EduCase TM EduCase TM Features Covers all aspects of EduCase TM features and supporting components. Scott Kaylor, M.Ed. Instructional Technologies: CEO Arthur L. Boyer, PhD: Physics Education Director Robert Amdur, MD: Physician Education Director Yulong Yan, PhD: Physics DICOM Director February 2013
2 Table of Contents Table of Contents Table of Contents... 2 Feature Overview... 4 Viewing Authors contours and User s Practice contours... 4 User Roles... 5 Contouring Tools... 6 General Tools... 6 Drawing Tools... 7 Interpolation Tool... 8 Contour Expansion Tool... 9 Eraser Tool... 12 Magnifying Tool... 12 Spyglass Tool... 13 Measuring Tool... 13 Window Leveling... 14 Image Series Controls... 15 DVH Charting Tools... 15 Annotations... 16 Saving Drawn Contours... 16 Load and Export Contours (Caseowners only)... 18 Exporting saved contours... 18 Loading saved contours... 19 Loading Area Domain DICE scores... 22 View Tools... 24
3 Table of Contents View Tools Menu... 24 Single Window mode... 24 Two Window mode... 24 Four Window mode... 25 Orthogonal Window mode... 26 Multi Window mode... 26 Metric Tools... 26 Metric Tools... 26 Caseowner view: Area Domain Quantitative Results... 27 Caseowner view: Area Domain Image Map Results (submission #1)... 28 Caseowner view: Area Domain Image Map Results (submission #2)... 28 PDF result data export... 29 MS Excel result data export... 29 MS Excel group result data export... 30 Caseowner view: Line Domain Metrics... 30 Author Tools... 31 Author Tools... 31 Annotation Tools... 31 View Annotations... 31 Creating Annotations (caseowners only)... 34 Sidebar Menus... 39 Left Side Menu: Images... 39 Left Side Menu: Slices... 40 Right Side Menu: Author's Structures... 40
4 Feature Overview Right Side Menu: Your Practice Structures... 42 Right Side Menu: All User's Structures... 43 EduCase Uploader Tool... 43 EduCase Uploader Tool... 43 EduCase TM Features: Feature Overview Viewing Authors contours and User s Practice contours The graphic user interface of EduCase consists of a basic viewing and navigation layout from which display, contouring, and assessment tools can be accessed and used. Once a case is loaded from the Internet, this GUI appears as below. The imaging studies are handled as conventional DICOM objects. A thumbnail panel on the left helps the user determine what slice within the study they wish to view in the main central window. A Zoom tool in the upper right corner of the window is always available to adjust the viewing scale.
5 Feature Overview The right panel contains the list of names given to the structures by the mentor. The colors of the boundaries and fill of the structures are controlled by the colored boxes beside the names. The check boxes are used to control which structures are displayed as lines (first column) and/or as fill (second column). The Navigation Tab provides users the ability to change the desired menu tool display. There are five primary menu tool display options including: Contouring Tools, View Tools, Metric Tools, Author Tools (case owners only), and Annotation Tools (case owners and students). To make the Navigation Tab appear, move the cursor into the upper gray menu bar and then draw it down into the next lower bar in the center of the page. This will cause the Navigation Tab to be populated with icons. Users will roll over the thin grey line under the menu bar in order to initiate the Navigation Tab for changing the menu display. Contouring Tools View Tools Metric Tools Author Tools (Case owners only) Annotation Tools (Case owners and students) User Roles Throughout the following documentation you will see references to two user types. The different roles indicate which capabilities will be available to each specific user type. They include:
6 Contouring Tools Caseowner, faculty, administrator: There is only on individual user in the EduCase system that can be associated with this user role. The caseowner has complete administrative capabilities to the case they are assigned to. General user, student: All other users with this role type will not have access to the administrative features described in the documentation. Contouring Tools General Tools The "Contouring Tools" folder contains the following menu items: Continuous (freehand) line contouring Point-to-point contouring Interpolation tool Expansion tool Structure erasing Magnification within the main view window Spy-glass viewing of secondary and tertiary studies Measurement between two selected points Window and leveling
