Endeavor™ User Manual Manual
Contents
1. 000008 31 Online Collaborative Annotation csceseseeeees 34 Starting Endeavor as a Server ceccceecccceeceseeeeeeeeeeeeeeeseeeeeeseeees 35 Starting Endeavor as a CIiQnt cccecccceececeeeeeseeeeseeeeseeeeseeeeeas 35 Online Annotation Procedure cceceecececeecececeececeeeecesaeeecneaeens 36 Onine Chater a a 43 2D 3D VisualizationS aannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 44 SD NIOWO P apei AE e EIE 44 2D7 3D OnNogonal MPR sree e debt hace e Ged 47 Maximum Intensity Projection MIP ccccccecceeeseeseeeseeeeeeeees 50 VOIUME Rendering eree a eer eceact eee ecoaes 53 White Matter Lesion PIUQ IN cccssceeseseeeeeeeeeeees 58 HOW VV IVIL VV OF KS coh cairn eee as rh coda Yad rah ark a h 59 Skull Stripper Seting serne A A A 60 Brain Tissue Classification ctiacs sete toes tie veney cera ce cemavar een teenenens 62 Segmented White Matter LESION cccccccseeeeseeeeeeeeeseeeeeeeeeeees 62 EXeCUIING VV MILF IUG INcuchivbretivtiaatiiutneuis EAE AEN 62 Starting the White Matter Lesion Plug in ccccseceeseeeeeeeeees 63 WV IVI VIG NU oh eciche bine cntn sched tts cade Mn a ccleds ON 66 Starting with a Fresh VOlUMG ccecccceeceseeeeeseeeseeeeeseeeeseeeeees 67 Processing WM ieissa n E E 70 Load a Volume that is Already ProcesSSed ccccsseeeeseeeeeeees 72 Simplified Explanation of Histogram Analysis cccseeceees 72. General ifffo Patient ID R 226 Patient s Age 06 Patient Sex M Image width 512 Image height 51 Total Images Se Original image FLAIR Skull stripped image FLAIR IM 0004 0001 dcm IM 0004 0002 dcm Spacing betweer Pixel Spacing 0 4 Intensity 1042 x IM 0004 0003 dcem Result of Brain Tissue Classification Tl Weig Segmented White Matter Lesi Information WMLs Detect r Skull Stripperet IM 0004 0004 dcm Radius Mean Curvature IM 0004 0005 dcm Inhomogeneity Brain Tissue la WMLs Detection IM 0004 0006 dcm Sensitivity dete 1 Select the image from the left column 2 To redo this image click on this Redo icon 3 A pop up Redo WML segmentation screen will ask for the Seed point area 78 Page Endeavor Software Manual WML Redo WML Segmentation Pop up Screen 4 In this screen use the rectangle box marked with a red oval and select the area around the centre where the Seed point is likely to be The miscalculated area must be included 5 Click the X at the top right corner close window 6 This will prompt for the T1 image file name Endeavor will direct you to the original files folder Select the image number 79 Page Endeavor Software Manual WML Select the T1 image screen a fi Open i l e ae JU d DICOM R227 SETLAX v 4 Search F a ee a By Organ
3. 3 Select any of the images on the left column The completed WML detection if any is shown on the screen WML Processed Output screen ES ENDEAVOR File View Help a yo ag Dicom image viewer WML plugin Endeavor White Matter Lesions Segmentation 54 Original i FLAIR Skull stripped i FLAIR riginal image ull stripped image eae 20 00 MEFE JN Mean Curvature 0 05 Inhomogeneity Correction Setting Signal threshold 1 00 Max Iterations 50 00 End tolerance 0 01 0 00001 0 001 Field distance mm 170 00 Subsampling factor 1 0 32 0 4 00 kernel FWHM 0 05 0 50 0 15 Wiener filter noise 0 0 0 1 0 01 jassification T1l Weighted Segmented White Matter Lesions Information a d N A Brain Tissue Classification Setting 9 NumberOfClusters 4 00 Maxlterations 100 00 Fuzziness 2 00 Epsilon 0 01 WMLs Detection Yetting Sensitivity detection 35 00 Outliers select an T1 Brain Tissue Red area is WML image Weighted only detection 73 Page Endeavor Software Manual WML Ay Show Analysis Results Purpose This icon will display the results of WML detection ina tabular format Calculating White Matter Lesions window Calculating White Matter Lesions PON I w d Current image is IM 0531 0005_detection dcm After the calculation process the results are displayed Calculating White Matter Lesions result Total No of Lesion P
4. Click on this icon to return to Main Perspective A message box pops up to ask if you want to close the Annotation Perspective Switch to Main Perspective E Switch to Main Ch Are you sure you want to switch to the Main Perspective This will clear all buffers P and close the 2D view Click OK to close the Annotation Perspective Click Cancel to stay in Annotation Perspective 31 Page Endeavor Software Manual ROI Drawing Board Icons Export DICOM File Directory Purpose This option will export a selection of DICOM files to a USB thumb drive or a folder on the local hard drive Use this option if a copy is required Select slides Select files to be exported From files number refers to Total number of file 83 h slide number toe copied From files number 1 To files number 3l To file gt number refers to the last slide number to be copied ok Cancel Please note The slide numbers DO NOT refer to the actual slide number of M 0001 0001 dcm After the slide numbers are entered into the From To fields click Ok To exit this option click Cancel lf copy of slides is initiated the next step is to identify the destination folder Save As ER Save As pl GQ m az p Search SempleExport Save as type jod o owse Folders Cancel The Filename is required Example SampleExport The file format types can be in jpg omp png tif or gif format Click on the drop
5. Endeavor Software Manual Online Collaboration ag Start Collaboration Server Continued Any PC that runs Endeavor can be a server The rest of the users are clients linked to the server How server collaboration is setup Steps 1 Ask the systems administrator for the authorization code and main port number and the IP address Click Save once the details are entered If you don t want to save click Cancel 2 Click Start to start a communications session To end the communications session click Stop 3 Inform other collaborators the IP address Once clients are connected to the server their IP addresses are displayed Click Refresh to view any connections Clear will clear the list Only shown on the PC which is the Collaboration Server 4 Start Annotation Perspective Collaborative annotation works by a who is holding the pen system The first person who clicks on Request to Annotate button holds the pen Other users have to wait in while the user holding the pen annotates lt is possible to view all connected Clients to the server and see which user is having the Request to Annotate or Update to Server To do this go to the Main Menu Select View In the drop down list select Other A Show View screen displays all choices available 38 Page Endeavor Software Manual Online Collaboration Show View screen pat Show View type filter text s 3D viewer Axial Corronal and
6. 68 Page Endeavor Software Manual WML C Where to store the output files step 2 Select Output Directory Select root directory to store intermedia and final result gt bb CER CT gt fy fYETS 0 Output F m R 227 Ax 72 FLAIR jb Output Folder New Folder Make New Folder Create a folder to store the output It is best to create a new folder in Desktop and use a filename like 227Output This will put all the generated files into the folder while maintaining the integrity of the original files Click OK 69 Page Endeavor Software Manual WML Processing WML From this point onwards the algorithm will process this new volume until the process is completed Process may take up to an hour Several progress screens will be displayed Skull Stripping in Process skull Stripping in Process Not Responding Current image is IM 0529 0001 dem While the process is running it will show that Endeavor is Not Responding Please wait for the process to complete Please note Should it happen that after an hour the process is not completed use the Task Manager to stop the program After Skull Stripping will be Brain Tissue Classification process Brain Tissue Classification Brain Tissue Classification in Process Create the task 70 Page Endeavor Software Manual WML After Brain Tissue Classification will be White Matter Lesion detection White Matter Lesion Detection C
7. Multiplatform support Endeavor has been known to run on Mac OS X Leopard and Ubuntu Linux 9 04 However we have not extensively tested this For optimal performance we recommend running Endeavor on Microsoft Windows System Requirements e Windows XP SP3 or higher Supports Windows 7 32 and 64 bit e Intel Dual Core based CPU or higher AMD Athlon X2 or higher At least processor speed of 2 8Ghz e 2GB RAM 250MB Hard disk space for installation e Sun Java Runtime Environment version 6 0 and above e Monitor screen resolution of at least 1024x768 pixels 16 bit color e DICOM images take up a lot of hard disk space Make sure there is ample free gigabyte GB hard disk space available 2 Page Endeavor User Manual Login Login Screen Username Password i EXTENSBLE MEDICAL IMAGE ANALYSIS AND VISUALIZATION 2 0 V rih ull al i COPYRIGHT i Computer Vision Research Group School of Computer Sciences Universiti Sains Malaysia All Rights Reserved Endeavor s login screen is setup by an administrator Username admin Password _ to be advised Click the Login button once after Username and Password is entered Click Clear if you want to reenter Username and Password Click Quit if you want to exit from Endeavor The administrator can create other user ids The icon User Manager will be available on the File Menu bar once the administrator is logged in To login without a user id please click on
