The Flex Tomo Window and Template Windows implement Regions of Interest (or ROIs) a little differently than MedView’s Standard Image window does. This chapter explains how to use ROIs in these newer windows. It discusses:
Creating ROIs
Using the tools below, you can create regions on your images. When you have created regions, their statistics can be displayed by either hovering your cursor over the region. When you do so, a popup window appears to display the statistics. The popup will automatically disappear after a moment. You can cause the popup to remain on screen by holding down the shift key. You can have multiple ROI popup statistics showing simulaneously by holding down shift and hovering over each desired ROI until its popup appears.
An alternative display, Show Statistics On Images (as shown below) writes the statistics directly into the image. You can then, if you wish, perform a Window Snapshot to capture the images and regions into a DICOM secondary capture study.
Note: the "O" hotkey allows you to easily turn the on image statistics display on and off.
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Rectangle ROI
You create a rectangular ROI by selecting the tool and clicking and dragging a box on an image. When you release the mouse button you’ll see your region and its statistics.
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Oval ROI
You create an oval ROI by selecting the tool and clicking and dragging an oval on an image. When you release the mouse button you’ll see your region and its statistics. Note that in this screen shot, the user has engaged the "opaque backgrounds" Miscellaneous Options - Template/Tomo option to improve on-image statistics readability.
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Freehand ROI
Use the Freehand ROI Tool to draw a border around any irregularly shaped region you wish to examine. The tool will automatically close the region (connect the start and end points) and calculate the area, sum, min, max and average.
Double-click on the region with the Grabber tool  (or any drawing tool) to display the “ROI Info” dialog. For a Freehand ROI you can change the line color, check or uncheck “Draw Filled,” and check or uncheck “Show Stats.” “Draw Filled” can be useful for complicated regions because it tells you exactly which pixels are included in the stats calculation.
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Threshold ROI
Use the Threshold Region of Interest tool (Threshold ROI) to exactly outline a region on an image for the purpose of gathering information about the region. This tool allows you to click once on the image, and the tool will automatically find the region boundary for you.
This tool uses a threshold to decide which points in the image are inside the region. For example, a threshold of 50% will include image pixels that are within 50% (above and below) the pixel you clicked. Therefore, raising the threshold grows the region, and lowering the threshold shrinks the region. In order to select exactly the region that you want, the threshold may need to be adjusted.
Double-click on the region with the Grabber tool (or any drawing tool) to display the “ROI Info” dialog. This allows you to change properties of the region. Use this dialog to adjust the threshold until the region is satisfactory. From this dialog, you can also change the line color by clicking in the colored box to open the color selection palette. Check “Draw Filled” to draw a solid region. This setting is useful for very complicated regions since it allows you to see exactly which pixels are included in the stats calculation. You can also uncheck the “Show Stats” checkbox to remove the region stats from image and display only the boundary line.
After drawing a threshold ROI on an image, if you scroll the slice/image stack, using the arrow keys, scroll wheel or click-and-drag navigations, the ROI will change shape as it recalculates the threshold pixel flow on the new image. The re-application uses the original pixel value and the pixel nearest the prior pixel location that is closest to the original see pixel value.
The above screen shot shows the result of scrolling the threshold ROI to a more posterior slice.
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Tool Use
To make it easier to work with ROIs you’ll notice that after you create a ROI when you move your cursor within the ROI’s bounds the cursor turns in to the arrow so that you can easily select the ROI to move, reshape or delete it. You can also select and use the Grabber tool to select ROIs.
After drawing a region, that region is automatically selected for you. This allows you to easily resize, relocate or delete the region.
To delete a region, select it and press the delete/clear/del key. Note that after deleting the region, if more than one region is present in the view, the next region in the region list in that view will be automatically selected for you. Thus, you can delete all, or part of, the regions in a view by repeatedly pressing the delete key.
Moving ROIs
Use the Grabber tool (or any drawing tool) to move an existing region.
- Select the grabber tool by clicking on it.
- Click and drag the region to position it elsewhere on the image.
- Note that you cannot move Threshold ROIs.
Resizing ROIs
Use the Grabber tool (or any drawing tool) to resize an existing region.
- Select the grabber tool by clicking on it.
- Click an existing region to select it. You’ll see handles appear on the region.
- Click and drag a handle to alter the shape of the region.
- Note that you cannot resize Freehand and Threshold ROIs.
Note that you can propagate ROI's between views and windows. See ROI Menu below for details.
Deleting ROIs
Use the Grabber tool (or any drawing tool) to delete an existing region.
- Select the grabber tool by clicking on it.
- Click an existing region to select it. You’ll see handles appear on the region to show that it’s selected.