7 Contouring Tools Viewing of DVHs Viewing of annotations Saving contours and submitting contours for metric scoring Loading students contours (for case owners) Drawing Tools Continuous line contours can be drawn using the freehand contouring tool. Facilities are available for editing the contour by drawing a cut line from outside the contour, into the interior of the contour, and back to the outside of the contour. Similarly, a contour can be extended by drawing a line starting inside the contour, extending across the original contour boundary, and returning to the
8 Contouring Tools interior of the contour. The contours are stored as polygons defined by an ordered sequence of vertices. The individual vertices of a contour can be selected by the point-to-point tool that fills the space between the vertices by a Bezier fit. The displayed vertices can be selectively moved to edit the contour. The eraser tool removes the last completed contour. Interpolation Tool The Interpolation tool allows users to draw a contour on any slice, draw a second contour on any other slice, and click the Interpolation button to produce contours in between drawn slices. Draw your first contour on any slice Draw your second contour on any other slice
9 Contouring Tools Click the Interpolation icon Confirm by clicking OK when prompted View interpolated contours and edit when necessary Contour Expansion Tool The Contour Expansion tool allows users to select an existing primary source contour, define the measurement in millimeters to expand, and select the secondary source contour to be expanded. Examine caseowner contours and determine expansion size with ruler tool
10 Contouring Tools Draw your primary source contour (ex. GTV). Once complete, click the Expansion icon on the menu bar Select the primary source contour that will be expanded from (ex. GTV). Click the Next button to continue. Select the number of millimeters you want for your expansion (ex. 5mm). Click the Next button to continue.
11 Contouring Tools Select the secondary source contour that will be expanded to (ex. CTV). Click the Finish button to complete the expansion process. New expansion will appear on the main screen Compare your expansion against the caseowner s contour Edit your expanded contours as needed
12 Contouring Tools Examine your expansion results with the ruler tool for field expansion approval and verification. Finally, do the same process on another slice and take advantage of the interpolation tool to complete contours on other slices. If the expansion tool is used with contour already drawn on other slices, the expansion will be incorporated on to those slices as well Eraser Tool The Eraser tool allows users to click the eraser icon and delete their drawn contour. Each click will erase each previous drawn contour currently selected on the Select Contour to draw pull down list. Magnifying Tool The Magnifying tool produces a boxed selection that allows users to roll their mouse wheel to enlarge or reduce the image area.
13 Contouring Tools Spyglass Tool When multiple modality studies are available, a spyglass tool is available to view the secondary study through the primary study. The window/levels of each study are still individually adjustable. Measuring Tool A basic measuring tool is also included in the contouring kit. It maintains its scale during the image zoom.
14 Contouring Tools Window Leveling The window and level of the study can be adjusted during the contouring process to optimize the contrast of a given study for the particular tissue imaging properties of the structure under consideration. When invoked, the window/level tool is pinned to the upper right corner of the main viewing window. The upper and lower bounds of the window can be adjusted individually as well as the window center.
15 Contouring Tools Image Series Controls When multiple studies are downloaded, such as a planning CT and an MRI study, the studies can be viewed individually or as blended images. When viewed as blended images the overall intensity of each study can be adjusted as well as the window and level of each individual image. The user can bring out features of either study that lend to the determination of structure boundaries in the blended view. The user can then edit contours drawn initially with one study or the other and with window settings that explore the visualization of structure boundaries viewed with a particular window in one individual study modality or the other. Any number of stacked modalities can be displayed in addition to 4D gated respiratory phases. DVH Charting Tools When treatment planning dose tables are uploaded with the study, the DVHs of the named structures can be displayed to illustrate advantages and disadvantages of structure boundaries in various clinical scenarios. The DVH charting can display Cumulative and Differential values when data is available.