8. Original image Process Selection Skull Stripper showing skull listing Setting and brain 1 Skull Stripper Seed X Seed Y tissues 2 Brain Tissue Radius Classification Mean Curvature 3 WMLs Detection Image details Spacing is 6mm This WML screen shows the layout The images need to be processed before the results are displayed in the remaining empty screens listed as follows 1 Skull stripped image 2 Result of Brain Tissue Classification and 3 Segmented White Matter Lesion 65 Page Endeavor Software Manual WML WML Menu The Menu Icons are explained below Load Volume Images icon This is the first step to Load selected image from database process WML The volume or image must either be loaded or imported Images can be the whole volume or Import external volume selected images Run Algorithm icon After the images are loaded imported the WML algorithm Run current image can be executed The Run volume images current image or the volume images can be processed Load selected volume from database Import external image al Runs the WML 3D viewer Show analysis results DICOM image header Histogram Analysis Load the parameter settings save the parameter settings 66 Page Endeavor Software Manual WML Starting with a Fresh Volume A fresh volume of images is given for processing of White Matter Lesion This volume contains Flair and T1 images Load only the Flair images into th
9. ert a 7GEFFOGbzqCNo43Yd0 Ibu zQSSX Patient ID 5YpO0E Study Date 200 2 Patient Name BRAINIX 4 Patient Sex 0000 we Study Time 141645 ma Modality MR Current slice 12 1 W 596 C 342 Slice position 116 91600066778 114 11810720305 17 9074919766740 Slice position 116 91600161953 114 11810815424 17 9074918851256 4 The scout line will appear automatically if correct images are loaded All images will change synchronously if a different image is selected in one of the window f gt F X zS Patient ID SYpoE 7GEFFOGb2zqCNo43Yd0 Ibu P q Patient ID SYpOE Patient Name BRAINIX Patient Sec 0000 Study Time 14164 Study Time 14164 3 706296564094 1 33 023791253566 5 121 76236948929 118 67295193766 11 4448198676109 19 Page Endeavor Software Manual Annotation Perspective Annotation Perspective Purpose Individual images can be selected viewed and annotated ba j ES ENDEAVOR i E File Wiew Help Patient ID Patient Name r Date Imported Modality No of images FYET5 0 COMUNIX 2010 09 01 EI 166 IM 0001 0001 dem User Guest Each slide will show the slide number and image resolution In this example image number is IM 0001 0001 dcm and resolution is 512 x 512 pixels To view the annotation perspective do the following a Steps K 1 Select the slide 2 Click once on the slide 20 Page Endea
10. Display multiple axis sequence images in Standard View Purpose To display multiple axis or sequence images in Standard View Note You will need to use images from a single patient Images can be from any sequence but must be different axis in order for the scout line to appear In order to have synchronized view of the images images need to be from same axis but must be different sequence In Standard view to view images from multiple axis or sequences side by side do the following 4 Steps 1 Select the folder as shown by the RED box PatientID Patient Name Age Sex Date Imported Modality No of images Description Dataset Size 5Yp0E BRAINIX 0000 2011 03 18 MR 232 T1 3D FFE C 53 MB FPMETp OSIRIX 0 2011 03 16 CT 593 Thorax Abdo 2 0 B25f 297 MB 2 Click the following icon as shown by the RED circle as 18 Page Endeavor Software Manual Standard 2D Viewer 3 Choose the images to display from the thumbnails viewer Multiple images selected then can be arrange as required on multiple windows sous amp gt O st2 Tse T Z te Qa Q E fee E s 3 9am E Patient ID 5Yp0E Patient ID 5Yp0E 7GEFFOGbzqCNo43 Patient Name BRAINIX Study m 200 Patient Name BRAINIX Study Date 20061201 A092 J Patient Sex 0000 Study Time 141 5 0 Patient Sex 0000 Study Time 141645 000000 Modality MR Current slice 12 1 sT2W FLAIR 3 zy N ce Wy ET
11. Front Viewin X Y Axis LUT Thermal Original 3 Side Frame urr_on off 3 Side Frame Angle of Rotation A 1150 Markers Scale Distance Threshold Depth Scale 1 0 Change Scale Distance 0 Distance thot Threshold and Depth Depth 88 Page Endeavor Software Manual Oblique MPR Viewer Main Frame Purpose This frame gives the overall volume rendering of the MRI scan and plays as a movie Steps 1 To view in moving pictures hold the cursor down and move it a few times Release and the images will start to play 2 The show is by frames per second fps Main Frame in Play mode 3 Click anywhere on the image to stop play Note This sample movie is scaled down from 1 to 0 5 89 Page Endeavor Software Manual Oblique MPR Viewer 3 Side Frame This frame displays the view of 3 sides The lines across the diagram shows how the image is displayed on the Main Frame 3 Sides Frame 90 Page Endeavor Software Manual Oblique MPR Viewer Software Update Introduction Endeavor software update functionality allows you to download the latest version of each plugins currently installed We encourage you to check the software for updates from time to time as currently the software update function does not automatically check for updates Updating Endeavor 1 From the menu select File then select Endeavor Software Update Manager G 2 The following window will b
12. Saggital view Connected Users Database Patient Dicom image viewer fF Event Log Image Explorer ca Image series Bal Patient image folder As Patient information pa Preview amp User Manager Welcome Er annotationView Use F2 to display the description for a selected view select Connected Users and Click OK This will bring up a new window next to the Embedded Server Configuration window View all Connected Clients Screen ol Welcome Embedded Server Configuration Connected Users 4 Node IP UserName Status No 1 1020715059 guest Click X at the tab to close this Connected Users window 39 Page Endeavor Software Manual Online Collaboration Online Collaboration Purpose This connects a client to the Collaboration Server A user needs to know the main port of the Collaboration Server to get connected A new tab screen Embedded Client Configuration is displayed marked with RED arrow in the Information Window How to setup a client to a server a Preview S Embedded Client Configuration 24 gt F Authentication Setting Username henry Tirri Password Use Currently Connected Username Password Connection Setting Authorization Code 12007 Server s IP 10 207 150 27 Server s Port 17704 Save Status Endeavor currently runs as a client Active Start Stop Steps 1 Obtain the IP address from the initiator of the collaboration Fill in the Authorizatio
13. Set up Camera Once the setup is complete a new Window is opened File View Help n X i cal 0O Dicom image viewer Sm 3D viewer 3 L ND X Tissue properties 2D Image plane selection Tissue skin Opacity Enable Saggital plane selection Saggital Specular m Diffuser Enable Coronal plane selection Coronal User Guest The RED arrow shows the new 3D Viewer To close click X Endeavor Software Manual 2D 3D Visualizations 3D Viewer Menu 2D Plane LUT fee xe w Black White Hue Saturation 2D Plane LUT stands for 2D Plane Lookup Table Users can choose any option of Black White Hue or Saturation 29 ManclUT Tissue K Tissue highlights both Bone and Skin Resets the 3D Viewer to default settings ipl Allows users to change 3D Viewer settings 3D Viewer Settings 3D viewer control setting ColorDialog Demo m Gradient Background Background color E Outline color Viewers can change background color and outline color using the Color Dialog demo 45 Page Endeavor Software Manual 2D 3D Visualizations 3D Rendering allows the user to turn the image into any position for viewing 3D Positions 1 Place the cursor on the image click once and hold the cursor 2 Move the cursor anywhere and the image will follow the movement of the cursor 2D Image Plane S
14. annotate received This notification does not require any user action Similarly when a user has completed the annotation and wants all the users in the collaboration session to view the annotation the user clicks the Update to Server button and a Notification window box pops up to inform the user Notification The annotation is successfully send to server This notification does not require any user action The annotation changes are then updated to all other users in the session 42 Page Endeavor Software Manual Online Collaboration Online Chat Chat This chat button is used to initiate a chat session between all collaborators Any collaborator that is connected to a particular online Collaboration Server can use this button to initiate a chat session Chat Session Window Box Le Endeavor Chat Client Default User Default User Testing 123 Default User Testing 45678 A chat session window box pops up on the screen and each user is identified with their login id In this example the user is listed in square brackets as Default User me q Steps gt 43 Page Endeavor Software Manual 2D 3D Visualizations 2D 3D Visualizations 3D Viewer ra 3D Viewer Purpose The user will view 3D rendering with a 2D image plane selection of Sagittal Coronal or Axial Click on this icon to view 3D Rendering Please wait for 3D Rendering to be setup 3D Rendering Setup 3D viewer
