extraction process only the grayvalues within the ex tracted segments will remain In the example shown here a segment was extracted out of a signed 8 bit integer data set data range 128 to 127 The voxels with grayvalues below the extracted segments data range will be mapped to 128 while the voxels with values above the extracted segments data range will be mapped to 127 Only the grayvalues within the extracted segments data range will remain In most cases the size of the bounding box of an extracted object will differ from the size of the original object The new bounding box will be cropped so that the extracted object will fit ex actly into the bounding box In the following you will find a description of the remaining context menu entries of the Opacity manipulation area e Histogram Select this command to open the histogram menu Disable histogram foam in Zoom out Soom reset VGStudio 1 1 User s Manual 127 4 VGStudio Interface amp Tool
162. y the number of voxels to be skipped in each direction When choosing a value of 1 every second voxel will be skipped in the selected direction The follow ing image shows the example for skip values of 1 in each direction t skipped voxel BD inportea voxel Fig 177 For each direction a skip value of 1 was chosen 178 VGStudio 1 1 User s Manual 5 1 Importing Data Step 5 Internal data representation fae Import tool unsigned Skit Fig 178 Use this dialog to specify the internal data representation The data type may be changed while loading data into VGStudio e g a 32 bit floating point data set on your hard disk may be mapped to a 16 bit integer data representation In this case this would reduce the amount of memory needed for visualization by a factor of two Any data type may be mapped to any other data type The only exception are RGBA data sets Reminder RGBA data can not be mapped to any other data representation Also monochrome data types may not be mapped to RGBA data VGStudio 1 1 User s Manual 179 5 Importing amp Exporting Data unsigned 8bit unsigned 8bit signed 8bit signed 8bit unsigned 16bit unsigned 16bit signed 16bit may be mapped to signed 16bit unsigned 32bit unsigned 32bit signed 32bit signed 32bit 32bit float 32bit float 32bit RGBA no mapping possible 32bit RGBA The voxel Resolution may be adjusted for data sets with non isotropic voxel dimensions el
163. yscale f Color Previous Pest Cancel Fig 164 Select the data type for TIFF JPEG BMP and PPM images Image slices may be imported as grayscale or color data 166 VGStudio 1 1 User s Manual 5 1 Importing Data Step 7 ROI and Skip selection E Import tool OF x ROL and Skip selection Choose your Region of Interest RON and the skip rate Region of Interest Min Preview Previous Mext Cancel Fig 165 Define Regions of Interest and choose the skip rate Use this dialog of the import wizard to define a region of interest within the imported stack of images or to define the number of voxels to be skipped in each direction of the image planes by dragging the sliders or typing in the desired values These functions may be of special interest for very large data volumes in order to reduce the amount of data loaded in VGStudio Use the four Region of Interest sliders to define a sub volume within the data set which should be loaded into VGStudio Only the x and y direction can be manipulated here To reduce the number of slices in z direction deselect several of the images to be imported in the file selection dialog see steps 1 and 2 VGStudio 1 1 User s Manual 167 5 Importing amp Exporting Data Fig 166 Define a Region of Interest that is to be loaded into VGStudio Use the two Skip sliders to specify the number of voxels to be skipped in x and y direction When choosing a valu
164. yvalue seg ments defined The classification tool above shows three grayvalue segments within the CT data set Segment 1 includes the grayvalue range from 0 to 658 It represents the noise and air within the CT data set Segment 2 ranges from 659 to 1443 and represents the soft tissue Segment 3 includes the bright est grayvalues from 1444 to 4095 It represents the bone structures and the metal of the braces in the CT data set As we can see in Chapter 4 6 1 Classification Tool the opacity and color map ping of the three segments can be handled independently of each other However the geometric settings such as position rotation scaling and clipping of one of the segments cannot be handled independently from the rest of the CT scan The Extract function is an easy to use and powerful tool to generate images as shown below in Fig 123 where the soft tissue is removed from half of the jaw In the example shown here we need to clip the soft tissue only In order to clip only one segment the segment has to be extracted VGStudio 1 1 User s Manual 123 4 VGStudio Interface amp Tools Classification oe selection AAA roe ka Object overview i i ii ii Opacity manipulation area noise f air soft tissue bone matal Insert handle Pelete handle Reset opacity curve Gray values I Color Color manipulation are are Copy opacity curve a Haste opacity CUE Hew segment b Cut segment

documentation

Contents

Download Pdf Manuals

Related Search

Related Contents