The 3D ROI operator provides advanced tools for drawing, visualizing, saving, and quanitfying both 2- and 3-dimensional regions. The acronym "ROI" stands for "region of interest" and is used to describe a particular area or volume within an image for which the user wishes to characterize some quantity or quality.
The 3D ROI tool can be accessed via the tool pull-down menu on the VQ front panel.
When the 3D ROI Tool is selected a 3D ROI Tool operator window is displayed.
Each panel of the 3D ROI Operator window provides a grouped set of functionalities. Use the tabs to move between panels.
| Tab | Description |
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ROI Loading, Saving, and Quantification Tools |
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Painting Tools |
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2D Drawing Tools |
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3D Segmentation Tools |
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Expert Settings |
ROIs can be created and deleted from the strip of icons at the bottom of the 3D ROI Operator.
| Icon | Description |
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Add an ROI |
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Edit an ROI |
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Delete an ROI |
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Reset an ROI |
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Hide an ROI |
Add an ROI. To add an ROI, click on the plus-sign "Add ROI" button. Use the interface that appears to specify a name and color for the ROI. To alter the transparency of the ROI in the slice and MIP views, respectively, increase or decrease the alpha values (a lower percentage will increase the transparency of an ROI). Check "Hidden" to turn the ROI off in all views. Check "Immutable" to prevent edits to an ROI.
Another option is to select any one or shift select more than one of the ROIs in the operator, right click, and select Add ROI. This will append a new ROI to the end of the list, regardless of which ROI is selected.
Edit an ROI. To edit an ROI, click on the pencil "Edit ROI" button. Use the interface that appears to change the name, color, transparency, visibility, or state of immutability.
This will edit whichever ROI is selected in the ROI dropdown menu.
Another option is to right click on any ROI in the operator and select Edit ROI.
Delete an ROI. To delete an ROI, click on the red X "Delete ROI" button. Use the interface that appears to move the pixels of the selected ROI to either the background or another selected ROI. The ROI will no longer appear in the drop-down menu of ROIs after being deleted. This will only delete the ROI that is selected in the ROI dropdown menu.
Another option is to select any one or shift select more than one of the ROIs in the operator, right click, and select Delete ROI(s).
Reset an ROI. To reset an ROI, click on the broom "Reset ROI" button. Use the interface that appears to move the pixels of the selected ROI to either the background or another selected ROI. The ROI will still exist after it has been reset, but it will no longer have any voxels associated with it. This will only reset the ROI that is selected in the ROI dropdown menu.
Another option is to select any one or shift select more than one of the ROIs in the operator, right click, and select Reset ROI(s).
Hide an ROI. To make an ROI invisible in the slice and MIP views without deleting the ROI, click on the Nazarm "Hide ROI" button. If the ROI is not immutable, it will be possible to edit the ROI even if it is hidden. This will only hide the ROI that is selected in the ROI dropdown menu
Another option is to select any one or all of the desired ROIs, right click, and select Toggle Hide ROI(s).
All selected ROIs will become hidden.
The left-most panel in the 3D ROI Operator presents the interface for basic input/output operations, quantification, and viewing functionality. To freely naviagate through the slices with the cursor, it is necessary for this panel to be active.
The buttons at the top of the operator window perform various functions within the operator.
Load an ROI from disk. The 3D ROI tool supports file formats of VQ 3D ROI (.rmha) and vtkStructuredPoints (.vtk). To load an ROI from disk, click the "Load ROI" button and select the desired ROI.
Save an ROI to disk. To save an ROI to disk, click the "Save ROI" button and specify a name and location for the file. The ROI will be written as an VQ 3D ROI (.rmha) file. All existing regions will be written to the same ROI file.
Load an ROI from an iPACS. To load an ROI from an iPACS, click the "Load from iPACS" button. The image data currently loaded must have been retrieved from an iPACS, and there must be an ROI associated with that particular image already stored on the iPACS. If only one ROI exists for the image, that ROI will automatically be loaded. If multiple ROIs exist, the user will be given a drop-down menu of available ROIs to choose from. The choices can be distinguished by the ROI creator's iPACS username, the date and time of creation, and the region names for that file.
