TexRAD Research Version Client User Guide 1.1

Transcription

1 The Barn, Manor Road Church Lane Chilcompton Somerset BA3 4HP TexRAD Research Version Client User Guide 1.1 Release date 27/02/2013 Number of Pages 21 Replaces None Status Draft Comment Copyright 2013 Date Name Signature Prepared by: 27/02/2013 Mike Hayball Reviewed by: Approved by:

2 Table of contents Contents 1 Scope Getting started Client requirements Login and registration Managing Users Starting Image Processing What next? TexRAD Data Miner Date:27/02/2013 Draft Page 2 of 21 Copyright 2013

3 1 Scope This document is intended to assist users with the operation of the TexRAD web server / cloud application. It does not cover the applications or operation of the algorithm. 2 Getting started 2.1 Client requirements Operating systems: Windows XP SP3 or higher or Mac OSX or higher Browser: Internet Explorer 7+, Chrome 12+, Firefox 3.6+ (PC); Safari 4+ (Mac) 2.2 Login and registration Point your browser at the web page you have been given. You should see the screen below in Figure 1. Figure 1. Login Screen If this is the first time you ve used the system and you don t have a username and password, click on Register. This will bring up a screen as in Figure 2. Enter a username and password then click Create User. You will need to contact your site administrator (for a cloud install, that will be support@texrad.co.uk) to grant access to your user. Date:27/02/2013 Draft Page 3 of 21 Copyright 2013

4 Figure 2. Registering 2.3 Managing Users If you are the administrator of your site, you will see the below (Figure 3) when you log in. Figure 3. Start screen for administrators Click on the Administer Users link to show the list of users (Figure 4). Date:27/02/2013 Draft Page 4 of 21 Copyright 2013

5 Figure 4. Managing users To add a new user, Click on the Add User link and fill in the form (Figure 5). If you want the user to access the TexRAD clients, you must enable the CadranUser Role as shown. To allow a user access to the TexRAD clients, click on the User Name in the User List and set the CadranUser role. Figure 5. Add a user 3 Starting Image Processing Log in as described above. Date:27/02/2013 Draft Page 5 of 21 Copyright 2013

6 Figure 6. Start screen for a logged in user Click on TexRAD Client to start the client. If this is the first time you have used the client in your browser you may be asked to install Silverlight (see below). Once Silverlight has been installed, the client will load. If Silverlight is not installed on your computer you will see the page shown in Figure 7. Click on Click now to install. Figure 7. If you do not have SIlverlight 5 on your system, you will see this. Depending on the security setup on your computer you may need to ask for assistance to install Silverlight on your PC. If all goes well, you should be able to answer the installation questions and progress to the client. Date:27/02/2013 Draft Page 6 of 21 Copyright 2013

7 Figure 8. If you are able to install Silverlight, you should see a screen similar to this. Once Silverlight has loaded, the client will start. There may be a delay of a few seconds while it loads (a progress wheel will appear and the count will increase from 0% to 100%). The start screen for the TexRAD client is shown in Figure 9. You can select a project at this point. Click on OK to continue to the client (you do not need to enter the password as you are already logged in at this point). A project is used to collect the results from TexRAD analysis for later processing. You can change the destination project when you save the results. Projects can be created and managed in the Data Miner. Figure 9. Starting the TexRAD Client A list of studies will be shown as in Figure 10. If there are no studies, you will need to upload some data (see Adding Studies). Note: All of your uploaded studies will appear here, the selection is not dependent on the project selected. At the top of the page you can filter by various patient information including Patient Name and Patient ID. If necessary, use * as a wildcard. Click on the heading for a column to sort. Date:27/02/2013 Draft Page 7 of 21 Copyright 2013

8 Figure 10. Selecting your study Once you have selected your study, it will be loaded into the client and displayed as in Figure 11. Note for large studies this can take a few seconds. Each series of images will be displayed as a thumbnail on the left of the screen. The first image of the series will be displayed (Figure 12). Date:27/02/2013 Draft Page 8 of 21 Copyright 2013