- Hit the “delete” or “backspace” key on your keyboard to delete the ROI. After deleting the selected ROI, the next ROI, if any, on the image will be auto-matically selected. Thus you can delete all ROI's on an image by simply repeatedly deleting.
Viewing and Editing ROI Properties
Use the Grabber tool (or any drawing tool) to access a region’s properties.
- Select the grabber tool by clicking on it.
- Double-click an existing region to display its properties.
Rectangle, Oval and Freehand ROIs have these types of properties:
You can change the color of the ROI, choose to have it displayed in outline or solid form by clicking the “Draw Filled” checkbox and you can choose to show or hide the ROI’s statistics by clicking the “Show Stats” checkbox.
Threshold ROIs have these types of properties:
In addition to the same properties as other ROIs, with threshold ROIs you can set the threshold a region should use when finding “similar” pixels.
ROI Table View
The Template window has a disclosable scrollable ROI table which appears on the left of template windows, when displayed. This table can be formatted in two ways: Full Statistics View and Reduced Statistics View, as shown below.
Full Statistics View
Reduced Statistics View
You can display the ROI list using the Hide/Show ROI Table View menu items in the contextual and menu bar menus or the F5 hotkey.
Show/Hide ROI Table View menu items
Menu items in the ROI List View contextual menu
allow you to toggle the display between the Full and Reduced statistics display (F6 hotkey).
The existing ROI menu is expanded and has Template Window specific items added:
Show/Hide ROI Table View will show or hide the ROI table view.
Show More/Fewer statistics toggles the ROI Table View between its two statistics display modes.
Sum/Different/Average ROI Statistics take the selected ROIs' statistics, perform the requested mathematical composition and place an entry in the ROI table displaying the resultant statistics as show below:
Sum (F8)
Difference (F9)
Average
Note that the Difference operator displays the results in percentage change. This can be very useful when comparing lesion ROI statistics between current and prior studies.
Clone ROI/Ruler to Similar Views will duplicate the selected shapes (ROI's, Rulers, Annotations) into any views in the current window whose type matches that of the view type of the source shape. That is, if a ROI was drawn on a Transverse view originally, the ROI will be duplicated onto all Transverse views of the current window. See also Paste to Similar Views.
Clone ROI/Ruler to All Views duplicates all selected shapes to all views of the current window, regardless of source view type.
Note: you can clone to windows other than the window on which the shape was created.
Graph ROI Statistics takes the selected ROI's and displays a graph window of their statistics. See ROI Graph Window below.
The Save/Load Shapes to/from XML File commands allow you to export and shapes to and from text based XML files.
In addition, the main menu bar Edit menu has commands that apply to all Shapes (ROI's and Annotations):
Cut and Copy operate on selected shapes (ROI's). Cut will remove the selected ROI and place a copy on the Pasteboard, Copy simply places a copy of the selected objects there.
Paste will paste any shapes (ROI's, Annotations) on the Pasteboard into the currently selected view of the current window.
Paste to Similar Views will paste any shapes (ROI's, Annotations) on the Pasteboard into any views in the current window whose type matches that of the view type of the source shape. That is, if a ROI was drawn on a Transverse view originally, the ROI will be pasted onto all Transverse views of the current window.
Paste to All Views copies all shapes on the Pasteboard to all views of the current window, regardless of source view type.
Duplicate will create copies of all selected shapes in their respective views.
ROI Graph Window
ROI Graph window (F10 and also ctrl-g on Windows). Displays the ROI Graph window, showing the selected ROI's.
To use, first select some ROI's, then use the Graph ROI Statistics menu item or associated hot-key. When you select and graph one or more of regions, for each image of the source view, the region is applied to the image, generating a series of ROI's from each primary ROI you drew and selected.
There are 3 graph types:
- The graph type All Images shows a graph of each of the regions you had drawn and selected, applied to the images of the view.
- The graph type Regions simply graphs each ROI you drew and selected.
- The graph type Generate 3-D Results shows a graph of each of the regions you had drawn and selected, projected into 3-D and applied to the images of the view as indicated above for each ROI type.
Generate 3-D Results graph type
Oval and Rectangular ROI's
When you select and graph one of these types of regions with the Generate 3-D Results graph type, the region is not applied to every image of the view. Instead, the region is "projected" into adjacent views as if it was the 3-d equivalent of the source primary region. So an oval becomes an ovoid and a rectangle becomes a prism. The corresponding regions are generated as if the primary region is the center of a 3-d object and extends on either "side" to one-half of the primary regions smallest axis.
Threshold (Magic wand) ROI
When you use this graph type with a Threshold ROI selected, the region is applied to all images but bounded by the primary region's bounding box. The effect is as if the original threshold region expanded in 3 dimensions from the start 3-d location you originally clicked.