16 Contouring Tools Annotations Annotations can be assigned to structures by the author using a suite of annotation facilities. The annotations can then be viewed by the user using tags viewed on the annotated structures. This feature allows the mentor to embed teaching material in the contouring process to enhance the student s learning experience. READ MORE... Saving Drawn Contours Once the contours of a structure are completed on all axial reconstruction
17 Contouring Tools planes, they can be saved by the student. The contours can be edited further and saved repeatedly, overwriting the previously saved contour by the same name by clicking the "Save Contours" button in the save pop-up window.
18 Contouring Tools Clicking the "Submit Final" button in the save pop-up window: The contour metric scoring tools operate on the areas within the boundaries of the contours (Area Domain) and on the contour lines themselves (Line Domain). The contours are scored by comparing the students contours with the mentor s contours. The Dice Similarity Metric (DSC) uses counts of pixels that fall within both student and mentor contours (true positive, TP), and pixels that fall in the student contour alone (false positive, FP) or the mentor s area alone (false negative, FN). Pixels outside each area that still fall within a rectangle that bounds both contours are counted as true negatives. The Dice Similarity Metric is computed as 2(TP)/(FP+2TP+FN) for the Area Domain. The line domain metric utilizes the distances between matched vertices in the mentor s and student s regularized contours. All calculations for the Area Domain and Line Domain are immediately available to students and mentors upon clicking the "Submit Final" button in the save pop-up window. READ MORE... Load and Export Contours (Caseowners only) Caseowners have several options for loading and exporting saved/submitted contours. Case owners have following options when clicking the load icon: Export individual and/or group contours Load individual and/or group contours Load individual and/or group Area Domain DICE submissions Exporting saved contours
19 Contouring Tools After selecting the "Load" icon in the Contouring Tools menu, caseowners can select any number of students from the "Saved user contours" bar. They can select users by holding the ctrl key on their keyboard and click any number of random users. They can also select users by holding the shift key on their keyboard and click a top-to-bottom list of users. Once the user group has been selected, click the "Export Contours" button. The caseowner must select an export destination folder and click "Save" to complete the export process. Contours are exported out in a zipped XML format which provides an ubiquitous language for use in research and programming. Loading saved contours
20 Contouring Tools After selecting the "Load" icon in the Contouring Tools menu, caseowners can select any number of students from the "Saved user contours" bar. They can select users by holding the ctrl key on their keyboard and click any number of random users. They can also select users by holding the shift key on their keyboard and click a top-to-bottom list of users. Once the user group has been selected, click the "Load Contours" button. Select the "Load Users as group" button Caseowners can toggle on/off the group's latest saved contours. (This will only display the latest contours and does not necessarily reflect DICE submitted scores)
21 Contouring Tools Another loading alternative is to load a group of users as "Individuals". The difference will be that each individual user selected will display in their own unique menu with their names in the menu header bar. Select the "Load each user" button
22 Contouring Tools Caseowners can now toggle on/off each individual user by selecting the menu bar with the user's name. To expand and reduce the menu bar, simply click the bar title or arrow on the right-hand corner of the menu header. To close the menu, click the File > Close drop-down button in the secondary menu header. Loading Area Domain DICE scores To view multiple Area Domain DICE submissions by student groups, start by: Opening the case in "Two window" mode. (see "View Tools") Click the "Load" icon to bring up the "Load and Export User Contours" popup window.
23 Contouring Tools Click the "Submitted user contours" header bar to open DICE contour submissions. (When the popup first opens the header bar will be on the bottom of the default list) Select any number of students from the "Submitted user contours" bar. You can select users by holding the ctrl key on your keyboard and click any number of random users. You can also select users by holding the shift key on their keyboard and click a top-to-bottom list of users. You can also sort columns to make your selection easier. (In this example we have sorted the column by clicking the "Attempt" column header and only selecting the 1st attempt users) Once the user group has been selected, click the "Load Contours" button. Repeat the process for second attempt users Once the 1st attempt group and the 2nd attempt group has been loaded as two unique group menus: Click the 1st main image and then select the contours from the 1st menu group Click the 2nd main image and then select the contours from the 2nd menu group This will allow caseowners to visually compare 1st and 2nd attempt Area Domain DICE contours. If you wish to view the actual Area Domain DICE scores you will need to load them from the Metric Tools menu. READ MORE...