15. box Choose Maximum Intensity Projection MIP on the sub category Press OK to proceed pe Show View Srm fy ie So j type filter text 4 2 2D SD Visualization EE 2D 3D Orthogonal MPR p ES Maximum Iptensity Projection MIP J ES Volume Rendering g gt Communication gt E Volume Rendering Oblique MPR View 4 Other 3D Viewer amp Connected Users O Database Patient Event Log Image Explorer Bi Image Preview Browser ea Image Series al Patient image folder Use F2 to display the description for a selected view Siero 4 Maximum Intensity Projection MIP view will be loaded 51 Page Endeavor Software Manual 2D 3D Visualizations MIP Viewer Menu Pantuncion Rotate function bial Most of the icons are self explanatory They will be discussed here To pan the visualization To rotate the visualization Gl To zoom into the visualization cah To change the viewer s setting 52 Page Endeavor Software Manual 2D 3D Visualizations Volume Rendering Purpose Allows for 3D visualization from 2D DICOM images fi a Steps 1 Click on the patient list to select which patient data to visualize Patient ID Patient Name Age Sex Date Imported Modality No of images Description Dataset Size fYET5 O 2011 03 23 CT 166 CT HEAD NK 5 0 B30s 2 Click View on the menu bar Select Other on the menu Fi
16. down to select or accept the default Click Save to save the slides into SampleExport and in jpg format To abort this operation click Cancel 32 Page Endeavor Software Manual ROI Drawing Board Icons Export DICOM File Directory Continued The file name is actually a folder name In this folder all the copied slides are stored The Desktop contains this folder sampleExport Open the SampleExport folder The folder should contain 3 slides with the following names SampleExport_1 jpg SampleExport_2 jpg SampelExport_3 jpog 33 Page Endeavor Software Manual Online Collaboration Online Collaborative Annotation How Endeavor Tackles Multiuser Collaboration The collaboration works by through the token passing mechanism This token is passed around among all users to enable orderly annotation of images in turn The user who holds the token is analogous to one who is holding the one and only pen Only this user can make annotations to the image during this time Once the token is released using Update to Server the token can be taken up by another user when he or she sends a Request to Annotate This technique avoids traffic jams and serves on a first come first served basis The second or third Request to Annotate is held in a queue In Diagram 1 the server talks to the clients and clients talk to the server When the token is released by Update to Server the annotation is updated For each client to see th
17. from the initiator of the invitation 1 Server s IP address 2 Authorization code 3 Server port number These setup details are required before a connection to the server can be established Please see Online Collaboration on how to start a Collaborative Client 35 Page Endeavor Software Manual Online Collaboration Online Annotation Procedure The online annotation procedure involves the use of drawing tools like drawing a line drawing a rectangle freehand drawing and typing notes or comments of the drawings on a text screen After setting up a Server or a Client start the Annotation Perspective and you will be able to see the images If you have setup the Server or Client Successfully the ROI Drawing Board now includes the buttons Request to Annotate and Update to Server Note that if you already use the ROI Drawing Board in the current session you need to close Endeavor first and start a new session select a particular image and click the Request to Annotate button This will give you the pen if you are the first requester Else you will be on the queue A Notification Window Box will pop up to inform you if the Request to Annotate is successful Once you hold the pen do the necessary drawings and comments After completion click the Update to Server button This will update the server and all the clients after a short delay The Collaboration Server or Client can be closed after the collaboration session is
18. is useful if the setting is going to be used repetitively A Save Parameter Dialog screen pops up to ask for the folder and file name save Parameter Dialog screen fis Y param Dialog gt p t gQ Cna Search Test Organize v New folder Ft Favorites BB Desktop Je Downloads Recent Places ParameterSave pr Libraries m Documents a Music Pictures E Videos jE Computer amp Local Disk C ees Removable Disk File name Save as type prm a Hide Folders The file extension is prm Select an appropriate folder and type in the file name Click Save to save the parameters Click Cancel to exit the operation 82 Page Endeavor Software Manual WML b Load Parameters Bes This icon loads the parameter settings like Seed X Seed Y Radius Sensitivity detection etc Click this icon to load the saved parameter settings A load parameter dialog screen asks for the folder and file name Load Parameter Dialog screen E load param Dialog p t TQ gt Test E en ee a E Organize v New folder s fi yr Favorites MB Desktop mI Downloads Recent Places ParameterSave pr Libraries m Documents a Music t Pictures z Videos JE Computer amp Local Disk C a Removable Disk Ciu Network File name v prm X Select the appropriate folder and file name Then
19. the Guest button No password Is required 3 Page Endeavor Software Manual Main Perspective Main Perspective 3 ENDEAVOR File View Help Patient ID Patient Name gi 5 Date Imported Modality No of images FYETS O COMUMNIX 2010 09 01 CT 166 iha Welcome isi ENDEAVOR Build 01072010 Description Endeavor fully supports the DICOM image format and therefore allows users to load browse view and analyze medical imagery In addition our software allows users to add graphical and textual annotations on the image as dynamic graphic overlays Accurate measurements can be performed on the 2D images Interactive 3D visualization of medical datasets allows medical experts to visualize bones tumours and other tissues c Copyright Computer Vision Research Group USM 2007 2010 All rights reserved Visit http cvrg cs usm my T Event Log 4 2 9 2010 13 31 11 gt gt Finished Creating components 2 9 2010 13 31 11 gt gt DVTRS ready The Main Perspective screen is divided into three parts a Patient Window b Information Window c Event Log Window The Information Window and the Event Log Window can be maximized and minimized AC v The Event Log Window is used for technical t troubleshooting The Event Log can be saved O H Save file 4 Page Endeavor Software Manual Main Perspective Menu Bar icons B romeo menoon A encans E foecs e e Switch to Main Perspective Exp
20. the RED box PatientID Patient Name Age Sex Date Imported Modality No of images Description Dataset Size 5Yp0E BRAINIX 0000 2011 03 18 MR 232 T1 3D FFE C 53 MB FPMETp OSIRIX 0 2011 03 16 CT 593 Thorax Abdo 2 0 B25f 297 MB 2 Click the following icon as shown by the RED circle A Ea ENDEAVOR _ a File View Help Patient ID 5Yp0E 7GEFFOGbzqCNo43Yd0 Ibu zQSSXx Patient Name BRAINIX Study Date 20061201 Patient Sex 0000 Study Time 141645 000000 Modality MR Current slice 12 1 W 2475 C 2856 may Slice position 121 90592369996 119 10512119626 17 4275144934654 13 Page Endeavor Software Manual Standard 2D Viewer Standard 2D Viewer Menu Bar Standard Viewer Menu Bar as shown by the big RED arrow can be used within the viewer to do few operations related to the standard viewer j i ENDEAVOR n T iin Patient ID 5Yp0E 7GEFFOGbzqCNo43Yd0 Ibu zQSSX Patient Name BRAINIX Study Date 20061201 Patient Sex 0000 Study Time 141645 000000 Modality MR Current slice 12 1 W 2475 C 2856 Slice position 121 90592369996 119 10512119626 17 4275144934654 Display the metadata a Zoom in Adjust contrast i Zoom out brightness Reset fit to window Pan the image Reset revert to original Set contrast brightness JA Multi view to a predefined setting 14 Page Rotate the image Endeavor Software Manual Standard 2D Viewer Most
21. 7 Volume Rendering Oblique MPR Viewer 85 WAOOUGTI OM tscosseteneeeceecianeadnsedaetekecaenane enneeeadeneieeaadebeanueneieseanted 85 Volume Rendering Oblique MPR Viewer Menu icons 87 Software Uppdal crsa 91 MTOdUCHO Nac haseacce a eette salamat adabct E OT 91 91 Updating ENGCAV Ol exitc tiuettestieudlcitiertleiic ous icsignssiccausteitiaulieisionas Endeavor User Manual Introduction Introduction Endeavor Extensible Medical Image Analysis and Visualization Platform Endeavor is a Java based software for medical image analysis and visualization developed by the Computer Vision Research Group School of Computer Sciences Universiti Sains Malaysia We have been actively developing various versions of Endeavor since 2008 The Endeavor website is here http cvrg cs usm my dvtrs Note Endeavor s development thus far is supported by University Science Malaysia s Research University Grant Endeavor fully supports the DICOM image format and therefore allows users to load browse view and analyze medical imagery In addition our software allows users to add graphical and textual annotations on the image as dynamic graphic overlays Accurate measurements can be performed on the 2D images Interactive 3D visualization of medical datasets allows medical experts to visualize bones tumours and other tissues Endeavor leverages on the Eclipse plug in architecture and this enables advanced imag