Save an ROI to an iPACS. To save an ROI to an iPACS, click the "Save to iPACS" button. The ROI will be automatically associated with the current image. Unique filenames will be generated based on the creator's username and the patient name from the image header. Previously saved ROIs will never be overwritten. The files will be saved to a subdirectory of the current project on the WebDisk, named "roi".
Merge ROIs from an iPACS or disk. If you wish to append previously stored ROIs to a set of ROIs currently open in the 3D ROI tool, the merge ROIs function can be utilized as follows:
If there is any overlap of existing and merged ROIs, a new ROI will be created and named a combination of the two ROIs listed names. For example, if a portion of a "Heart" and "Liver" ROI overlap after a merge, the new combined ROI created would be named "Heart/Liver" and consist of only the specific volume of Heart and Liver that overlap.
To associate the combined ROI with the proper ROI, right-click the combined ROI and select "delete ROI". The option to move pixels to either "background" or other ROIs will be presented for your selection. Selecting "background" will delete the ROI all together.
Center view on ROI. To center the field of view on the center of mass of a particular ROI, double click the ROI in the ROI Table.
Render ROIs in the MIP view. To trigger a new rendering of the current viewed ROIs in the MIP view, click the "VTK" button.
Reset the camera view. To reset the MIP view to the original orientation and size, click the "Reset Camera" button.
Reset all ROIs. To clear only the contents of all existing ROIs, click the X then the "Reset All" button. Empty ROIs will still exist under the same naming and coloring scheme. To delete all ROIs completely, click the X then the "Delete All" button. The background will be the only thing left in the ROI menu.
Show the image histogram. To view a histogram of the image or any subset of the image determined by an ROI, click the "Histogram" button. Choose the Image used to generate the histogram by selecting from the "Data set" drop-down menu. The portion of the image contributing to the histogram can be set under the ROI Controls by selecting an ROI from the drop-down menu.
Set quantification table columns. To determine which quantitative fields will be displayed in the quantification table, and stored to the iPACS if applicable, use the selection widget under Operator -> Quantification Table List.
The available quantification values are described below:
| Option | Description |
| ROI | Name of the ROI |
| Patient | PatientsName from the header |
| Series | SeriesDescription from the header |
| Modality | Modality from the header |
| Color | Color of the ROI |
| Voxels | Number of voxels contained in the ROI |
| Volume | Volume of the ROI in mm3 |
| Mean | Arithmetic mean of values of voxels contained in the ROI |
| StdDev | Standard Deviation of values of voxels contained in the ROI |
| Min | Minimum value of all voxels contained in the ROI |
| Max | Maximum value of all voxels contained in the ROI |
| Median | Median value of all voxels contained in the ROI |
| Sum | Sum of all voxels contained in the ROI, sometimes interchangeable with 'Uptake' |
| Unit | Unit of voxels in the selected dataset |
| Conc 10% | Concentration (mean/volume) of the 10th Percentile of voxels contained in the ROI |
| Conc 50% | Concentration (mean/volume) of the 50th Percentile of voxels contained in the ROI |
| Conc Peakregion | Concentration (mean/volume) of the 3x3x3 cube of voxels with the greatest mean of all 3x3x3 cubes of voxels contained within the ROI. Referred to below as Highest-uptake region |
| Conc Peakmax | Concentration (mean/volume) of the 3x3x3 cube of voxels that has at its center the maximum voxel of the voxels contained in the ROI. Referred to below as SUVmax. |
| Conc Max | Concentration (mean/volume) of the maximum voxel of the voxels contained in the ROI |
| Conc | Concentration (mean/volume) of all the voxels contained in the ROI |
| Conc Unit | Unit of voxels in the selected data set over volume (mm3) |
Show the quantification table. To display the quantification table including all existing ROIs, click the "Show Table" button.
Save the quantification table to disk. To save the quantification table to disk as a comma-separated values (.csv) file, click the "Save Table" button.
Perform a cut on an image using an ROI. To remove voxels from image data based on an ROI, choose the desired ROI from the ROI selector and click the "Perform Cut" button. All visible images will be cut; the ROI remains unchanged. The cut tool is useful for eliminating undesired features in images, such as metal instrumentation that may appear in some CTs.
Show/hide the 3D ROI table. Click the "Show/hide ROI Table" button to turn the ROI table on or off. ROI names can be edited within the ROI table by clicking on the desired field to set the cursor. Check the boxes in the 'H' column to hide ROIs. Check the boxes in the 'I' column to make ROIs immutable.
