www.rcr.ac.uk

COAST USER GUIDE

This guide refers to the 1.7 (July 2014) Release of COAST

Faculty of Clinical Oncology

www.rcr.ac.uk

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Contents

1. Getting started 2 Prerequisites 2 Downloading and installing COAST 2 Running COAST for the first time 2 Terminology 2 Initial Datapacks 3 Loading a case 3 Deleting datapacks 4

2. Getting to know COAST 5 Working your way round the COAST screen 5

3. Contouring 6 Reviewing the case prior to contouring 6 COAST Image Viewer 6 Image settings for contouring 7 Using the contouring tools 8 Start contouring 9 Editing a contour 9

Adding a margin to a contour 10 Deleting a contour 11 Copying an ROI 11 Renaming an ROI 11 Saving your contouring 11 Returning to previously saved contouring 12

4. Scoring your contouring 14 Scoring your contouring 14 Contouring analysis – what’s happening under the hood? 17 Reviewing your contouring 18

5. Using the COAST datapack manager 19

6. Conclusion 21 Feedback 21 How to contribute to COAST’s ongoing development Error! Bookmark not defined.

1. Getting started

Prerequisites

§ To run coast you need a PC running Microsoft Windows XP, Vista, 7 or 8, or a Mac running Windows via Apple Bootcamp, Virtualbox, or VMWare player (note that VMware fusion is not supported)

§ COAST is designed for use on your own computer, for which you have administrative privileges. However, it can also be installed on your hospital PC by an IT engineer. Please check your local IT policy regarding this.

§ You need a screen resolution of at least 1024 x 768 pixels (XGA)

§ COAST should configure itself correctly on large screen setups, but any display problems can be fixed by setting your font size to 100%

§ COAST needs at least 2GB of RAM to run, and around 500Mb of free hard drive space for each datapack

Downloading and installing COAST

§ To download COAST from the College website click the installer file, and follow the instructions on screen. You will need to accept the terms and conditions before COAST will install.

§ You can view the Readme file to see any last minute notices about the current version of COAST.

Running COAST for the first time

§ For Windows 8 users, select the Coast application tile from the charms bar

§ For earlier versions of Windows, go to Start | COAST | Coast to run the application

§ NHS Use: If you have asked an IT engineer to install COAST on your Hospital computer, COAST will automatically configure itself for your personal use when you log in.

§ The first time you run COAST, you will be prompted to enter your name. This is used for the creation of CPD certificates.

Terminology

COAST uses several different kinds of data files.

§ The first is a datapack file (which ends in .zip). This contains all the image data and annotation data that goes with a specific planning case. Datapack files are downloaded from the college web site.

§ The next is a Coastguard file (which ends in .cgf). This file holds all the information for a specific clinical assessment. Note that it is possible that one datapack has more than one Coastguard file associated with it.

§ The final one is a Coastline file (which ends in .cln). If you save your work in COAST, then your contours are stored in a Coastline file.

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Initial Datapacks

Home Use: The install file for COAST includes two datapacks which will be ready for use on installation. The first is a CNS case of Glioblastoma, with a fused MRI scan, and the second is a prostate cancer case. If you wish to load any additional datapacks, you will need to use the COAST Datapack Manager. Further details appear in Section 5 – Using the Datapack Manager. NHS Use: If you had COAST installed on your work computer by an IT engineer there will usually not be any datapacks available when you first run COAST. Please refer to Section 5 – Using the Datapack Manager for details on how to download some datapacks.

Loading a case

When you first load COAST, you will see that the task window is asking you to select a case file

Click on the ‘Load a case’ button and you will see that a new window appears. This will initially just show the two datapacks that come with the installer. To access more datapacks you will first have to install them using the datapack manager (see Section 5 of the user guide):

First you must choose a datapack that has been imported into COAST. Once you select a datapack on the left, then you can choose a coastguard file on the right that contains the case you are interested in. Finally click ‘Load a case’ and COAST will start loading the data. Depending on the speed of your computer, it may take a few minutes for COAST to load all the data. Most datapacks can now include an extensive contouring guide, including illustrations and scan images. In some cases, the contouring guide is prepared from the guidance notes for a clinical trial. If a guide is available, COAST will ask you if you wish to view it whilst the datapack is loading:

In some Datapacks, the author of the datapack has provided some of the diagnostic imaging associated with the case. This is helpful because we usually refer to diagnostic scans before and during contouring. We will return to the topic of viewing diagnostic images in section 3.

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Once you have loaded the case, you will see a screen like this. COAST is now ready for you to use!

Deleting datapacks

If for some reason you wish to remove a datapack from your computer, you can use the COAST datapack explorer to do this for you. Click on the delete selected datapack button and the computer will remove the datapack from your hard drive. Please note that deleting a datapack will also delete any contours that you have saved that are associated with the datapack.

