InVols software user manual Menu bar items
Contents
1. clipping box MPR planes and measurement tools Tool Translate Switches mouse buttons functionality for the camera translation mode Tool Zoom in out S Switches mouse buttons functionality for zooming in out Tool Rotate Switches mouse buttons functionality for the camera rotation mode in 3D mode only Tool Window edition Switches mouse buttons functionality for adjusting window level values Tool W L presets 450 Level 40 v Presets Default WL 450 40 z View BG E Wi Tools MPR 3D Planes and Transfer function have the same functionality as the corresponding menu bar items Measurements zagar Tool Line Measurement of distances 1n cm Setting this tool on changes mouse buttons functionality to begin creation of Line objects This also counts for any other measurement tool To stop creation mode press right mouse button To delete selected object or its point press DELETE Objects can be created only in MPR mode Use context menu to add new points Tool Lines loop Measurement of the mean data value inside an area inside a lines loop Tool Ellipse Measurement of the mean data value inside an area inside an ellipse Tool Angle 4 Measurement of the angle in degrees between two lines the first and the last in the line sequence Tool Clear notes Remove all measurement tools MPR mode2. Planes Background colour Transfer Function Use MPR and 3D or tools to switch between MPR and 3D visualization modes that are presented below for the same medical dataset a MPR mode dj InVols Viewer W 450 L 40 EN BW 450 40 W 450 L 40 Wa m W 450 L 40 fps 12 42 b 3D mode File View Settings Help CT abdomen CT anatomy CT broncus tf DVR CT lungs 1 CT lungs 2 CT muscles CT skin MRT angio MRT angio 2 MRT angio 3 fps 8 34 2 Use Planes or tool to switch on off MPR oblique plane visualization in 3D mode Viewer d o u Gea E 7 eng Sex 5 2 ES 8 5 9 TP EN CT abdomen IE CT anatomy CT angio CT bone 1 CT bone 2 CT bone 3 CT broncus CT lungs 1 CT lungs 2 CT muscles CT skin MRT angio MRT angio 2 MRT angio 3 tf DVR v mM EXD fps 6 69 Use Background color to change the background color for 3D mode it is black by default Use Transfer Function or tool i coloring transfer function for the volumetric dataset can be chosen from the presets or you can yourself change and create new transfer functions see Transfer Function to show hide the Transfer function window where a di InVols Viewer o ES w23 a Joga 2 File View Settings Hel CT abdomen CT anatomy CT angio CT bone 1 CT bone 2 CT bone 3 CT bronc
3. 0 60 format SHORT data values offset 0 data values scale 1 window level 40 window width 450 modality CT To obtain data values in Hounsfield units one should do the following operation with all dataset cvalues Output units m S V b Where Output units the resulting value 1n HU m corresponds to the Rescale Slope 0028 1053 parameter in DICOM file b Rescale Intercept 0028 1052 SV source value from the file Transfer Function Transfer Function window allows for choosing a predefined transfer function TF from the presets list 1 and for creation of new user defined transfer functions To show hide this window use tool On the histogram area 2 you may adjust current transfer function to change the appearance of the dataset in 3D mode please note that changes would be seen only when using tf DVR rendering algorithm which is used by default To add or remove control points of the current TF use buttons below on the left 3 You can also use the right mouse button to create delete control points To select and drag points use left mouse button Mouse wheel can be used to scale histogram area by scrolling and to translate 1t press amp drag CT bone 1 CT broncus CT lungs 1 CT lungs 2 CT muscles CT skin MRT angio MRT angio 2 MRT angio 3 To save changes press button 4 a new TF will be created Please note that the current rendering image of 3
4. D mode will be saved as well and used as a preview image on the right 5 To remove a TF from the list 1 you may use button 4
5. InVols software user manual The InVols software application is intended for MPR and 3D visualization of medical datasets in Dicom 3 0 and RAW file formats When starting the program you will see the MPR browsing mode by default Graphical user interface 1s represented by the window header 1 the menu bar below 2 toolbar 3 and the working area 4 a _ e MT Be 3 InVols Viewer File View Settings Help KAKE E W 450 L 40 1 W 450 L 40 Menu bar items File 1 Open folder with DICOM files 2 Save to raw 3 Load raw file 4 Make screenshot 5 Exit dj InVols Viewer 0 File View Settings Help Open folder with DICOM files Save to raw Load raw file Make screenshot Choose Open folder with DICOM files to load medical CT or MRI data in DICOM file format Please note that not all DICOM format issues are supported like decoding compressed images for instance a InVols Viewer File Vie Settings Help Choose folder with the DICOM files Ss imgl 4s img2 MEE 4 STT mars J sa dA SE2 J client 4 invols presets lib releases Folder SE2 Make New Folder Cancel Once you have managed to load a dataset into the system you can always save the dataset in binary format using Save to raw To load a dataset from the binary file choose L
6. It is a viewing mode by default In this mode the main window is divided into four windows for browsing MPR sections sagittal 1 frontal 2 axial 3 and oblique 4 When starting the program the oblique plane is not defined and the corresponding window is empty Using selection mode tool I you can 1 Drag MPR center on one of the MPR planes blue arrows 2 Define oblique plane yellow arrows 3 Change clipping box red arrows MPR center is a point where all four MPR planes a intersecting j tnvols Viewer m ED T bet n File View Settings Help IE NG OM FG w W 450 L 40 W 450 L 40 When the oblique MPR plane is defined user can rotate the plane in windows 1 2 and 3 yellow arrows c mo fe InVols Viewer 5 2 m a EE File View Settings Help JE ES 50 1 ES 2 mM 6 Val 1003 W 450 L 40 W 450 L 40 W 450 L 40 J W 450 L 40 3D mode In 3D mode the main window is divided into the 3D visualization window 1 and presets window 2 1 Rendering is performed in 3D visualization window you can adjust control points of the clipping box 4 using mouse and selection mode tool 5 2 You can select a transfer function from the list Double click on any preset will open th Transfer Function window 5 3 i e m m mem moo Ha fd InVols iewer 1 A w Fi
7. le View Settings Help Beebe AOE 90 2 bones2 CT abdomen CT anatomy 1 1 Fa 1 K 47 CT bone 1 CT bone 2 CT bone 3 CT broncus tf DVR MRT om 3 3 Presets 2 fps 0 68 You can choose visualization algorithm from list 3 1 tf DVR Direct Volume Rendering with colored transfer function 2 wIDVR Direct Volume Rendering with gray scaled transfer function defined by W L values 3 SSD Shaded Surface Display The iso value is defined by Level value of W L 4 MIP Maximal Intensity Projection is defined by current W L 5 MinIP Minimal Intensity Projection is defined by current W L RAW file format A dataset in RAW file format are stored into raw file slice by slice while additional information 1s stored in corresponding raw txt file For example File name raw 1s a binary file that contains the dataset as a 3 dimensional matrix considering Vijk to be the value of cell of index 1 j k the file will contain the following values V000 V100 200 Vn 1 00 VOIO V110 V210 Vn 1 m 1 0 VOOI Vn 1 m 1 p 1 File name raw txt contains the information below default size ivec3 3 integer values Dataset sizes O Z o Z format enum SHORT USHORT or Data values format UBYTE Here is an example of txt file from the Datasets floder size 256 256 277 spacing 0 86 0 86
8. oad raw file n X InVols Viewer e 6 File View Settings Help fd Load volume data gt invols Datasets ee UO Organize v New folder YF Favorites gt ct head 256 raw RE Desktop 4 amp Downloads Recent Places 5 Google Drive SS libraries RH A MEE EE Documents 2 Music Pictures Subversion B Videos E Homegroup jW Computer L Local Disk C 7 File name ct head 256 raw v raw files raw W 450 L 40 B W 450 L 40 Make screenshot makes a screenshot of the 3D rendering area so it does not work in MPR mode and stores the image in PNG format into the file specified by the user Please note that you should switch to 3D mode before making screenshot fey InVols Viewer I Ss ENES ES E mM 26 6 5 b CT abdomen CT anatomy CT angio CT bone 1 CT bone 2 CT bone 3 CT broncus CT lungs 1 CT lungs 2 CT muscles CT skin tf DVR Y Organize v New folder e YF Favorites RE Desktop ll Downloads Recent Places a Google Drive 2l Libraries Documents a Music E Dirkiuirer File name LUERIUTBPERVES UBER fps 12 42 To end working in InVols choose Exit View 1 MPR 2 3D 3 Planes 4 Background colour 5 Transfer Function InVols Viewer File View Settings Help E v MPR Ai 30
9. us tf DVR Y MRT angio MRT angio 2 MRT angio 3 CT muscles an Tas 912 892 fps 1 56 Settings 1 Shading 2 Tricubic filtering 3 Save default window position InVols Viewe File View Settings Help Shading Tricubic filtering Save defailt window position Use Shading to switch on off the shading for the 3D mode Switching this option off should accelerate the rendering performance Rendering with left and without right the shading option Use Tricubic filtering to switch between trilinear by default and tricubic data interpolation for the 3D mode Please note that switching this option on will significantly slow down the output In some occasions though it will improve rendering quality Rendering with left and without right the tricubic filtering option Use Set default window position to use the current window position when starting the program next time Help 1 Help 2 About File View Settings Help iid Help opens this manual About shows information about the program itself and the author Toolbar items All Tools arranged into 3 groups 1 Control 2 View 3 Measurements Some of the tools double menu bar fun functionality The tooltip of each tool is defined by its name Control ONE Tool Object edition KI Switches mouse buttons functionality for objects edition
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