The ROI Graph Window plots the statistic selected in the Value menu on an x/y graph
Note, in the screen shot below, that each ROI line is drawn with the ROI's original color (All Images and Generate 3-D Results graph types).
Statistics/Results export
You can export the statistics of the associated ROI's to a text file using the ROI Graph Window's Save As popup menu
Also, choosing the Copy command from the Edit menu (or hot-key command/control-C) will place both a text version of all statistics as well as a screen shot of the ROI Graph window in the system clipboard/pasteboard for pasting into another application such as a spread-sheet, word processor or presentation application.
In both cases, for each original ROI given to the ROI Graph window, two sets of statistics will be generated. The first is the ROI applied to all slices/images in the home view of the original ROI. The second is the set of statistics resulting from extending the ROI as a 3-D ROI (Generate 3-D Results) into the slices/images of the home view.
The statistics exported will be expressed in the units currently selected in the Value menu.
ROIs and Save Screen Arrangements/Bookmarks
ROI's, and indeed all shape objects (ROI's/Annotations/Rulers) are saved and restored with Save Screen Arrangements and Bookmarks. Indeed with Bookmarks, you can save several different views of the window set with varying ROI types, placements, etc to demonstrate specific image diagnostic characteristics.
ROI Persistence and Propagation Mechanisms
- Save/restore ROI's to/from disk files. For caching frequently used sets of Regions/Rulers.
- save ROI's along with SSA
- save ROI's to disk, load ROI's from disk. Separate, independent xml file
- if ROI's or Rulers are selected, those are exported to a text XML file
- if there are no ROI's or rulers selected, all shapes are exported to a text XML file
- Export ROI/Ruler statistics
- Copy to clipboard as text.
- In addition to the ROI's themselves, when you select a ROI or ROI's and choose "Copy" from edit menu (or use command/control-C keyboard shortcut) a tab/return delimited text version of the statistics is also placed on the clipboard so if you switch to a text editor or spreadsheet (or whatever) and "Paste" the statistics will be pasted into that application's document.
- Save to text file
- Current implementation: choose Graph ROI stats and then "Save as Text" from right-most popup menu.
- ROI Copy/Paste between windows/views
- select ROIs (on views or in table, hold down shift or command/control to select multiple), choose Copy from Edit menu or press cmd/control-c
- Paste. Just pasting takes the ROI's and applies them to matching view type. For example, if source view of ROI was coronal, the paste function will find another coronal and paste the region there. Prefers last clicked viewer, if applicable.
- shift Paste: pastes to selected viewer without requiring the view types to match. To paste a ROI into a specific view regardless of its view type, click on the view first to select, then hold down shift then Paste. Only pastes into different view type if shift is down.
- Paste to Similar Views: applies all pasted ROI's to all matching view types.
- Paste to All Views: applies all pasted ROI's to all views (regardles of view type).
- Command-A selects all ROIs
- Clone ROI's to other views - takes selected ROI or ROIs and duplicates them into other views of the window whose view type matches that of the source ROI view (hot-key F7). Cloning differs from simple pasting in that each selected ROI is copied into all views of matching view type (sagittal, coronal, transverse). Cloning is also smarter about choosing views to clone to. Paste can result in adding a ROI to a view that already has an identical ROI. Cloning attempts to avoid that.
- The Clone ROI/Ruler to Similar Views command (ROI menu) takes the selected ROI's and duplicates them into all views whose type matches that of the source view (ie a ROI drawn in a coronal will only be cloned into coronal views).
- To use "Clone", for example:
- open a CT/PET study in a dual study template window with views for all view types for each study
- draw a ROI on one view of each type (coronal, sagittal, transverse)
- select these ROI's using shift/control/command click or Select All with command/control-A
- choose the Clone ROI/Ruler to Similar Views menu item
- the ROI's will be cloned to all like views in the window. That is, if, for example, you drew the ROI's on the PET views, they will all be cloned to both all remaining PET views, if any, as well as all corresponding CT views.
- The Clone ROI/Ruler to All Views command (ROI menu) takes the selected ROI's and duplicates them into all other views, whether or not the destination view type matches that of the ROI's source view.
Exercises for Exploring ROI Feaatures
- Cloning Regions: you can easily duplicate drawn Regions into other views.
- Multiple regions into multiple views
- In a complex pet/ct template (eg GE Volumetrix), draw a region (eg irregular) on each view type of the CT only views (sagittal, coronal, transverse and rendered). You should have 4 regions. Do a Control/Command-A to select all.
- Right click on one fhe regions and choose "Clone ROI/Ruler to Similar Views".