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2. Getting to know COAST

Working your way round the COAST screen

COAST looks a little different to your conventional treatment planning system, as it performs a slightly different task. Let's look at the main screen:

1 Image display area. It will show axial CT and MRI/PET data.

2 Status box. You will see that COAST shows what it is doing in this box. You can ignore the display in this box unless something goes wrong, and you notice a fault. Copying the contents of the box and sending it to us will help us understand what caused the error.

3 Slice slider. You use this slider to move up and down through the dataset. You can do the same thing with the PageUp and PageDown keys on your keyboard.

4 Sliders that allow you to move the image around to centre on a specific area of interest. This is helpful when you are working with a 2x or 4x zoomed image.

5 Task window that allows you to perform major functions in COAST. You will see that functions are grouped together in tabs e.g. for contour editing, reviewing your contouring, or setting your display settings. Click on the tab for the task you wish to perform and then you will see more controls appear.

6 Menu bar. Some functions like loading and saving files are found here.

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3. Contouring

Reviewing the case prior to contouring

At this point the system is ready for you to start contouring. However, as in real life, it is necessary to take some time and acquaint yourself with the clinical task, the imaging, and the image settings. COAST Image Viewer

Some datapacks will contain diagnostic quality imaging for you to look at before you start contouring. If this imaging is available, you will see a button in the Display settings tab that allows you to launch the COAST image viewer.

The viewer pops up in a different window, and operates independently from the COAST application. When you click the button, you will see something like this:

You can use the scroll bars to move around the image, and the zoom bar to change the magnification from 25% to 400%. Unlike the scan window in COAST itself, you can enlarge the display window in the image viewer by making the application larger. COAST image viewer can display multiple image datasets. If you go to the scan selector tab, you will see a list of available images available for viewing, together with a brief description of the scan:

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Image settings for contouring

Before you start contouring, it is necessary to ensure that the best display settings are in use for the image data. Use the display settings tab to do this. You can set window settings using the sliders, enter values directly as numbers or set them automagically from a preset windowing level.

You may also want to change the zoom level to make it easier to see what you are doing. Note that only 2 magnification levels are available. By default, COAST will apply smoothing the image during zoom, though in some situations, it may be easier to see the tumour with the smoothing turned off. You can change this by unchecking the Smooth Zoom box in the Display Magnification panel.

400% Zoom. No Smoothing.

400% Zoom. Smoothing Switched on.

Some datapacks will have a secondary image dataset such as an MRI scan or PET-CT scan, which have been co-registered to the CT scan. In this case you can press the Enable MRI/PET fusion to see the additional controls. You can set window levels for the secondary image, and switch between the CT, secondary image or a blend of the two.

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Now you have finished reviewing the imaging, it's time to start contouring. The contouring tools have been made as simple to use as possible, so that they conform to the way that most other Windows software works. However, there may be some things that are different from your own treatment planning system and it might take a little while to unlearn these habits. Using the contouring tools

First, switch the task pane to display contouring tools by clicking on the Contour tab. You will see that by default all the contouring tools are turned off. This is to stop you inadvertently contouring when you are still reviewing the imaging. Click on the enable editing box and the tools will appear:

First thing is to create a new region of interest. Click the New ROI button and a box will appear asking you to enter the name of your region of interest. Usually you will be contouring the GTV, so this is what appears by default.

Note that due to a quirk in Windows, COAST will not be aware if you click the red cancel button on this box, and will still go ahead and create a new contour. You will need to use the delete ROI button to get rid of the new ROI. Once you have entered the name of your ROI, you will see that COAST automagically moves you on to draw mode. You can tell which mode you are in because a red box appears around the appropriate button.

Start contouring

When you are in draw mode, move the pointer over the display window and you will see it change to an arrow with a box by it. This means that COAST is waiting for you to start clicking points round your target.

Use the left mouse button and click several times round the edge of your target. If you click a point by mistake, then press the right mouse button to undo the last point.

When you are finished, double click the left mouse button and COAST will close the loop and store the contour. Now move to a new slice and continue contouring. If you want to exit drawing mode, Click the Draw button again and the red box round the button will disappear. Editing a contour

To edit a contour, click the Edit button and choose the slice that holds the contour you wish to edit. You will see a red box appear round the Edit button. Now move the pointer onto the screen. You will see the pointer changes to an arrow with a question mark next to it:

This is because there may be more than one contour in your ROI on a single slice (e.g. a bifurcating structure) so you need to tell COAST which one you are working on. Click somewhere near the contour you wish to edit and you will see it turn yellow and the pointer will change to a hand indicating that you can move the points around.