22. DE EXTENSIBLE MEDICAL IMASE ANALYSIS AND VISUALIZATION ENDEAVOR Endeavor User Manual Computer Vision Research Group School of Computer Sciences Universiti Sains Malaysia Last updated 28 September 2010 This page is left intentionally blank Table of Contents IU O CLIC CO IN P EEA 1 Primary FUNCIONANIUCS vsiscsacssdissncinisasncnistehcnischandissednactennmeda 1 Who needs ENO SCAV ORS crrercerao rE E E EDE 2 LOGIN SCVO Moriri aa 3 Main Perspective ccccssccsscessesssnsenseesseeseeneensenseeseeaes 4 Meni Bar IGONS aaea A A ONE 5 Menu Bar ICONS Explained ccccceecceeceeceeceeeceeeeeeceeeeeeseeeaeeees 6 Preview Screen Qu ccececcecececececeeeeeececececneneeeeeceeeeeeaeeeaes 9 View DICOM IMaQes cccceecceeeecseeceeeececeeeeeeeteueeseeteneeesees 12 Standard 2D ViCWEL 2c1ceccccececeececececeecececneeececeeeees 13 Standard 2D Viewer Menu Bat cccececcececeecececeececeeeeeeeeeaeees 14 Display multiple images as a matrix cccecceeceeceeeceeeeeeeeeeeeeeaes 16 Display multiple axis sequence images in Standard View 18 Annotation Perspective cccccsscsscesssssenseensenseeeeeas 20 NINA CS CIOS seca aecicneciec oie oe E re eee een ace 22 POD FAWING BO ANG a e2ecesshe satel nanei Ei 23 ROI Drawing Board Menu Bar icons Explained ccceeeeees 24 WserAnnotation Tet BOX veloc ence ender ie 29 Main Menu Bar Icons in Annotation Perspective
23. ain in Picture 1 Each image slice is taken at an angle Spacing between each slice of the brain scan Is fixed scans can be 5mm or 6mm apart The metadata will show the spacing There is better clarity of White Matter Lesion WML if the spacing is smaller However the algorithm will still detect WML regardless of the spacing between each slice a is the top of the Cerebral Cortex and b is the last slide of the brain scan at the Cerebellum 59 Page Endeavor Software Manual WML Skull Stripper Setting The algorithm works by first removing the surrounding skull and bone tissue This is a necessary step to separate out the brain tissue from bone tissue In order to do this the skull stripper setting includes several parameters These parameters involve the process of identifying Seed X and Seed Y the radius and the curvature These settings are preset and should run optimally However flexibility is given to the user to adjust these settings accordingly Seed X and Seed Y To identify the best position for Seed X and Seed Y the last slice located at the Cerebellum b and the top of the brain image slice a is displayed Settings for Seed X and Seed Y Radius and Seed Setting Referring to Picture 1 the image on the left side is b Cerebellum with nose structure and the image on the right is a Cerebral Cortex The optimum setting is displayed by the GREEN crosshairs The radius is shown as a circle at the intersectio
24. and brain tissue is classified into different classifications At this point the algorithm compares what looks normal to what looks abnormal Segmented White Matter Lesion From brain tissue classification White Matter Lesion can be easily segmented The algorithm shows clearly in the brain areas affected by White Matter Lesion Executing WML Plug in The WML Plug in requires T1 and Flair DICOM images The first step involves importing these sets of images into the local hard drive Once these images are imported the patient ID and name is displayed in the Patient Window in the Main Perspective screen a ay Fa Co g Steps l K Me 62 Page Endeavor Software Manual WML Starting the White Matter Lesion Plug in 1 At the Patient Window select the Patient ID with the T2 Flair description Click Once 2 Atthe Preview Screen select the Ax T2 Flair folder Click once 3 Click on the first image This will start the Annotation Perspective 4 From the File menu select View and then select Other be ENDEAVOR l aad File View Help 5 3D rendering a Export DICOM File Directory Sex Date Imported Modality No of images fri 2010 09 01 CT 166 a t Start Collaboration Server rs Online Collaboration a Add new Plugin Ctrl 3 Other gt fp i i t E e E 63 Page Endeavor Software Manual WML 5 The Show View will display a list Select WML
25. are Manual 2D 3D Visualizations This page is left intentionally blank 5 Page Endeavor Software Manual WML White Matter Lesion Plug in Introduction This plug in is an enhancement to the existing Endeavor package It is an algorithm that covers 3 basic areas These are as follows 1 Skull Stripper 2 Run Tissue Classification 3 White Matter Lesion detection The approach of this module is to make use of the T2 weighted Flair and T1 weighted images First step is to load or import the Flair images After that the algorithm will need to compare with the T1 images The user will be asked for the folder which contains the T1 images The first process is to strip away bone tissue from brain tissue This is done by using the skull stripper algorithm In this step the settings for the Seed point is important because this position identifies the center of the brain The curvature of the skull must also be identified After this stripping process the brain tissue is analyzed from its intensity and classified as normal or abnormal tissue This is best pictured by using a histogram analysis From this classification comes the segmentation of White Matter Lesion 58 Page Endeavor Software Manual WML How WML Works A diagram of the human brain is displayed below View of the Brain man scanned images Picture 1 The scan is not perpendicular This is illustrated by the RED lines across the br
26. click Open to load the parameters Click Cancel to exit the operation 83 Page Endeavor Software Manual WML re WMLs 3D Viewer This icon displays the WMLs in 3D Click this icon and a new 3D window is displayed WMLs 3D Viewer hii E AWIR EON oo File View Help Tissue prope rties Tissue WMLs Specular Show edge C The image is in 3D and the severity of WML is clearly seen Background colors can be changed by using the Settings icon 84 Page Endeavor Software Manual Oblique MPR Viewer Volume Rendering Oblique MPR Viewer Introduction In MRI scans there are T1 weighted and T2 weighted Flair images These images can be rendered in 2D or 3D This plug in offers volume rendering of MRI scans 1 Go to File View and select Other List of plug ins EA Show View type filter text 4 2 2D SD Visualization EE 2D 3D Orthogonal MPR ER Maximum Intensity Projection MIP BE Standard 2D Viewer S EE Volume Rendering t Communication 4 Volume Rendering Oblique MPR View Sle me Rendering Oblique MPR V 4 2 Other 3D Viewer amp Connected Users Database Patient Event Log 4 Th 2 Click OK to select this plug in Click Cancel to exit Page 85 Endeavor Software Manual Oblique MPR Viewer There is a short delay while Volume Rendering is loaded A Java applet window Is displayed Java applet window Once the app is comple
27. dow is closed An Information Window will display that all annotations and drawings are saved Information Window Oh Saving complete database is updated This action will bring the User Annotation Section up to date 29 Page Endeavor Software Manual ROI Drawing Board Icons User Annotation Description User Annotation Section User Annotation Action recorder Usenthtarnn Annotation guest 7 Rectangle Sample annotation For each color that is used the annotation reflects that color an it also describes the drawing tool used The r Name column is the user login name The Annotation column records down all the text that was keye into the Annotation text box OD WACOM Col com Orarclale ERROR EIEI ERS sometimes changes to the saved annotations are required To make changes do the following Steps T F 1 Click to load the annotations Sy 2 Check tick that particular drawing by going to the User Name column User Name W quest 7 Rectangle 3 and then click 4 Click to save the changes 30 Page Endeavor Software Manual ROI Drawing Board Icons Main Menu Bar Icons in Annotation Perspective Once the Annotation Perspective is initiated 2 other menu bar icons are also activated in RED boxes Switch to Main Perspective es Export DICOM File Directory Switch to Main Perspective Purpose It returns the user to the Main Perspective screen
28. e Patient Window a ok ae I Steps Starting with Flair images loaded from DICOM into Patient Window select the Patient ID Go into the Annotation Perspective From File menu select View then Other Start WML plug in At the WML Load Volume Images icon select Load Selected Volume from Database The Selected Volume From Database window will display This will take a short while for all the images to load into WML from the Database Selected Volume From Database selected volume from database Select __ the Run Algorithm icon and select Run Volume Images This is a 3 step process It will A Ask for the Seed point B Where are the T1 images and then C Where to store the output file 67 Page Endeavor Software Manual WML A Seed point select the position of the Seed point and double click Close this window by clicking the X at the top right corner B Where are the 11 files Step 1 Select T1 Weight Series Directory Select the directory containing the T1 Weight series for skull stripping and brain tissue dassification d metadata p database a DICOM ib CER CT i fYET50 di Output E i Folder R 227 Make New Folder OK Cancel In this example the T1 files should be found in the patient ID folder of R 227 or another Patient ID Endeavor automatically locates this folder when the Patient ID was imported from DICOM Click Ok