- Note that the regions you have drawn are copied, scaled appropriately, to all corresponding views of that type (transverse region to all transverse views and so forth).
- One region into multiple views
- open a PET in a coronal only template.
- Draw a region on any view.
- Select that region (it may already be selected), right-click on it and choose"Clone ROI/Ruler to Similar Views".
- Note that the region is duplicated into all views of the window.
- Copying/pasting Regions: you can copy and paste regions between views in a template window and between windows.
- In a single study template (displaying all views, sag. cor, trans), display a CT in a CT/PET study.
- Draw 4 regions, one in each view as above.
- Select all using Command/Control-A and then choose copy.
- Open the PT in a similar template, choose paste. Note that the regions are copied into one each of the corresponding views.
- Reopen the complex PT/CT template (eg GE Volumetrix) as before.
- Choose "Paste ROI/Ruler to Similar Views). Note that the 4 regions are pasted into all matching view types.
- In the complex template as before, delete any current ROI's by selecting all (Command/Control-A) and pressing delete.
- Draw a single ROI in a coronal view.
- Select it and choose Copy (Command/Control-C).
- Click on another coronal view to select it (it will be highlighted by a thin maroon rectangle) and choose Paste (Command/Control-V). The ROI will be copyied into that view.
Note that by default, you cannot copy ROI's between views of different types (sagittal ROI cannot be copied/cloned into transverse view). You can override this by holding down the shift key or choosing the "All Views" form of paste/clone.
- Save Screen Arrangements (and Bookmarks): ROI's are saved and restored.
- open the template window of your choice.
- Draw regions, choose "Save Screen Arrangement" from the File menu or press Command/Control-S
- Save for this visit only.
- Close the visit/window,
- ensure that Save Screen Arrangements are not disabled (ensure the Preferences "No Saved Arrangements" item is unchecked) and re-open the visit. Your ROI's should be restored as they were.
ROI's are stored with Bookmarks and both SSA's for this visit and Protocol based SSA's.
You can export ROI's (and all annotation shapes) to XML files, and import them back in as needed.
- ROI mathematical operations
- open a template window, draw two regions, display the ROI Table view by right clicking on a view and choosing the "Show ROI Table View" item, press the F5 hot-key or choose the item from the main ROI menu You will see entries for both of your regions.
- Select both of the regions and choose "Sum Selected ROI Statistics" from the ROI menu, or press th F8 hot-key or right-click on a ROI and choose the "Sum" item from the contextual menu.
- A new entry in the ROI table will appear showing the summed statistics of the two regions.
- Select the two ROI's again, if needed, and choose "Difference ROI Statistics" as above (hot-key is F9).
- Note the new ROI Table entry showing the percent change.
- Provide a name/label for a ROI
- Draw a ROI
- display the ROI Table view (f5)
- in the ROI Table, double click the ROI you just created to open the Edit ROI dialog
- in the Label edit text item, type a name for your ROI
- click OK
- note that the new name/label for the ROI is displayed in the ROI Table view and on-image with the ROI itself
- Change the text size/font in which ROI statistics are displayed on screen
- Draw a ROI, note its statistics as displayed on screen, either via the ROI statistics popup window or the on image line (toggle with the 'O' hot-key)
- choose Miscellaneous Options from the Preferences menu
- click the Appearance tab
- note the item at the bottom displaying the current ROI text statistics display font/size
- click the Change button
- choose a new text font and size and close the font selection dialog
- note that the text item in the Appearance panel is modified to show your new font/size selection
- click Apply (Macintosh) or OK (Windows) to apply the settings
- note that the font/size of the statistics of the ROI you drew are now drawn in the new font/size.
- ROI Graph Window
- In a single study template (displaying all views, sag. cor, trans), display a PET series.
- Choose the Threshold (Magic Wand) ROI tool, click on a pixel on a lesion or other area with distinct boundaries
- Choose the Oval ROI tool and draw an oval ROI around the threshold ROI area
- Repeat (press the "p" hotkey to reselect the previous Oval ROI tool) and draw an Oval ROI on a comparison region (eg, liver)
- Press the cmd/ctrl-a hot key to select all regions
- Press the F10 or cmd/ctrl-G hotkey or choose the Graph ROI Statistics menu item from the ROI or contextual menu
- You should see a Graph window with your 3 regions graphed in the Generate 3-D Results graph type
- Choose the "All Images" graph type and notice the change in curves
- Try each of the different statistics value types from the Value menu.
- Choose Copy (command/control-C) from the Edit menu and paste results into spreadsheet or presentation application document.
- Choose Text from the ROI Graph window's Save popup menu and open resulting text file in text editor to view results or import into spreadsheet.