24 View Tools View Tools View Tools Menu The "View Tools" folder allows the user to view reconstructions in one plane or multiple planes. Once viewed as preferred by the user, contouring tools are deployed to execute the segmentation. Single Window mode This is the default mode for viewing each axial reconstruction in a single window. Two Window mode In this example we have opened two windows, revealed the primary CT from the Image Series controls in the first window, and revealed only the secondary CT/PET images in the second window.
25 View Tools Four Window mode In this example we have opened the four window mode and revealed only one of the data sets from the Image Series controls for each window.
26 Metric Tools Orthogonal Window mode Multi Window mode In this example we created a custom view that allows for the top row as orthogonal view and the bottom row for Axial and Sagittal MR image sets. Custom views must be requested and are not part of the standard window view modes. Metric Tools Metric Tools
27 Metric Tools The contour metric scoring tools operate on the areas within the boundaries of the contours (Area Domain) and on the contour lines themselves (Line Domain). The contours are scored by comparing the students contours with the mentor s contours. The Dice Similarity Metric (DSC) uses counts of pixels that fall within both student and mentor contours (true positive, TP), and pixels that fall in the student contour alone (false positive, FP) or the mentor s area alone (false negative, FN). Pixels outside each area that still fall within a rectangle that bounds both contours are counted as true negatives. The Dice Similarity Metric is computed as 2(TP)/(FP+2TP+FN) for the Area Domain. * Caseowners: Can view users that have been assigned to the case group and drill down to each user's results. * General Users: Can only see their own results. Caseowner view: Area Domain Quantitative Results
28 Metric Tools Caseowner view: Area Domain Image Map Results (submission #1) Caseowner view: Area Domain Image Map Results (submission #2)
29 Metric Tools PDF result data export MS Excel result data export
30 Metric Tools MS Excel group result data export Caseowner view: Line Domain Metrics The line domain metric utilizes the distances between matched vertices in the mentor s and student s regularized contours.
31 Author Tools Author Tools Author Tools Author tools are only available to caseowners and administrators. This feature provides the caseowner to co-register image study sets, adjust the fusion registration variables, and hide unwanted or extra slices within a case. Annotation Tools View Annotations All users have access to any annotations that have been added by the caseowner. A popup alert will inform user if annotations have not been added to a specific case. Click the "Annotation" icon in the Contouring Tools menu bar to initiate the annotations. Annotations are contour specific and will have a colored open icon attached to the contour with the same color. Click the icon to open the "View Annotation" description center.
32 Annotation Tools The first column contains: Title: Which is the title of the annotation the caseowner gave to this annotation. Author: Is the name of the user (caseowner) that created the annotation. ROI: Is the name of the contour the annotation is parented to. Date: List the creation date and time. Tags: Are the meta tag the caseowner added to the annotation. The Media column can contain following media assets: Image files including:.jpg,.png, and.pdf. Audio files including:.mp3 only Video files including:.flv,.mp4, and.avi.
33 Annotation Tools The Description column contains: Text description created by caseowner Add Comment button: Allows user to add their comments on the specific annotation they are viewing. Clicking anyone of the listed Media assets produces a popup window displaying the asset and scroll feature to show all other listed assets. You can close the popup by clicking the "x" in the upper left-hand corner of the popup window.