29. e analysis segmentation and visualization algorithms to be added in the form of plug ins To date we have added DICOM communication capabilities which allow users to retrieve remotely stored medical data from Picture Archiving and Communication Systems PACS Primary Functionalities The primary functionalities provided by the Endeavor include e DICOM Compliant Medical Image Viewer and dataset browser which supports MRI CT X Ray ultrasound and other modalities e Revolutionary real time medical image sharing and annotation for instantaneous medical expert collaboration e Includes a built in relational database to store patient dataset and annotation information 1 Page Endeavor Software Manual Introduction e DICOM query and image retrieval from a PACS Server or medical image repositories e Provides nondestructive medical image annotation and measurement capabilities to the user in a user friendly interface e Includes basic image processing capabilities and could be extended to include more sophisticated image analysis algorithms e Includes powerful iteractive 3D visualization capabilities for medical image datasets Who needs Endeavor Endeavor can be used in hospitals clinics and research and educational institutions and can be installed on personal computers or laptops With its low hardware requirements and low cost of entry Endeavor is the ideal software tool for improved healthcare delivery
30. e opened please select your product Product Selection T 3 Now you may exit the running Endeavor window Note that the software update will fail to perform update if the Endeavor software still running 4 Upon pressing the OK button the following windoe will be opened 2 ENDEAVOR Update Manager Selected Product Endeavo Partial Update Full Download Configuration Back Page 91 Endeavor Software Manual Oblique MPR Viewer 5 6 To start check for new updates from the our centralized update server press the Partial Update button Then when asked to choose folder select your Endeavor software installation folder usually will be in Program Files Press OK and the for check update process will start followed by the update installation itself i ENDEAVOR re shane Selected Product Endeavor a Partial upate Full Download Configuration Back 207 ko pies ces ee 207 kalie com dvtrs core_1 0 0 201012081430 jar 31 ko done Average speed 31 kols com dvtrs extinsightToolkit_1 0 0 201012081430 jar 268 ko done Average speed 768 kols Plugin found org eclipse ui workbench 3 amp 0 I20100 03 1100 jar fj Plugin found org eclipse ui 3 6 0 120100 03 1100 jar Blugin found org itk 1 0 0 feature r Blugin found org vtk 1 0 0 feature Plugin found reIR 1lib 1 0 0 feature Update Mode Partial update Compare plugins Diffe
31. e updated annotation each client must poll the server Endeavor uses hash polling where each client checks for updates The update occurs in seconds When the update is done all users can see on their respective screen the update under the respective user name How the Server and Clients Interact Client 1 Server Client 2 x Client 3 34 Page Endeavor Software Manual Online Collaboration Starting Endeavor as a Server To use online collaborative annotation the first step is to be the initiator and by default the initiators PC becomes a server Only one PC can be a server at any one time To identify that your PC is a server you need to give your IP address to fellow collaborators Inform other users of your intention and then provide them with the authorization code and main port This is the tricky part The authorization code and main port is under the control of your own organisation s systems administrator or the IT department head To enable other users to connect to your PC the systems administrator must open a specific port in the computer network That is why this authorization code and main port number is required Please see Start Collaboration Server below on how to start a Collaborative Server Starting Endeavor as a Client After you have received an email or an invitation to participate in an Online Collaborative Annotation event you can start Endeavor as a Client To do this you need 3 things
32. eate multiple image display from multiple images just double click the images to load it into the Standard View E Patient image folder E sous st2 Tseym 3 SOUS Patient ID 5Yp0E Patient Name BRAINIX Patient Sex 0000 7GEFFOGbzqCNo43Y d0 Ibu zQSSXx Study Date 20061201 Study Time 141645 000000 sT2 TSE T sT2W FLAIR T1 3D FFE C T1 SE extrp T1 SE extrp T2W FE EPI 6 Dragging the individual windows will align the windows and snapping it in place Multiple numbers of windows can be created sous X sT2 TSE T X a E H QQRS H EI S T 93993 m Patient ID 5Yp0E 7GEFFOGbzqCNo43Yd0 Ibu zQSSX Patient Name BRAINIX Study Date 200612 e i 1988 Patient Sex 0000 Study Time 141645 Patient ID 5Yp0E 7GEFFOGbzqCNo43Yd0 Ibu zQSSX Patient Name BRAINIX Study Date 20061201 Patient Sex 0000 Study Time 141645 000000 Modality MR 119 10512119626 17 4275144934654 sT2W FLAIR 53 lm Patient ID 5Yp0E 7GEFFOGbzqCNo43Yd0 Ibu zQSSX Patient Name BRAINIX Study Date 20 640 Patient Sex 0000 siaN Study Time 141645 me Modality MR Current slice 12 1 W 596 C 342 Slice position 116 91600066778 114 11810720305 17 9074919766740 Modality MR Current slice 12 1 W 558 C 321 Slice position 116 91600161953 114 11810815424 17 9074918851256 17 Page Endeavor Software Manual Standard 2D Viewer
33. election 2D Image plane selection Enable aggital plane selection Saggite Enable Coronal plane selection Corona Enable axial plane selection Axial i Users can enable Sagittal Coronal and Axial plane selection by checking ticking the respective boxes 46 Page Endeavor Software Manual 2D 3D Visualizations 2D 3D Orthogonal MPR Purpose The user could visualize sagittal coronal axial and 3D view in a single window d p 4 Steps y 1 Click on the patient list to select which patient data to visualize Patient ID Patient Name Age Sex Date Imported Modality No of images Description Dataset Size fYET5 O 2011 03 23 CT 166 CT HEAD NK 5 0 B30s 2 Click View on the menu bar Select Other on the menu File Help 3D q Export DICOM File Directory Start Collaboration Server Online Collaboration Add new Plugin Other 47 Page Endeavor Software Manual 2D 3D Visualizations 3 Select 2D 3D Visualization category on the dialog box Choose 2D 3D Orthogonal MPR on the sub category Press OK to proceed ES Show View type filter text a 2D 3D Visualization ER 2D 3D Orthbgonal MPR z te Maximum Intensity Projection MIP ER Volume Rendering Communication E Volume Rendering Oblique MPR View 4 Other 3D Viewer Connected Users O Database Patient Event L
34. ewer Event Log Image Explorer val Image series Patient image folder As Patient information ia User Manager QO WML plugin Endeavor White Matte O WMLs 3D view ce Welcome Er annotationView Cancel Select Preview highlighted by a RED arrow Note This Show View option gives many different choices and can be used if there is a need to open the Volume Rendering DICOM image viewer WML plug in Preview and others 11 Page Endeavor Software Manual Preview View DICOM images Purpose Opens folder and see individual images In Preview to view the individual images of each folder of a patient do the following Steps 1 Select the particular folder as shown by the RED arrow 2 Double click the folder 2 ENDEAVOR m p j File View Help i Patient ID Patient Name Age Sex Date Imported Modality No of images FYETS O COMUMNIX 62 2010 09 01 CT 166 4 Preview 25 CT HEAD HK 5 0 B305 a E In this example there are 83 images in the folder and all these 83 images will be displayed Page 12 Endeavor Software Manual Standard 2D Viewer Standard 2D Viewer Purpose Opens folder and load the patient image on multiple windows In Standard view to view patient images on multiple display windows do the following Fi Steps k 1 Select the folder as shown by
35. finished To do that click the Home button on the File Menu to Switch to Main Perspective Then click on the X on the tab to close the server or client window The following sections describe how to use the Online Collaborative Annotation 36 Page Endeavor Software Manual Online Collaboration _ Start Collaboration Server Purpose The Collaboration Server acts as a server and clients can link to the server This enables various users specialists medical researchers surgeons in different locations to come together and discuss in a collaborative manner using Endeavor s visual imaging software Collaboration can also occur ina classroom setting with a teacher and students situated in different geographical locations Clicking this icon will start a new tab Embedded Server Configuration screen marked with RED arrow This means that one user must initiate the collaboration The server IP address must be communicated to other users to enable them to connect to the initiator Le ENDEAVOR z eee File View Help Patient ID Patient Name ge Se Date Imported Modality No of images FYETS O COMUNIX 2 2010 09 01 CT 166 joo Preview Embedded Server Configuration Connection Setting Authorization Code Main Port List of Connected Endeavor Client No Connected From Refresh Clear Status Inactive Press the Start button if want to start a communication session Stop 3 Page
36. ixels Lesion Area mm 2 Volume mm 3 Detection result s File Name 127 670 8 Estimate total volume 96 820 0 21 278 5 la Save X Close The image numbers or rows in RED are WML positive Green rows are WML negative To save this tabular result in a text format click Save 74 Page Endeavor Software Manual WML A Save As screen will display i Text File Save Dialog 7 eS sar 1e SHE patient T1 W File name Save as type Jock Browse Folders Save select the appropriate folder to save the file Type in a file name and click Save Click Cancel to exit this operation I Histogram analysis Purpose This icon will produce an analysis based on intensity of the pixels From this classification potential areas of WML can be segmented A histogram setting screen is displayed Histogram Setting screen Histogram Setting Number of bins 898 0 User specified minimum 1 0 User specified maximum 897 0 i Smooth histogram Cancel oo Accept the default settings Click Ok to run the analysis Click Cancel to exit this operation The result is displayed in a histogram 75 Page Endeavor Software Manual WML Histogram Analysis Description Histogram Analysis Diagram Histogram Analysis WML Histogram Analysis 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 Intensi
37. ize seo Views fy New Folder Name Date modified E IM 0529 0001 dcm IM 0529 0002 dem IM 0529 0003 dem IM 0529 0004 dem More IM 0529 0005 dem Folders IM 0529 0006 dem ib CER CT IM 0529 0007 dcm Ji fYETS 0 IM 0529 0008 dem J Output IM 0529 0009 dem W R227 F IM 0529 0010 dcm DQ AxT2 FLAIR IM 0529 0011 dem U SETIAX IM 0529 0012 dem Favorite Links E Documents W Desktop T E Recent Places File name Please note The image numbers are different for Flair and T1 In this example Flair image was IM 0531 0005 dcm The T1 image was IM 0529 0005 dcm select the matching T1 image number the last 4 digits In this example it is IM 0529 0005 dcm 7 Click Open The Skull Stripping process begins It will take a few minutes a al fetes al i Initializing the Skull stripping process 80 Page Endeavor Software Manual WML The images will be redisplayed correctly in the next screen After Redo image screen Original image FLAIR Skull stripped image FLAIR Result of Brain Tissue Classification T1 Weighted Segmented White Matter Lesions FLAIR Information Missing lobe is shown after Redo an image When images are miscalculated the WML analysis is no longer accurate Use this Redo icon as and when needed for selected images 81 Page Endeavor Software Manual WML ET Save Parameters Click this icon to save all parameter settings This
38. le Help 4U nq Export DICOM File Directory Start Collaboration Server Online Collaboration Add new Plugin Other m 53 Page Endeavor Software Manual 2D 3D Visualizations 3 Select 2D 3D Visualization category on the dialog box Choose Volume Rendering on the sub category Press OK to proceed ES Show View Sa type filter text 4 2 2D SD Visualization a CE 2D 3D Orthogonal MPR p ES Maximum Intensity Projection MIP gt Communication gt gt Volume Rendering Oblique MPR View 4 Other 3D Viewer T Connected Users O Database Patient Event Log Image Explorer Bi Image Preview Browser ea Image Series a Patient image folder E m o e 4 ls T Use F2 to display the description for a selected wiew Sime 4 Volume Rendering view will be loaded 54 Page Endeavor Software Manual 2D 3D Visualizations Volume Rendering Viewer Menu Pantunction Rotate function HAB Most of the icons are self explanatory They will be discussed here To pan the visualization To rotate the visualization Gl To zoom into the visualization To change the viewer s setting 55 Page Endeavor Software Manual 2D 3D Visualizations Plug ins The following pages will now look at the Plug ins available in Endeavor s Medical Image Analysis and Visualization package 56 Page Endeavor Softw
39. n 60 Page Endeavor Software Manual WML Radius and Seed Setting of Skull Stripper Radius of seed point 20 Seed 258 397 ok The radius is set at 20 as default The radius can be changed by keying in a different number To increase the radius type in a larger number To dearease the radius type in a smaller number The Seed coordinates will also change as the crosshairs are moved around the images o select the Seed coordinates position the crosshairs to he desired position ole click on the position Seed numbers are changed Click Ok Close this Settings window by clicking the X at the top right corner oe 0010 The above steps will set Seed X and Seed Y coordinates and the radius of the Seed point The Mean Curvature refers to the skull curvature The optimum setting is 0 05 Executing the algorithm will take up CPU processor time and as the algorithm checks from the Seed point and moves outward individual images are processed and comparison between brain tissue and skull tissue is performed The algorithm will strip away all skull tissue leaving only brain tissue This process may take up to an hour depending on the processor speed and memory available After the skull stripper is completed next comes brain tissue classification 61 Page Endeavor Software Manual WML Brain Tissue Classification This part of the algorithm is fast Each slice is read by the algorithm
40. n Code and Server s IP address 2 Click Save to save the connection setting If you don t want to save click Cancel 3 Click Start to start the communications session In this example the client is active Click Stop to end the communications session 4 Start Annotation Perspective 40 Page Endeavor Software Manual Online Collaboration Online Collaboration Annotation Screen Description Online Collaboration Annotation Screen Pixel information Property Annotation 23 x 25 575 mm2 Potential tumour region Styles SOLID v Pic IM 0001 0001 dcm Size D 12bits W 512px H 512px SE Color Contrast T Rotate i Brightness Reset Update to Server At the block RED arrow the button is greyed out once a user clicks on this button After the annotation is complete the user who is holding the pen can now Update to Server mee pass the pen to other users by clicking this button The changes are then sent to the Server and later updated to all the other Clients Please note Each time a user clicks on any of these buttons a Notification Window Box is displayed see thin RED arrow Page 41 Endeavor Software Manual Online Collaboration Notification Window Box Once there is a Request to Annotate a Notification window box pops up to inform the user at the bottom right of the screen Notification Waiting for approval to annotate Notification Approval to
41. n the process is repeated for the eft tail of the histogram This identifies the cerebrospinal fluid CSF and White Matter Lesion WML In Picture 2 in between the cerebrospinal fluid CSF and white matter lesion WML is normal brain tissue From the tangent points obtained from HTLD the WML can be segmented The bins here refer to the level of bins found in 16 bit or 8 bit images For 16 bit images the maximum level can be as high as 65535 bins but only 1000 bins are used For 8 bit images the maximum level of bins is only 255 WMLs Detection Setting screen WMLs Detection Setting A Sensitivity detection 35 00 Fhretevel Outliers 1 50 of bins Extreme Outliers 3 00 The default bins setting is 35 00 and this is in most cases good enough But when there are issues with sensitivity it is recommended to change the setting to 1 00 to adjust for 8 bit images The smaller the level of bins the higher the sensitivity becomes 7 Page Endeavor Software Manual WML Redo WML segmentation for selected image 4 Purpose There are certain peculiarities in the images obtained from DICOM These peculiarities can cause the WML algorithm to miscalculate the intensities When this occurs the skull stripper cannot process the image correctly An example is shown below Miscalculation of Intensities example Dicom image viewer WML plugin Endeavor White Matter Lesions Segmentation a SnaeaRB
42. o a Stop icon To stop playing the images click on the Stop icon 22 Page Endeavor Software Manual ROI Drawing Board Icons ROI Drawing Board ROI Drawing Board Dicom image viewer 2 QA Q eg a3 a b E 7 Sm amp fi Raa Pixel information Property Annotation Pic IM 0001 0001 dcm Size 1 D 12bits W 512px H 512px Contrast 5 Brightness 5 Reset ROI Drawing Board Menu Bar Icons Reset to Original Load previous annotation from xml H Metadata 4 Save annotation to xml Save annotation to xml to xml Dette sosces ject 2 Measure disano 5 eccamoiaton R Piet itrmaion 23 Page Endeavor Software Manual ROI Drawing Board Icons ROI Drawing Board Menu Bar icons Explained Most of the icons are self explanatory Some of them will be discussed here Cy To see a larger image zoom in Gl To reduce the image size zoom out To get back to original size use reset to original Displays all pixel information by default To save the annotations to database click this icon To view all the annotations click this icon Annotations can be retrieved from xml Annotations can be saved in xml b Draws an arrow to highlight a particular area 4 Please note XML format can be used in other applications 24 Page Endeavor Software Manual ROI Drawing Board Icons Drawing tools include rectangle freehand arrow and measurements Measure a distance How to Meas
43. of the icons are self explanatory They are discussed here i 9 i ty O Fhe oF amp To display the DICOM metadata To adjust the brightness contrast level After selecting this icon left click the image and drag sideways to change the contrast Drag upward or downward will change the brightness To pan the image within its window To rotate the image To set brightness contrast in predefined setting To see a larger image zoom in To reduce the image size zoom out To maximize the image to window size To reset the image window to its original size To load images as a matrix display 15 Page Endeavor Software Manual Standard 2D Viewer Display multiple images as a matrix Purpose Opens multiple images for comparative study In Standard view to view multiple images as a matrix do the following f Steps 1 Click Please enter matrix colurnns Please enter matrix rows 2 Enter the number of columns and rows to display 3 Press Ok to proceed 4 Multiple images will be loaded into the window as shown below Patient ID 5Yp0E 7GEFFOGbzqCNo43Yd0 Patient Name BRAINIX Study Date 200 Patient Sex 0000 Study Time 141645 Patient ID 5Yp0E 7GEFFOGbzqCNo43Yd0 Patient Name BRAINIX Study Date 200 Patient Sex 0000 Study Time 141645 0 Patient ID 5YpOE 7GEFFOGbzqCNo43Yd0 Patient Name BRAINIX Study Date 20 Patient Sex 0000 S
44. og S Image Explorer Bi Image Preview Browser Image Series ea Fi pi Sa Patient image folder t Use F2 to display the description for a selected view Sens 4 2D 3D Orthogonal MPR view will be loaded a Image Preview Browser he 2D 3D Orthogonal MPR 3 Computed image Axial Computed image Corronal 2D 3D Orthogonal MPR Viewer Menu 48 Page Endeavor Software Manual 2D 3D Visualizations i Y zomen o Most of the icons are self explanatory They will be discussed here Gl To see a larger image zoom in To reload the image currently loaded E To load image from external folder 49 Page Endeavor Software Manual 2D 3D Visualizations Maximum Intensity Projection MIP Purpose Maximum Intensity Projection MIP allows users to view projected 3D data that represents the plane of the voxels with maximum intensity step k steps A 1 Click on the patient list to select which patient data to visualize Patient ID Patient Name Age Sex Date Imported Modality No of images Description Dataset Size fYET5 0 2011 03 23 CT 166 CT HEAD NK 5 0 B30s 2 Click View on the menu bar Select Other on the menu Export DICOM File Directory ie Fi Start Collaboration Server La Online Collaboration Add new Plugin Other gt 50 Page Endeavor Software Manual 2D 3D Visualizations 3 Select 2D 3D Visualization category on the dialog
45. ort DICOM File Directory 3D Rendering k Manager Manages Usernames and Passwords Note DICOM stands for Digital Imaging and Communications in Medicine 5 Page Endeavor Software Manual Main Perspective Menu Bar Icons Explained This section explains the functions of all the icons found in the menu bar P Import DICOM File Directory Purpose To view images DICOM files must first be imported to the local hard drive to a specific folder A specific named folder helps Endeavor to bookmark that folder for easier retrieval Clicking this icon will display the Open Directory window to select the folder to place the new DICOM files to be imported Open Directory window Open Directory Sa Directory for DICOM File Desktop gt E cvrgshare Public JE Computer i Network di Bug Traq Doc Screenshots m Endeavor Installation Screenshots updated Folder cvrgshare Make New Folder select your directory or Make New Folder Then click OK The new DICOM files will be imported to the directory or folder of your choice The patient details will be displayed on the Patient Window 6 Page Endeavor Software Manual Main Perspective 4 Import DICOM From PACS Purpose In a hospital environment all MRI or CT scans or other forms of images are stored in PACS Picture Archiving and Communications Systems These DICOM files must be imported to a specific named folder in the local hard drive of the PC befo
46. plugin Endeavor White Matter Lesion LS Show View 2 a P Axial Corronal and Saggital view Database Patient Dicom image viewer Event Log Image Explorer va Image series Patient image folder As Patient information peal Preview cl User Manager lugin Endeavor White Matte O WMLs 3D view ce Welcome Er annotationView i Use F2 to display the description for a selected view Click Ok to start the White Matter Lesion plug in Click Cancel to exit this operation 64 Page Endeavor Software Manual WML White Matter Lesion Screen Dicom image viewer WML plugin Endeavor White Matter Lesions Segmentation 3 ome E c C s al SoARBo KB Original image FLAIR Skull stripped image FLAIR General information i Patient ID R 227 Patient s Age 063Y Patient Sex F Image width 512 px IM C Image height 512 px Total Images Series 19 Seacing between slices 6 0 mm Spacing 0 4688 0 4688 mm psity 0 123 y 4 gt gt PT amp Process Selection J Skull Stripper v Brain Tissue Classification Segmented Whit va Result of Brain Tissue Classificfti gt ay Skull Stripper S tting a Megh Curvature 0 05 pmogeneity Correction Setting p fin Tissue Classification Setting gt gt lt lt lt lt WMLs Detection Setting Sensitivity detection 35 00 Outliers 1 50
47. re image analysis can be performed To retrieve from PACS you need to know the connection to the server This information is obtained from your internal PACS systems administrator Steps pr 1 Select Import DICOM from PACS Import DICOM from PACS window Import DICOM From PACS Connectior New Server v Save Connection Name New Connection Server IP Server Port Server AET Client IP 10 207 150 5 Client Port 11112 Client AET CLIENT Today Yesterday This Week Last Week Others 2010 09 CT CR MR US NM SG XA XRF DX MG PR KO SR All Modalies Patient Name Patient ID Transfer Syntax None z Query Instance Availa Study Date Modality Modality in St Study Desc Patient Name Patient ID Sex Related Series 7 Page Endeavor Software Manual Main Perspective 2 To establish a connection to the PACS server please get the following information from your own organisation s systems administrator or IT department head a Server IP b Server Port c Server AET d Client Port e Client AET The following information is displayed by Endeavor a Client IP Once the connection server is setup correctly you will be able to query and retrieve any DICOM file Any DICOM file retrieved from PACS can be stored directly to a local folder 8 Page Endeavor Software Manual Preview Preview Screen Purpose A screen for viewing titles of folders The Preview Screen is di
48. reate the task After White Matter Lesion Detection process is done the next screen will show that Process is complete Process Complete LE Process Comp e3ts iii ae Oh White Matter Lesions detection and segmentation have been completed 7 Time taken 1998 sec In this example the time taken is 1998 seconds or 33 3 minutes Please note In the drop down list for Load Volume Images the Load Selected Image From Database work the same way 71 Page Endeavor Software Manual WML Load a Volume that is Already Processed When a volume is already processed the images can be copied over to another PC or loaded onto the WML viewer for further analysis Note The following sample is a severe WML case 1 Select the Load Volume Images icon In the 7 drop down select Import External Volume 2 A directory of folders is displayed Make a new folder on the Desktop so that is easy to find Import External Volume folders Import external volume g Es Open volume images from Directory adi R227 Ax T2 FLAIR di Output 1 ote mR SETI di History m icons 1 Hi Folder R227 Make New Folder Click Ok This will import the images and start the loading process 72 Page Endeavor Software Manual WML Importing External Volume process Importing External Volume Current image IM 0531 0006 dcm This will take a while depending on the number of images to be imported
49. rent version found for plugin com_dvtrs_InterfaceController feature Local version 1 0 0 201012031112 remote version 1 0 0 201012081430 Different version found for plugin com dvtrs VolumeRendering jar Loral version 1 0 0 201012031112 remote version 1 0 0 201012081430 Different version found for plugin com dvtrs annotation jar a local version 1 0 0 201012031112 Upon completion you will get the following window and means your Endeavor software has successfully been updated ENDEAVOR Update Manager fs i Product Update finished OK To change the configuration such as the URL to our centralized update server press the Configuration button 92 Page