9 Figure 11. The start screen for images. Once you have selected the series, select the frame (image number) within the series using the Frame slider, or type the image number. Width and Level can be adjusted by typing in the boxes or pre-sets can be selected by right-clicking the image and selecting WL. Zoom is also available from the right-click menu. The mouse behaviour is controlled by selecting the option at the top left: Pan to move a zoomed image around the screen; W/L to control the width and level; ROI for region of interest editing (see later). The Layout control selects the number of images to be displayed on screen. You will not usually need to change this. Date:27/02/2013 Draft Page 9 of 21 Copyright 2013

10 Figure 12. Basic controls Once you have selected the image of interest, you can draw your regions and process the image. First select the ROI type from: Rectangle Ellipse Polygon a free drawn polygon. Click multiple points to draw a polygon or click and drag for a continuous line. Seed-point this is similar to the magic wand selector seen in some paint applications. It will draw around areas of similar density. Please consider this experimental at the moment. Lungs this is a work-in-progress lung detection algorithm. In addition, you can select the Fitting option which applies an Otsu threshold algorithm to the region drawn (Otsu selects the threshold which optimally separates the region into two contrast values). This is particularly useful in lung tumours. See Figure 13 and Figure 14 for an example. Date:27/02/2013 Draft Page 10 of 21 Copyright 2013

11 Figure 13. Drawing a region of interest with fitting enabled. First, draw round the tumour coarsely. Figure 14. Drawing a region of interest - showing the results of fitting on the region drawn in Figure 13 To edit the region of interest after drawing, first use Zoom and Pan to resize the image appropriately (Figure 15), then click within the region to select it (it will change from blue to red). Date:27/02/2013 Draft Page 11 of 21 Copyright 2013

12 Figure 15. Zooming the image for easier editing Hold down the shift key while you draw the new boundary (Figure 16) then doubleclick to finish. The new boundary will replace the old (Figure 17). Figure 16. Editing a region of interest Date:27/02/2013 Draft Page 12 of 21 Copyright 2013

13 Figure 17. After editing If you wish, especially if you have multiple regions, you can change the name (select the ROI, right click and select Annotations/Rename). Other features found in the annotation menu include: Save save a file on your local computer which allows you to restore the ROI later. Load load a file saved as above. Calculate properties prepare the ROI properties Show Properties show the properties after preparation above. Delete ROI Once you have drawn your region (or regions) you can process them (Figure 18). Click on the Algorithm drop-down list for to select the appropriate algorithm (you will need to discuss this with us). Select an Algorithm (from the drop-down menu) which includes: Liver - Includes only pixels between HU within ROI after erosion (scale = 1.8) for reducing edge artefacts in the case of large organ - Liver Lung - Includes only pixels above -50HU within ROI after erosion (scale = 0.5) for reducing edge artefacts in the case of lung tumours Small Tumour - Includes only pixels above -50HU within ROI after erosion (scale = 0.5) for reducing edge artefacts in the case of small tumours Phantom - Includes all pixels (no thresholds) within ROI after erosion (scale = 1.8) for reducing edge artefacts in the case of CT phantom studies Custom: LiveronCT (Recommended) - Includes only pixels between HU within ROI after erosion (scale = 1.0) for reducing edge artefacts in the case of large organ - Liver Date:27/02/2013 Draft Page 13 of 21 Copyright 2013

14 Custom: NonLiveronCT (Recommended) - Includes only pixels above -50HU within ROI after erosion (scale = 1.0) for reducing edge artefacts in the case of lung or small tumours Custom: PhantomonCT (Recommended) - Includes all pixels (no thresholds) within ROI after erosion (scale = 1.0) for reducing edge artefacts in the case of CT phantom studies If you have multiple regions on the image you can select the handling: all the software will analyse the texture within the ROIs individually but present the results (quantification) after combining all ROIs into one single ROI distinct - the software will analyse the texture within the ROIs individually and present the results (quantification) for each distinct ROI separately Figure 18. Processing the region of interest Click on Process to additionally display the conventional image (with all but the ROI masked out) and filtered derived images in false colour (positive pixel values in blue and negative pixel values in red ). If you have a customised algorithm to use, select Add. You will see the dialog in Figure 19. Please contact TexRAD to discuss the values to enter here. The algorithm settings can be saved to your computer and restored (an alternative save to the server will be available soon). Date:27/02/2013 Draft Page 14 of 21 Copyright 2013

15 Figure 19. A customised algorithm Click on Process to process the images. After a short pause, a screen similar to Figure 20 will appear. Figure 20. Results of processing The Analysis Results screen will show the results of the processing in a table. Selecting a row will also give a representation of the filtered image. This table can be copied or saved to comma-separated variable format (CSV) or copied by clicking in the table and using Control-A (select all), Control-C. Date:27/02/2013 Draft Page 15 of 21 Copyright 2013

16 We recommend saving the results for use in the data miner. This saves a rich set of information about the processing including the source study and image, the region(s), the processing parameters and much more. Select the Project in the drop-down box then click on Store results to save to a specific project. Save results will save the results as a file on your computer. Show full report (not currently in use) will show a report from a template for printing. Typically, five TexRAD filters are applied to the data and the first three are shown along with the source image in a 2x2 view (Figure 21). These images are displayed using a red / blue colour scale showing negative/positive pixels respectively. Note: The images are not intended for diagnosis but as a guide to the filter results. Figure 21. Processed images 4 What next? To process a different image, click on Select Image in the helper screen. To select another study click on Select CT Study in the helper screen. When you have finished, close the browser window or click on Home at the top right. 5 TexRAD Data Miner The data miner is used to analyse results stored using the Store Results option in the TexRAD client. Results are gathered into a Project and selections can be made from within the project and compared with each other or external results. Date:27/02/2013 Draft Page 16 of 21 Copyright 2013

17 This introduction will show you how to view the results, manage your projects and data. The advanced features of the Data Miner will be explained in training either onsite or via Web presentation. To start the Data Miner, either select the Miner: Open option within the client or click on the Data Miner option in the Home page. As with the TexRAD Client, the first time you start the app you may need to load Silverlight or the application. Occasionally you will see an error message Loading GUI failed this can be ignored and should only occur once. The slightly uninspiring start screen (Figure 22) allows the selection of source data. For the analysis of TexRAD Client output, click on the TexRAD Client check box. The Data source drop-down list will be filled with the list of current projects. Select one of these to load. Initial data load may take a few seconds. Figure 22. The Data Miner start page Once the data has loaded, the left-hand side of the Data Miner will show the list of analysis results (Figure 23). In the case of the TexRAD Client data, each row represents a single filtered image / region of interest combination with the analysis results, image information and intermediate information included. Date:27/02/2013 Draft Page 17 of 21 Copyright 2013

18 Figure 23. Sample data set from the TexRAD client At the bottom of the data grid you will see two expander bars Histogram and Images. If you click on these to expand, you will see the histogram from the filtered data and thumbnail images from the processing (Figure 24). Data can be copied to Excel or other destinations using the usual Control-C key combination. Date:27/02/2013 Draft Page 18 of 21 Copyright 2013

19 Figure 24. View the histogram and images from an analysis result. Right-click on a row to see some options (Figure 25). These include Remove and Move. Use these options to delete a processing result or move it to another project (delete actually moves to a hidden project in case of error, the data can be rescued). See Figure 26. Date:27/02/2013 Draft Page 19 of 21 Copyright 2013

20 Figure 25. The right-click menu in the Data Miner Figure 26. Moving a data object between projects in the Data Miner To manage projects create, rename, remove. Select the Edit Projects link on the right-hand side. You will be presented with an Edit Project dialog (Figure 27). Date:27/02/2013 Draft Page 20 of 21 Copyright 2013

21 Figure 27. Editing Projects in the Data Miner Date:27/02/2013 Draft Page 21 of 21 Copyright 2013