34 Annotation Tools To add a comment click the orange text link "Add Comment". A popup window will open displaying your user name and a text box to enter your comments. After clicking the "add comment" button your comment will display with all other user's comments in order as they were received. Before you post: Before posting, please ask yourself the following question: "Am I making a post which is either funny, informative, or interesting on any level?" If you can answer "yes" to this, then please post. If you cannot, then refrain from posting. If you post anyway, the admins will probably remove your thread. Before you reply: Before replying, please ask yourself the following question: "Does my reply offer any significant advice or help contribute to the conversation in any fashion?" If you can answer "yes" to this, then please reply. If you cannot, then refrain from replying. Creating Annotations (caseowners only) Caseowners have the ability to create media rich annotations to any of the contours associated with a case.
35 Annotation Tools Start by selecting the "Annotation Tools" folder from the main menu. Click the "Add" button in the upper-left menu bar to launch the annotation interface. Type a title for your annotation in the "Annotation Title" text box. The "Author" box will default to the logged in user name. Select an ROI to add your annotation from the "Select ROI" pull down menu. Type in the "Tags" text box to add meta data to our annotation. This will allow users and search engine to find your material more easily. Select the "Allow Comments" checkbox if you wish to allow users to comment on your annotation. Click the "Add Media" button to browse for and upload your annotation media assets. Type your annotation's didactic script in the "Description" text box. Click the "Save" button to save all you annotation work. Click the "Clear" button if you would like to re-write your description material.
36 Annotation Tools Adding Media assets to your annotation: Click the "Add Media" button to initiate the Add Media popup window. Click the "Browse" button to select the media asset from you computer. Type a caption in the "Media Caption" text box. You can also edit you caption with the text editor options. Click the "Upload" button to upload you media asset and media caption. Click the "Cancel" button or the popup window "X" in the upper right hand corner if you wish to close the "Add Media" asset popup window without saving. You can add any number of Media Assets by repeating the steps above. These can include image, audio, and video assets. Add your didactic text to you annotation:
37 Annotation Tools Type your annotation description in the "Description" text box Click the "Save" button to compete your annotation once all parameters have been set, all media assets have been added, and description text is complete. * Note: at this point your annotation is only available on the selected slice. Distributing your annotation to all slices containing the annotated contour: Click the "Duplicate" button if you want your annotation to appear on all slices with the given contour. Click the "Edit" button if you want to edit any of the annotation parameters in the previous steps. Viewing your annotation Media Assets:
38 Annotation Tools After saving your annotations, click any of the media assets listed in the "Media" box to launch you media asset. If you have more than one asset, click the navigation button in the asset popup to navigate through all assets listed. To close the asset popup window, click the "x" in the upper left hand corner of the asset popup window. Adding a "Comment" to the comment dialogue: Click the "Add Comment" button to launch the comment popup window. Type your comment in the "Comment" text box. Click the "Add Comment" button to add your comment. It will display along with all the other comments by users in the order it was received. This allows you to answer questions directly from other user that may have posted questions.
39 Sidebar Menus Sidebar Menus Left Side Menu: Images The upper left-hand menu labeled "Images" allows caseowners the ability to add various images to support their case. By clicking the green "+" icon, they will be prompted with a popup window to browse for images and add captions from their desktop. Select the appropriate checkbox to describe your image. After the upload process is complete, users can click on the image thumbnail to view the image in the main UI. By clicking any thumbnail in the "Slices" menu will bring the case images back into the main UI. Supporting images can include: DRRs, Daily Radiographs, jpg, png, and power point slides that have been converted to images.
40 Sidebar Menus Left Side Menu: Slices Click or drag-and-drop or click a thumbnail within the "Slices" menu to load a selected slice into the main UI. This allows for image reference quick navigation through a case. Additional methods for navigating through a case include the navigation button on the bottom of the main window or using the roller button on your mouse. Right Side Menu: Author's Structures The Author's structure menu offers several features that differ from caseowners and general users. All users have the ability to: Toggle on/off the contour "color-fill" button which is a green icon located left of the Author's Structures tile Toggle on/off any individual or all primary structures from any case (unless structures have been disabled by caseowner) Select a contour's color box to change the color of a structure from the color picker
41 Sidebar Menus Caseowners have additional features that include: Enabling and Disabling contours within the Author's Structure menu Editing the title on all structures. This feature allows caseowners to restrict access to any number of structures to students to insure they are able to perfect their drawing techniques without seeing the master contours. Click the "Disable" radio button to initiate the contour disable popup window, select the appropriate check boxes to disable the contours, click save, and Author's contours selected will be unavailable to general user for viewing. Click the "Enabled" radio button to turn them back on.
