TexRAD Research Version Client User Guide Version 3.9

Transcription

1 Imaging tools for medical decision makers Cambridge Computed Imaging Ltd Grange Park Broadway Bourn Cambridge CB23 2TA UK TexRAD Research Version Client User Guide Version 3.9 Release date 23/05/2016 Number of Pages 29 Replaces Status Comment None Release Page 1 Client User Guide 23/05/2016

2 Imaging tools for medical decision makers Contents 1 Scope Getting started Client requirements Login and registration Managing Users Adding Studies Starting Image Processing Log in and start the client Select a study Select images for processing Draw regions Algorithms Custom: SolidLesion_CT Custom: SolidLesion_CT_ex_Ca Custom: Liver_CT Custom: SolidLesion_MR Analysis Advanced features Saving algorithms What next? TexRAD Data Miner The import wizard Page one data selection Page 2 merge rows Page Other wizard options The data grid Other Data Grid options Import wizard Save Series editor Clear all series Edit TexRAD Projects Show TexRAD Histogram Restore TexRAD Session Page 2 Client User Guide 23/05/2016

3 Imaging tools for medical decision makers 7.3 Data analysis Statistics Correlations TexRAD histogram Bland-Altman Correlation Histogram Kaplan-Meier KNN, ROC and Scatter Plot Configuring the analysis options Page 3 Client User Guide 23/05/2016

4 1 Scope This document is intended to assist users with the operation of the TexRAD 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 to grant access to your user. Date:23/05/2016 Release Page 4 of 29

5 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:23/05/2016 Release Page 5 of 29

6 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 Adding Studies Image data must be added in DICOM format. If configured, you may be able to send directly from your PACS or image archive. Alternatively, you may be able to upload image data using the web browser. Date:23/05/2016 Release Page 6 of 29

7 If you have a DICOM Upload option on the TexRAD home page, selecting this menu option will show the dialog in Figure 6. Use the Select Files option to select one or more DICOM files. When you have selected the relevant files, click on Upload to push them to the server. After a few seconds you should see these files in the Image Processor. Figure 6. File upload screen. 4 Starting Image Processing 4.1 Log in and start the client Log in as described above. Date:23/05/2016 Release Page 7 of 29

8 Figure 7. 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 8. Click on Click now to install. Figure 8. 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:23/05/2016 Release Page 8 of 29

9 Figure 9. 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 10. 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 10. Starting the TexRAD Client 4.2 Select a study A list of studies will be shown as in Figure 11. 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:23/05/2016 Release Page 9 of 29

10 Figure 11. Selecting your study 4.3 Select images for processing Once you have selected your study, it will be loaded into the client and displayed as in Figure 12. 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 13). Date:23/05/2016 Release Page 10 of 29

11 Figure 12. 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:23/05/2016 Release Page 11 of 29

12 Figure 13. Basic controls 4.4 Draw regions 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 using the current window / level settings to set the data range). This is particularly useful in lung tumours. See Figure 14 and Figure 15 for an example. Date:23/05/2016 Release Page 12 of 29

13 Figure 14. Drawing a region of interest with fitting enabled. First, draw round the tumour coarsely. Figure 15. Drawing a region of interest - showing the results of fitting on the region drawn in Figure 14 To edit the region of interest after drawing, first use Zoom and Pan to resize the image appropriately (Figure 16), then click within the region to select it (it will change from blue to red). Date:23/05/2016 Release Page 13 of 29

14 Figure 16. Zooming the image for easier editing Hold down the shift key while you draw the new boundary (Figure 17) then double-click to finish. The new boundary will replace the old (Figure 18). Figure 17. Editing a region of interest Date:23/05/2016 Release Page 14 of 29

15 Figure 18. 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 (in xml format) on your local computer which allows you to restore the ROI later. Load load a file (in xml format) 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 19). 4.5 Algorithms Click on the Algorithm drop-down list for to select the appropriate algorithm (you will need to discuss this with us) Custom: SolidLesion_CT This algorithm includes only pixels between -50 and above HU within ROI using "threshold" as padding (erosion-scale=0) for reducing edge artefacts in the case of solid-tumours. Spatial scale filter - SSF values include 0,2,3,4,5,6mm Custom: SolidLesion_CT_ex_Ca This algorithm includes only pixels between -50 and 200HU (to exclude calcification if present) within ROI using "threshold" as padding (erosion-scale=0) for reducing edge artefacts in the case of solid-tumours. Spatial scale filter - SSF values include 0,2,3,4,5,6mm. Date:23/05/2016 Release Page 15 of 29

16 4.5.3 Custom: Liver_CT This algorithm includes only pixels between 0 and 300 HU within ROI using "threshold" as padding (erosion-scale=0) for reducing edge artefacts in the case of large organ such as liver. Spatial scale filter - SSF values include 0,2,3,4,5,6mm. This algorithm was being employed in the earlier liver studies. TexRAD research team have recently been using 'Custom:SolidLesion_ CT' algorithm settings for liver analysis on CT. So fine to use either but whichever algorithm you use be consistent Custom: SolidLesion_MR This algorithm includes all the pixels within ROI (with any signal-intensity) using "threshold" as padding (erosion-scale=0) for reducing edge artefacts in the case of solid-tumours. Spatial scale filter - SSF values include 0,2,3,4,5,6mm. In all the above algorithms, one can customise the erosion (scale = 0.5) to further reduce edge artefacts if present in cases where the ROI drawn around the lesion is located in a heterogeneous background. If in doubt, please do not hesitate to contact us to discuss this further before starting your image analysis. 4.6 Analysis 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 19. Processing the region of interest Date:23/05/2016 Release Page 16 of 29

17 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 20. 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). Figure 20. A customised algorithm Click on Process to process the images. After a short pause, a screen similar to Figure 21 will appear. Figure 21. Results of processing Date:23/05/2016 Release Page 17 of 29

18 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 commaseparated variable format (CSV) or copied by clicking in the table and using Control-A (select all), Control-C. 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 22). 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 22. Processed images Note: From version 3.9 an additional option appears on the Processing button ( Batch Process ). This allows multiple slices or regions to be processed simultaneously. Please contact us for information on using this feature. 5 Advanced features 5.1 Saving algorithms New versions of algorithms can be saved using the Add Date:23/05/2016 Release Page 18 of 29

19 Figure 23. Save algorithm menu 6 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. 7 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. 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 Data Miner starts with a Wizard view. Date:23/05/2016 Release Page 19 of 29

20 Figure 24. The TexRAD Miner Wizard which appears on startup 7.1 The import wizard Click on Start New to analyse a new dataset Page one data selection In the first page, select one of the data source icons to add data. Typically, you will use Project Data to select the results of analysis. Click on this icon and select the source project. Figure 25. First page of the data miner wizard with the DefaultProject data project selected. The Inject data icons allow clinical data to be merged with the project data. Please contact us for more information on using this. For example, to inject Excel data, first select a range of data including title from a spreadsheet. E.g. Date:23/05/2016 Release Page 20 of 29

21 The click on the second Inject Data Icon. Figure 26 shows the next screen. Label the source (red highlight), then click the green-highlighted box and paste the Excel data. You may see a warning asking you to confirm pasting into Silverlight you will need to confirm before continuing. Figure 26. Adding data from Excel. After pasting, the appearance should be as in Figure 27. Date:23/05/2016 Release Page 21 of 29

22 Figure 27. Wizard after pasting data from Excel Page 2 merge rows This page allows multiple filters to be displayed in a row, useful for comparing different filter sizes. Again, the details of this are best covered in training and we recommend leaving Enable unticked. Date:23/05/2016 Release Page 22 of 29

23 Figure 28. Page 2 of the Data Miner Wizard - merging rows Page 3 Page 3 is used with the Inject Data option in Page 1 to allow two datasets to be related. Date:23/05/2016 Release Page 23 of 29

24 Figure 29. Page 3 - linking related data Click finish to complete the import process Other wizard options Other options in the import wizard include: Edit current repeats the Start new wizard steps for the current dataset. Restore restore the last session. Load from file load a saved session from an XML file (see Save later). Load from DB load your saved session from the database (see Save later). 7.2 The data grid Once the data has loaded, the left-hand side of the Data Miner will show the list of analysis results (Figure 30). 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:23/05/2016 Release Page 24 of 29

25 Figure 30. Sample data set from the TexRAD client Data can be copied to Excel or other destinations using the usual Control-C key combination. Hover over a row to see the source and filtered image related to it. Right-click on a row to see some options (Figure 31). 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 32. Date:23/05/2016 Release Page 25 of 29

26 Figure 31. The right-click menu in the Data Miner Figure 32. Moving a data object between projects in the Data Miner Other Data Grid options At the top of the data grid you ll find a tool bar: In order, the options are: Import wizard This brings up the Import Wizard as described above Save You can save your current session as a file on your local machine, or in the database (only one database session is allowed at a time). Saved files can be shared with other users (if they have access to the same data). Date:23/05/2016 Release Page 26 of 29

27 7.2.4 Series editor The series editor will let you change the series used for analysis. Most often, you would use this to select rows corresponding to a particular filter value. Figure 33. Series edit dialog Clear all series This option removes any series created above Edit TexRAD Projects Use this dialog to manage projects create, rename, remove. You will be presented with an Edit Project dialog (Figure 34). Figure 34. Editing Projects in the Data Miner Show TexRAD Histogram This will show histogram data for the selected row. Date:23/05/2016 Release Page 27 of 29

28 7.2.8 Restore TexRAD Session This option will open a new browser tab and restore the TexRAD analysis associated with the current selected row. 7.3 Data analysis A number of analysis options are available for the data miner. Please note that these are experimental and should not be relied on for publication without crosschecking. Figure 35. Analysis options. Options include: Statistics This will show summary statistics for all current series Correlations This will show simple rank correlation coefficients between the columns in the current series TexRAD histogram This is used for internal testing shows a cumulative histogram of all rows (not very informative but can be pretty if you enable standard deviation) Bland-Altman Will show a Bland-Altman plot of two variables for the current series Correlation Will display a scatter plot of two variables and calculate statistics for the current series Histogram Will display a frequency histogram of a selected variable for the current series Kaplan-Meier Will display a Kaplan Meier plot for the current series. This requires the addition of clinical data contact us for training KNN, ROC and Scatter Plot These are used for development and not relevant to general use. Date:23/05/2016 Release Page 28 of 29

29 7.3.9 Configuring the analysis options Figure 36 shows an example configuration. Click on the spanner icon to set plot parameters. If you have multiple series, use the graph icon to the right to select which series are visible. When you have set the parameters, use the refresh button at the top right to refresh the view. Figure 36. Configuring the correlation plot Date:23/05/2016 Release Page 29 of 29