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A small box will appear round each of the points you clicked and you can now drag them to a new position using the left mouse button. Clicking the right mouse button will delete the point underneath the pointer. Once you have finished editing points, double click with the left mouse button and you will see the contour turn red again. This means that the changes have been saved. When you are editing or deleting points, it is the point under the index finger of the pointer that will be moved or deleted. Author’s note: In COAST 1.4, we had quite a lot of problems with contours reappearing, and not being saved correctly. COAST now automagically saves your contour if you move off the display window and as soon as you change slices. Adding a margin to a contour

You can grow a margin around an ROI that you have drawn, or around one of the visible structures included in the datapack. In the contouring panel, take a look at the margin tools box.

To add a margin, you must set the distance to be grown in the Left-Right, Ant-post, and Sup-Inf directions, and also specify a new name for the ROI formed by adding this margin. Note that the sup-inf margin will always be rounded to the nearest slice (i.e. if you have 3mm slice spacing in the datapack, and you specify a 10mm sup-inf margin, then the algorithm will grow the margin by 9mm in the sup-inf direction. This next bit is a little confusing but very important:

- If you want to add a margin to a structure you have drawn, then select your structure in the contour list and press the button add margin to user contour.

- If you are adding a margin to a structure that has been provided in the datapack, then select the structure in the datapack you wish to use as the basis for your margin, and press the button Add margin to preset contour.

The computer will set to work performing the margin growing calculation. As with the TPS you use at work, it can take a little while for this step to finish, particularly if you are adding a large margin. Important: Because of the way COAST works, you can only see one of your ROIs on the display at a time. When the margin growing is complete, you will need to select the new ROI to see the results of your volume growing. Also, please note that at the moment the margin growing cannot be constrained to include or exclude a specific structure. This will be implemented in a forthcoming update of COAST.

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Deleting a contour

To delete a contour, click on the delete button in the contouring tools. As you move the pointer over the display window, you will notice that the pointer changes to an arrow with a small question mark by it:

Move the pointer close to the contour you wish to delete and then left click. Note this cannot be undone so use this option with care. You may decide your contour is just not right, and you want to delete it and start again. To do this, select the contour you wish to delete, and press the Delete ROI button in the ROI controls box. Copying an ROI

There are also some circumstances where you may wish to make a copy of an ROI, and then edit it (say for example, an ROI for the Prostate CTV could be copied and edited to form the Prostate & Seminal Vesicles CTV).To do this, select the ROI you wish to copy, and press the Copy ROI button in the ROI controls box. A new ROI will appear at the bottom of the ROI list, with the word ‘copy’ appended to the name. Renaming an ROI

If you create a new ROI, you can change its name to distinguish it from other ROIs. Select the ROI you wish to rename, and press the Rename ROI button in the ROI Controls box of the editing panel. A small box will appear, asking you for the new name of the ROI. Hit OK and the name is changed.

Saving your contouring

It's a good idea to save your masterpiece as you go along. You can do this by saving the contours to a Coastline file. On the Menu bar click on File and Save Coastline to save your work:

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A window will appear asking you to give the Coastline file a name, and choose a folder. By default COAST will save your contouring in the same folder as the datapack you are working on. This makes it easier to find your work, and to keep datapacks tidy on your computer.

Returning to previously saved contouring

If you are returning to work on some contouring you have started previously, you will first need to reload the Case File (CGF) you were working on, and then load the Coastline (CLN) file. First click the ‘Load a case’ button and find the CGF file you were working on:

Then go to the File Menu and select ‘Load Coastline’:

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Then find the Coastline file and select Open. Your outlining will then be restored, together with the window levels you used when you saved your contouring.

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4. Scoring your contouring

Scoring your contouring

Once you have completed contouring your masterpiece it is time to score it against the outlines of the content author. To do this, you need to have selected your contour in the contour tab. If you have only contoured one structure, then COAST will use this one.

Next, you need to go to the review tab, and choose which contour you want to be scored against. In this example, there is only one contour available for scoring, and that is the GTV. Then hit the score outline button and COAST will start its analysis.

It should just take a few minutes for COAST to complete the analysis, and you will see things flashing on the screen as it goes. When it is finished, COAST selects the results tab and shows you the results.

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You get several bits of information. First is the sup and inf extent of your contour compared to that of the content author. You also get a conformity index, which tells you the volume of overlap between your contour and the reference contour. Finally, you get a breakdown on the axial conformity, which is used to judge whether or not you pass the case. If you have been successful in all contouring tasks, you will see this indicated in the box below the results, and a button will appear allowing you to generate a CPD certificate.

Click the button, and COAST will generate a certificate, signed by the Medical Director for Professional Practice, Clinical Oncology. By the way, the barcode authenticates the certificate to stop you making lots of copies, and COAST will remember all the cases you have completed, and only generate one certificate for each case. It is therefore a good idea to print and/or save the certificates as soon as they are generated.