50. splayed by clicking once on the Patient ID displayed at the Patient Window see big RED arrow To Delete or Refresh a Patient at the patient row right mouse click and select Refresh or Delete 2 ENDEAVOR n Patient ID Patient Name qi Si Date Imported Modality No of images COMUNIX 2010 09 01 CT 166 gt Number of folders In the Preview screen all the folders will be displayed for that patient This includes MRI images and CT scans Screen Navigation Right agrow key Laft arrow key Each folder contains a particular area of the body To read the descriptions of each file use the right and left arrows keys on the keyboard to move horizontally or click on the Left and Right arrows 9 Page Endeavor Software Manual Main Perspective Switch off Preview jd Preview 2 TO Close Preview click the X on the tab Switch on Preview DE ENDEAVOR a gt rie Ven Hel 3D rendering Export DICOM File Directory Se Dee opni eee ee 2010 09 01 ET 166 t Start Collaboration Server il Online Collaboration 8 Add new Plugin Ctrl 3 oh 4 ui ee eee ca To switch on Preview go to the View option in the menu bar Select Other marked by RED arrow 10 Page Endeavor Software Manual Main Perspective A new screen is displayed E Show View P Axial Corronal and Saggital view Database Patient E Dicom image vi
51. ted the Java applet closes and Volume Rendering screen displays Volume Rendering Oblique MPR Viewer Screen V3 ENDEAVOR e File View Help Details Type of View Volume Projection Trilinear Front Viewin X Y LUT Thermal Original 3 Side Frame ZAspects Z Aspects 64 Angle of Rotation X 115 0 V Markers Scale Distance Threshold Depth Scale 1 0 4 Distance 0 Threshold 128 lt Depijh 6 Main 3 Side Frame Settings Frame Frame 86 Page Endeavor Software Manual Oblique MPR Viewer Volume Rendering Oblique MPR Viewer Menu icons Viewing Options Slice Nearest Neighbour Slice Triline ar Slice and Borders The drop down option gives Slice and Volume Dots l Sa different viewing variations Volume Dots Volume 1 Projection Trilinear Front Volume 2 Projection Trilinear Back Original GrayScale l l Different color schemes give Spect Jame different perspectives Fire Thermal Viewing Axis select any combination of Axis to view 8 7 Page Endeavor Software Manual Oblique MPR Viewer Settings Frame Purpose This frame displays the selection of choices from the drop down menu icons and gives a little flexibility to users who want to experiment with different Z Aspects angle of rotation markers and scales settings Frame screen enlarged Details R View Options Type of View Volume 1 Projection Trilinear
52. th is 512 px and height is 512 px DICOM images are 12 bits If DICOM images are exported into jog or omp these formats will have a lower depth As the cursor moves around the image the intensity level is displayed along with the x and y coordinates 2 Page Endeavor Software Manual ROI Drawing Board Icons Property Information Description This column refers to the annotation drawing symbols applied over the image styles Choices Property Ar syes BEETS gt s SOLID Size i DOT Color DASH DASHDOT Rotate DASH DOT DOT Reset This refers to the line styles appearing on the rectangle rulers or freehand drawings By default it is a SOLID line Size This refers to the thickness of the lines Color This refers to the colors appearing on the lines Different colors can be used by different users Rotate The selected drawing can be rotated by selecting the bar Reset Button This will reset all the styles sizes color and rotation to the default setting 28 Page Endeavor Software Manual ROI Drawing Board Icons User Annotation Text Box Annotation text box Property Annotation Styles Selec Size 1 Color Rotate Type any relevant text into this Annotation text box i Save Annotation to Database Click this icon to save all the annotations and drawings Note If this icon is not clicked it means the drawings and annotations are not saved Data will be lost when the win
53. ties E Pixel intensities Histogram summary Smoothing original image Peak 433 with a count of 361 1776 show statistic annotation Max intensities level 899 End of Right Tail Intensity 11 End of Left Tail Intensity 899 V show HTLD annotation close HTLD is a marker Check this box gt W V show slope annotation The algorithm uses the Box Whisker Plot outlier method and from this process it generates the HILD markers HTLD stands for Histogram Tail Lesion Detection To the right of the peak the intensity increases This means that the tissue in this area would be classified as abnormal or white matter lesion Normal tissue has a lower intensity With this classification the WML tissues can be segmented The processing starts from the HTLD blue line to the red line Click Close to close the window Please note A detail explanation is found at this link Automated White Matter Lesion Segmentation in MRI using Box Whisker Plot Outlier Detection htto www2 warwick ac uk fac sci dcs events miuaZ20 1 0 proceed ings 76 Page Endeavor Software Manual WML Simplified Explanation of Histogram Analysis FWHM Picture 2 The use of Full Width Half Maximum FWHM is used to detect the starting point of the process of bins until the location of the tangent point The histogram of Flair images is used and to get the tangent point the right tail of the histogram is calculated The
54. tudy Time 141645 Modality MR Current slice 1 1 Modality MR Modality MR Slice position 123 48501954041 123 85898304080 83 23715 Patient ID 5Yp0E 7GEFFOGbzqCNo43Yd0 1 Patient Name BRAINIX Study Date 200 Patient ID 5Yp0E 7GEFFOGbzqCNo43Yd0 Patient Name BRAINIX Study Date 200 Patient ID 5Yp0E 7GEFFOGbzqCNo43Yd0 Patient Name BRAINIX Study Date 20 Patient Sex 0000 Study Time 141645 Modality MR Current slice 4 1 W 2475 C 2856 Slice position 123 05435714684 122 56247520541 65 2890 Patient ID 5Yp0E 7GEFFOGbzqCNo43Yd0 1 Patient Name BRAINIX Study Date 20 Patient Sex 0000 Study Time 141645 Modality MR Current slice 7 1 Slice position 122 62369451485 121 26596737002 47 3409 Patient Sex 0000 Study Time 141645 0 Modality MR Current slice 5 1 W 2475 C 2856 Slice position 122 91080293618 122 13030576800 59 3063 Patient ID 5Yp0E 7GEFFOGbzqCNo43Yd0 Patient Name BRAINIX Study Date 200 Patient Sex 0000 Study Time 141645 0 Modality MR Patient Sex 0000 Study Time 141645 0 Modality MR Current slice 6 1 W 2475 C 2856 Patient ID 5Yp0E 7GEFFOGbzqCNo43Yd0 Patient Name BRAINIX Study Date 20 Patient Sex 0000 Study Time 141645 Modality MR Current slice 9 1 W 2475 C 2856 Slice position 122 33 3194 120 40162891244 35 3755 16 Page Endeavor Software Manual Standard 2D Viewer 5 In order to cr
55. ure a distance 1 Click this icon The cursor changes to a cross hair 2 Click the start position and hold the mouse 3 Move the cursor to the end position and release the mouse The length is displayed in mm Remove all drawings This icon removes all drawings A pop up window box asks for confirmation How to Remove all Drawings iz Confirmation Do you want to clear all drawing Cancel 1 Click Ok to clear all drawings 2 Click Cancel if all drawings are to remain 25 Page Endeavor Software Manual ROI Drawing Board Icons Draw Rectangle How to Draw a Rectangle 1 Click this icon The mouse cursor changes to a crosshair Move the mouse to a starting position Click once and hold down the mouse 3 Move the mouse diagonally Release the mouse f Draw Freehand DOARDE Aea Click this icon The mouse cursor changes to a crosshair Move the mouse to a place on the image Click and hold the mouse and move the cursor in a circular shape 3 Release the mouse Ne 26 Page Endeavor Software Manual ROI Drawing Board Icons Pixel and Property Information Enlarged image Pixel information Property Has son Intensity 926 0 483 yi356 Styles SOUIG 01 0001 dem Size 1E 512px H 512 px T P P Color trast L Rotate Brighthess 5 Reset The picture resolution is given in depth width and height In this example depth is12 bits wid
56. vor Software Manual Annotation Perspective There will be a slight delay as the perspective is setup Annotation Perspective Setup 2D viewer i Setup 2D viewer Endeavor will now go into the Annotation Perspective screen I ENDEAVOR e T File View Help Dicom image viewer A User Annotatio z 1 User Name Anno ay R zy ry e ee Pixel information Property Annotation z Intensity 1081 0 4 Styles Sele v Pic IM 0001 0001 c Size Le Contrast 5 Cain Brightnes Rotate The annotation perspective is divided into 3 areas a Image Series b ROI Drawing Board c User Annotation 21 Page Endeavor Software Manual Annotation Perspective Image Series Image Series Image series m 7 oF Maxi a TeS ike sa IM 0001 0001 dcm 7 Scrokup and down bar 1 A ms IM 0001 0007 dem The Image Series screen displays all the individual images The navigation icon at the top bar gives flexibility for screen display The Play icon is to play all the images for quick viewing instead of viewing one image by one image This is displayed in the DICOM Image Viewer screen Click the Play icon There is a Timer Input screen to display in fast or slow speed The smaller the number the faster it plays Timer Input Timer Input Dialog Please enter a Timer rms 100 0 Ok Cancel Click Ok to start play To exit click Cancel The Play key will change t
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