42 Sidebar Menus Caseowners can click an Author's Structure title to initiate the title text box, rename the contour title, and hit the "Enter" key on your keyboard to complete the title change. Right Side Menu: Your Practice Structures Users can toggle on/off their structures as they go through their contouring process. To initiate the "Your Practice Structures" menu, click the menu header bar and/or header bar arrow to open and close the menu section.
43 EduCase Uploader Tool Right Side Menu: All User's Structures Caseowners and general users can view all structures that have been saved by all users. This is helpful to instructors to evaluate students progress and facilitate discussion amongst peers. To initiate the "All User's Structures" menu, click the menu header bar and/or header bar arrow to open and close the menu section. The same action could be performed by the casesowner "loading" user's saved structures. READ "Load and Export Structures"... EduCase Uploader Tool EduCase Uploader Tool The EduCase Uploader Tool is our proprietary tool that clients can use to upload a case to an EduCase server. The Uploader Tool is only available to clients with EduCase websites. The EduCase Uploader Tool can load the following DICOM file types: CT.xxxxx.dcm: CT images are parsed and uploaded as JPEG files PT.xxxxx.dcm: PET images are parsed and uploaded as JPEG files MR.xxxxx.dcm: MRI images are parsed and uploaded as JPEG files US.xxxxx.dcm: Ultrasound images are parsed and uploaded as JPEG files RD.xxxxx.dcm: RT Dose files are parsed and uploaded as XML data RS.xxxxx.dcm: Structure files are parsed and uploaded as XML data
44 EduCase Uploader Tool RE.xxxxx.dcm: Spatial Registration objects are parsed and transform secondary data sets to the primary data set for co-registration * Enter you User ID and Password * Click "Login" to continue * Read the "Terms of Service" * Click the "I agree to the terms" checkbox if you agree * Click the "Next" button to continue * Click the "Browse" button to browse for case data to upload * Select the root folder where your case data resides * Click "Open" to continue
45 EduCase Uploader Tool * Select the "Include subfolders" unless all of your data resides in the root folder * Click "Next" to continue * The Uploader Tool will scan your files to determine what to upload * Click the "See what we transmit" link for detail on what we upload * Click "OK" to close the popup window * Find and select your primary data set (In this case it is a CT data set) * Select the "There are multiple image series for this case" button if you have multiple data sets for a case * Select the "Flip primary image series" only if you have a prone case and need to see it in
46 EduCase Uploader Tool supine * Select all the secondary image set you wish to upload with your case * Select the "4D Case" checkbox only if the secondary image sets are gated 4D respiratory image sets * Click "Next" to continue * The Dose value window will appear only if your case data has a dose file * Click the "Default Setting" button to load a default list of values * Select the "Relative" or "Absolute" radio button * Double click and edit dose values if desired * Click the color box to change the dose value color if desired * Click "Next" to continue * Type the title of your case in the "Title" text box * Select the category from the "Category" pull down menu * Type a description of your case that will be posted in your case listing * Click "Next" to continue
47 EduCase Uploader Tool * The Uploader Tool will analyze your case data (no action required) * If there is a registration object, the Uploader Too will resample the secondary MR images and co-register them to the primary CT image * The Uploader Tool will analyze your case structure data (no action required) * The Uploader Tool will parse your case data for orthogonal images (no action required)
48 EduCase Uploader Tool * After the upload process is complete, the Uploader Tool will provide a link to you newly uploaded case to the EduCase server