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Contouring analysis – what’s happening under the hood?

It’s helpful to understand the process used by COAST to analyse your contouring. COAST uses several different metrics to make the Pass / Fail assessment, as follows:

1. Analysis of superior and inferior extent of contouring. Whilst we have 3d planning, we still tend to outline on a slice by slice basis, and it is often helpful to know whether or not you have contoured on the same slices as the datapack author. This is the first thing that COAST calculates, and it shows you in the results the top and bottom slices of your own contouring, and that of the author. Although this is calculated for reference, COAST won’t actually fail you if your superior and inferior extents don’t match up, because of the volume ratio assessment.

2. Volume ratio analysis. The next thing that COAST does is to look at the volume of your contour in 3D, compared to that of the datapack author. If it exceeds a tolerance value, then COAST decides that your contour is not similar enough to the Gold Standard contour to warrant further evaluation. This also helps COAST work out if you might have contoured a different structure.

3. Axial conformity analysis. This is the main part of the evaluation. What COAST does is to break up your contours into individual points, and then measure the distance from every point on the edge of your contour to its corresponding point on the Gold Standard contour. This is done by means of a two dimensional grid search.

Thus for every point on your contour, COAST has a measure of how far that point is from the gold standard contour. It works out the average for each slice and for the whole of your contour. This information is used to construct the error-volume histogram, showing how much of your contour falls within a certain distance (in millimetres). Finally COAST applies the pass/fail threshold specified by the datapack author for your axial conformity score.

Gold standard contour

User contour

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Reviewing your contouring

Now you have the results, you can go back to the review tab and go through your contouring slice by slice. The way in which COAST displays information about your contouring has changed. You will see a histogram appearing on the screen that looks something like this:

This shows the contouring errors of each and every point on each contour of your work, when compared to the gold standard contour. If you got a perfect score, you would have a single bar at zero.

Positive numbers, or bars to the right of zero, are overcontouring errors. These indicate that you have perhaps been a little generous in your contouring compared to the Gold Standard. The consequence of overcontouring errors for IMRT is an increase in normal tissue dose which will not be quantified downstream in treatment planning. Negative numbers, or bars to the left of zero, are under-contouring errors. These are potentially more serious because you may have underdosed the tumour and compromised tumour control.

If you scroll up and down through the slices, you will see the mean and maximum conformity measurements for that slice. A traffic light also appears alongside the numbers, where Green means within the contouring threshold and red means outside the contouring threshold.

You can use the zoom, pan and window controls to review your contouring against that of the content author. You can then go back into edit mode and try contouring again.

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5. Using the COAST datapack manager

Author’s note: In COAST 1.4, we found that quite a few users had problems with downloading datapacks from the College web site, and having to do the installation into COAST by hand. The COAST Datapack Manager makes datapack installation a simpler and more robust process.

Running the Datapack Manager

On Windows 7 and earlier, go to Start | Programs | Coast 1.7 | Coast Datapack Manager.

On Windows 8 go to the charms bar and find the COAST Datapack manager application tile. If you start typing COAST you will find it quickly.

You need to have a connection to the Internet to use the Datapack Manager. A few seconds after it opens, if you don’t do anything, you will see a little screen popup like this:

With your permission, COAST will then connect to the College server (Or COAST Central) and get a list of available datapacks. You will see a list of installed datapacks on the left of the screen, and a list of available datapacks on the right of the screen.

Select a datapack from the right hand list and click ‘Install selected datapack’. Depending on how big the datapack is, and how fast your connection is, it might take a few minutes to download the datapack. You will see a little window appear showing how far the download has got. If your connection fails during a download, simply reselect the datapack, click install, and your download will resume from where it left off.

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Once the datapack is downloaded, the Datapack manager performs a quick validity check, to confirm that the datapack you have downloaded is intact and was approved by the College. It will then be installed and appear in the left hand list of available datapacks. At this point, you can close the datapack manager and run COAST and your freshly downloaded datapack will be available for you.

If you download a datapack that you already have installed on your computer, the Datapack manager will delete the old copy and start with a fresh copy. This means that your saved contouring will be lost too.

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6. Conclusion

This is a quick walkthrough of the functionality of COAST. Please do not hesitate to make contact if you experience any problems with it.

Feedback

If you encounter any bugs in the software or experience any problems please complete the online feedback form and return it to the College as soon as possible.

Raj Jena& Anna Campbell May 2014

www.rcr.ac.uk

The Royal College of Radiologists.

COAST User Guide The Royal College of Radiologists, 2013.

Ref No. COAST2013 © The Royal College of Radiologists, August 2013.

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Faculty of Clinical Oncology