Copy/paste the 3D ROI. Click the "Copy or Paste ROI" button to copy and/or paste ROIs between instances of VivoQuant.
There are a variety of paintbrushes to choose from when creating an ROI. The sphere, cylinder, or cube paintbrush can be selected by clicking the corresponding radiobutton on the Painting tab. The radius of the paintbrush can be set by changing the number of pixels shown in the numerical spin box. These 3D paintbrushes extend across multiple slices; to activate 2D mode, mark the '2D only' checkbox. In 2D mode, the paintbrush will only paint on the current slice.
Note: an ROI must be added before utilizing the painting tools.
ROIs can be drawn freely on any of the three slice views. The view currently being drawn in will be denoted "Active" in the upper left corner.
Each voxel can only belong to a single ROI. Painting over an existing ROI with a new ROI will place the painted voxels in the new ROI unless the existing ROI is immutable. (See Editing an ROI to learn how to make an ROI immutable.)
To erase voxels from an existing ROI, paint over the existing ROI with the ROI selector set to Background. Alternatively, set the ROI selector to the existing ROI (from which to erase voxels) and hold down the Shift key while drawing. The Shift key activates the background ROI for the painting tool, even if another ROI is set in the ROI selector.
Sync Pos. If "Sync Pos" is checked, then the non-Active slice views will be updated in real time to match the position of the drawing tool on the Active slice. When this box is checked, drawing times will typically be slower.
Erode/Dilate. The Erode/Dilate tool can be used to remove or add up to 5 layers of voxels from the input ROI. The erosion or dilation will be applied to the currently selected ROI in the 'ROIs' drop-down menu near the bottom of the window.
If you would like the voxels that are being added or removed from the ROI to be put in an ROI other than the one currently selected, mark the 'Map to' checkbox and choose the ROI to put the new voxels in from the drop-down menu to the right.
To perform the erosion or dilation, click the green checkmark button.
The 2D drawing tools match the options available within the Quantification++ Tool.
Choose the desired tool from the drop-down menu to begin drawing. Use the red X button to delete a contour (this will not delete the ROI). Use the green checkmark button to add the voxels within a drawn contour to the currently selected ROI.
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Spline tool |
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Bully tool |
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Freehand tool |
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2D Thresholding tool |
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Apply Spline Path to ROI and move to next slice |
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Apply Spline Path to ROI |
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Clear Spline Path |
Spline tool. Use the spline tool to define points between which smooth curves will be filled in. The base points can be moved by using the left mouse button to drag them. Additionally, points can be deleted (middle click point) or added (double click position on curve). Once a shape has been closed (right mouse button), it can be re-opened by using Shift + middle click on a point.
Bully tool. Use the bully tool to nudge the drawn boundary inward or outward with a circle-shaped cursor. The cursor size can be changed using the paintbrush size selector in the Painting Tools panel. This mode provides an efficient way to fine-tune an ROI made in Spline or Freehand mode. You may select which image data you want to use as the input ("Ref" is the first image loaded in the Data Manager, "Inp1" is the second, etc.) and the thickness of the tool, in the bully tool and for the following three tools as well.
Freehand tool. A freehand region may be drawn by moving the mouse while holding down the left mouse button. The region may be drawn in segments through a series of L-clicks and closed with a right click.
2D Thresholding tool. Use the Percentage selector field to set a threshold for the ROI. Specify the image on which to base the thresholding using the drop-down menu.
Apply Spline Path to ROI and move to next slice. Creates 2D ROI within spline path and moves to next slice.
Apply Spline Path to ROI Creates 2D ROI within spline path
Clear Spline Path Clears spline path and all points
The 3D Segmentation Tools, located in the tab denoted by the magic wand icon, can be used to apply different thresholding techniques across input images and user-defined ROIs, as well as advanced ROI processing.
Note: an ROI must be added before utilizing the segmentation tools.
Setting the Input and Output ROI. The Input ROI must be selected from the 'Input' drop-down menu before applying thresholding. If an ROI other than the background is selected, only image pixels within the chosen ROI will be considered when thresholding is performed.
The Output ROI is the ROI specified in the ROI drop-down menu located at the bottom of the 3D ROI Operator window. If the Output ROI is not empty prior to thresholding, the result of the thresholding will be added to the existing voxels of the Output ROI.
Keep in mind that other ROIs may be overwritten if the result of a thresholding technique intersects them. To prevent other ROIs from being altered, set them to immutable. (See Editing an ROI to learn how to make an ROI immutable.)
Choosing the Image Data. The segmentation algorithm will work on the data from the image specified in the Image drop-down (where Ref is the first image loaded according to the data manager, Inp1 is the second image, etc.).
Setting the Seed Point. For methods that require a seed, the cursor location at the time the thresholding is performed will be used.
Setting the Thresholds. For methods that require thresholds, use the number fields beneath the Image Selection drop-down. Click the 'Min' and 'Max' buttons to the left of each threshold field to fill in the minimum and maximum values, respectively, from the selected image. The unit is assumed to match that specified in the header.
Available Thresholding Methods. The thresholding methods available are in the Segmentation Algorithm drop down menu. After selecting a seed and thresholds as necessary, click 'Apply' to perform the segmentation. It may be necessary to wait approximately a minute for the thresholding to complete.
| Requires Seed? | Requires Thresholds? | |
| Global Thresholding | ||
| Connected Thresholding | ||
| Neighborhood Thresholding | ||
| Otsu Thresholding | ||
| Confidence Connected | ||
| ROI Connected | ||
| Interpolate Slices | ||
| Connected Components |
ROI Max Size. The ROI Max Size filter can be used to fill holes in existing ROIs. Any connected components in the Input ROI that are comprised of fewer voxels than the 'Max size' specified will be mapped to the output ROI.
Low-pass Smoothing. Use the Low-pass Smoothing filter to remove jagged surfaces from manually created ROIs. The amount of smoothing can be controlled with the Low-pass radius parameter. Smaller radii will result in smoother ROIs.
NOTE: Smoothing ROIs contained in images with large dimensions can take upwards of 30 seconds.
Modal Smoothing. Use modal smoothing to reassign every voxel's ROI value to the mode of the surrounding region specified by the given radius. The amount of smoothing can be controlled by the Mode Radius and Iterations parameters.
Bounding Cylinders. The Bounding Cylinders tool can be used to generate cylindrical ROIs that encompass each animal of a multi-animal image. The number of animals is automatically determined, and the cylinder radius can be configured. This algorithm works best on NM images, but may also work on some CT images.
If there are any ROIs present prior to using this tool, they will be deleted.
The Expert tab, denoted by "Exp" presents the advanced settings of the 3D ROI Operator. For the typical user, these settings will not need to be changed.
Data. By default, VQ ROIs are written in a compressed format. To extend compatibility with other tools (e.g., ITK), uncheck "compressed." If the ROI files will only be used within VQ, leave the "compressed" box checked.
Importing and Exporting ROIs.To import an ROI loaded in the Data Manager from an image file, click the 'I' button and select the corresponding dataset to import. To export a 3D ROI as an image to allow manipulations outside of the 3D ROI tool, click the 'X' button.
Rendering. If "auto" is checked, ROIs will be re-rendered in the MIP view automatically upon certain triggers. When unchecked, rendering will only occur when the VTK button is used. For systems with less speed and memory, it may be helpful to select a less demanding setting from the rendering quality combo box.
Segmentation. To add a curvature flow smoothing preprocessing step to the segmentation methods, check the "Smoothing" box. Use the fields beside Segmentation to tune the parameters of the smoothing and various segmentation methods (mouse over the each field to view the field name). The Smoothing filter will use the Iterations and TimeStep settings; the Confidence Connected Thresholding will use the Multiplier and NeighborRad (neighborhood radius) settings; the Neighborhoood Thresholding will use the NeighborRad setting.
Crop Range. To perform any of the thresholding segmentation methods on only a sub-region of the input image, follow these steps:
To undo/redo operations performed in the 3D ROI tool go to View->Undo or View->Redo. The operation being undone or redone will appear in the View drop down menu (as seen in the image below). Keyboard shortcuts are also available for undoing or redoing an operation.
The undo/redo function is applicable to all functions performed on 3D ROI data itself, i.e. operations performed to actual volume image data cannot be undone or redone. For example, performing a cut on an image using an ROI cannot be undone since it is applied to actual volume data and not just 3D ROI data.
Important Notes:
