3D ROI Tool

Overview

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 operator provides advanced tools for drawing, visualizing, saving, and quantifying both 2- and 3-dimensional regions. This tool allows for having a voxel belonging to more than one ROI. For example, a user could have an ROI that contains the whole brain and other ROIs for regions of the brain, meaning that each voxel of the whole brain ROI would need to simultaneously be part of two different ROIs.

Invicro implemented overlapping of ROIs by adding layers. The user is able to add new layers in the 3D ROI Operator, select an active layer, and create and modify ROIs in that layer independent of the contents of other layers. Overlapping is then possible as each voxel can belong to various ROIs on each layer.

The previous ROIs approach limited the user to 256 ROIs, as it used an internal buffer of unsigned chars (1 byte per voxel). To allow for multiple layers, the new approach keeps a list of buffers of unsigned chars that can be increased on demand by the user up to a potential of 8 layers if the RAM allows it. The new maximum total number of ROIs was then increased to 2048, and each voxel now supports up to 8 overlapping ROIs. However, the allocated RAM for the ROIs object increases significantly as the user adds more layers. We can also expect a small overhead execution cost when drawing the ROIs on the image for display purposes, as the blending or the handling of the different layer will require more processing.

Getting There

The 3D ROI tool can be accessed via the operators pull-down menu on the VivoQuant front panel.

When the 3D ROI Tool is selected, a 3D ROI Tool operator window is displayed.

Each tab of the 3D ROI Operator window provides a grouped set of functionalities.

Tab	Description
	ROI Loading, Saving, and Quantification Tools
	Painting Tools
	2D Drawing Tools
	3D Segmentation Tools
	Expert Settings

Layers

We use ROIs to label voxels in the image as belonging to a region, so we can extract quantitative information about that region from the image. Layers allow the user to specify that a particular voxel belongs to multiple regions. Within a layer, a given voxel can only belong to one region; that is, ROIs are associated with a layer. For example, one layer could contain different brain sections, while another layer defines the entire brain.

Whole brain ROI (in green) defined in Layer 1 — Whole brain ROI (green) defined in Layer 1

Brain sections separately defined as ROIs in Layer 0

Cortex brain section (red) defined in Layer 0 over whole brain (green) of Layer 1

Whole brain section (green) layered over cortex brain section (red)

Layers can be created and deleted from the strip of icons at the bottom of the 3D ROI Operator.

Relevant layer actions are described in the table below.

Icon	Description
	Add a Layer
	Edit a Layer
	Hide a Layer
	Reset a Layer
	Delete a Layer

Add a Layer

Click the Add Layer button to create a new layer.

A popup window will open, prompting the user to name the new layer and set the transparency of the ROIs by selecting an alpha value.

Decrease the alpha value to increase the transparency of all ROIs in the layer.
Values range from 0% - 100% and change by 10% increments.
The option to make the layer hidden is not available during the layer creation process and appears greyed-out.

Note: The maximum limit of layers in one session is 8.

Edit a Layer

Click the Edit Layer button Add Layer to edit a existing layer.

A popup window will open, allowing the user to edit the name of the selected layer, change the transparency of the ROIs by adjusting the alpha value, or hide/unhide the layer.

Decrease the alpha value to increase the transparency of all ROIs in the layer.
Values range from 0% - 100% and change by 10% increments.

Select Active Layer

Select the layer of interest from the dropdown Layer to set it as the Active Layer. The display will show the active layer, and any layer actions, such as editing or deleting, will be performed on the current active layer.

Hide a Layer

Click the Hide Layer button to hide the active layer. Click the Hide Layer button again to show the layer.

Reset a Layer

Click the Reset Layer button Hide Layer to clear the contents of all ROIs in the active layer.

Delete a Layer

Click the Delete Layer button to open options for the active layer.

A popup window will open, prompting the user to delete or reassign the ROIs associated with the specified layer.

To delete all ROIs in the layer, click OK.
To reassign the ROIs to another layer, click the Re-assign ROI Pixels check box and the greyed-out options underneath will become active.

Verify that the layer selected in Target Layer is the layer of interest then select the Move Policy to apply.

Available Move Policies are described in the table below.

Move Policy	Description
Overwrite	ROIs from the layer being deleted (active layer) will trump any overlapping ROIs existing on the destination layer. Use this option if you do not want any of the ROIs being moved to be changed.
Keep Destination	ROIs on the destination layer will trump any overlapping ROIs existing on the layer being deleted (active layer). Use this option if you do not want the ROIs in the destination layer to be changed.
Respect Immutable (default)	Use this option if the user wants ROIs from both the destination layer and layer being deleted (active layer) to be preserved or overwritten based on pre-specified information. ROIs marked immutable from the destination layer will trump any overlapping ROIs. ROIs not marked immutable from the destination layer will be trumped by the ROIs from the source layer if overlapping.
New ROIs from Overlap	Using this option will create new ROIs in areas where the destination ROIs and the ROIs being moved overlap. Use this option if you want the flexibility to decide how the overlap is handled.

ROI Creation and Deletion

ROIs can be created and deleted from the strip of icons at the bottom of the 3D ROI Operator.

Icon	Description
	Add an ROI
	Edit an ROI
	Delete an ROI
	Reset an ROI
	Hide an ROI

Add an ROI

There are two methods for adding an ROI:

1. Add Via ROI Section Buttons

Click the Add ROI button Add ROI to open options for adding a new ROI.

A popup window will open, prompting the user to provide specific information for the new ROI, including:

The ROI’s name and color.
The layer to which the ROI should be added
Note: The Number of ROIs per layer should not exceed the limit of 256.
The transparency of the ROI in the slice and MIP views.
- To alter the transparency, increase or decrease the alpha values (a lower percentage will increase the transparency of an ROI).
The ROI’s visibility by checking “Hidden” to turn the ROI off in all views.
The ROI’s ability to be edited by selecting “Immutable.”

Another option is to select any (or many) of the existing ROIs is to right click and select Add ROI. This will append a new ROI to the end of the list.

Edit an ROI

To edit an ROI, double-click the ROI to be edited to select it and click on the Edit ROI button . A popup window will opens and allow the user to change the name, color, transparency (Alpha), visibility, and state of immutability of the ROI. To make ROIs immutable, check the boxes in the ‘I’ column.

Another option is to right-click on any ROI in the operator and select Edit ROI.

Delete an ROI

To delete an ROI, double-click the ROI to be deleted to select it and click on the Delete ROI button . A popup window will open and allow the user to move the pixels of the selected ROI to either the background or another ROI.

Another option is to select one or many of the existing ROIs, right click, and select Delete ROI.

Note: The ROI will no longer appear in the drop-down menu after being deleted.

Reset an ROI

To reset an ROI, double-click the ROI to be reset to select it and click on the Reset ROI button . A popup window will open and allow the user to move the pixels of the selected ROI to either the background or another ROI.

Another option is to select one or many of the existing ROIs, right click, and select Reset ROI.

Note: The ROI will still exist after it has been reset, but it will no longer have any voxels associated with it.

Hide an ROI

To hide an ROI in the slice and MIP views without deleting it, double-click the ROI to select it and click on the Hide ROI button .

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.

Note: If the ROI is not immutable, it can be edited even if it is hidden.

ROI Loading, Saving, and Quantification Tools

The first tab in the 3D ROI Operator window features tools for basic input/output operations, quantification, and viewing functionality. To freely navigate through the slices with the cursor, this panel must be active.

The buttons in this tab perform several functions within the operator.

Button	Function
	Load or save an ROI from disk or iPACS
	Render ROIs in the MIP view
	Reset the camera view
	Reset all ROIs
	Show the image histogram
	Show the quantification table
	Export the quantification table to disk
	Perform a cut on an image using an ROI
	Perform a copy or paste on an image using an ROI
	Export ROIs into the Bed Removal tool

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 , select the Load from disk option and choose the desired ROI from the file browser.

Save an ROI to Disk

To save an ROI to disk, click the Load ROI button , select the Store to disk option 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 ROI button and select the Load from iPACS option. The image data currently loaded must have been retrieved from an iPACS, and there must be an ROI associated with that 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 ROI creator’s iPACS username, date and time of creation, as well as the region names for that file.

Save an ROI to an iPACS

To save an ROI to an iPACS, click the Load ROI button and select the Store to iPACS option. The ROI will be automatically associated with the current image. Unique filenames will be generated based on the creator’s username and the patient’s name from the image header. Previously saved ROIs will not be overwritten. The files will be saved to a subdirectory of the current project on the WebDisk, named roi.

Select Current Layer

By default, all layers are load or saved when loading or saving an ROI. However, the user can specify to save only a single layer by loading or saving the current layer.

Merge ROIs from an iPACS or Disk

To append previously stored ROIs to a set of ROIs currently open in the 3D ROI tool, click the Load ROI button and select Merge from iPACS or Merge from disk, depending on where the additional ROIs are stored. The additional ROIs associated with that image will be appended to the currently open ROI set in the 3D ROI viewer. Previously saved ROIs will not be overwritten.

If there is any overlap of existing and merged ROIs, a new ROI will be created and named as 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 will 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. A popup window will open and allows the user to move the pixels of the selected ROI to either the background or another ROI. 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 Add ROI .

Reset the Camera View

To reset the MIP view to the original orientation and size, click the Reset Camera button Add ROI .

Reset all ROIs

To reset all existing ROIs, click the Add ROI button and select Reset All. Empty ROIs will still exist under the same naming and coloring scheme.

To delete all ROIs completely, click Add ROI and select Delete All. 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 Show Histogram Add ROI button. Choose the image used to generate the histogram by selecting it 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, go to the Operator tab on the main menu, then select Quantification Table List.

The available quantification values are described below:

Option	Description
ROI	Name of the ROI. You can left-click this field to enter comments.
Patient	Patient’s name for the current study.
Series	Specific data set in the study from which the data was calculated.
Modality	Modality from which the data values for the row were calculated.
Color	Color of the ROI as drawn in the display.
Voxels	Total number of voxels contained in the selected ROI.
Volume	Volume of the selected ROI in units of cubic millimeters.
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).

Concentration Peaks

“Impact of the Definition of Peak Standardized Uptake Value on Quantification of Treatment Response”. Vanderhoek, et al. J Nuclear Medicine, 2012. Link.

Show the quantification table.

To display the quantification table, including all existing ROIs, click the Show Table button .

Export the quantification table to disk.

To export the quantification table to disk as a comma-separated values (.csv) file, click the Export 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 Cut ROI button Cut ROI . All visible images will be cut and the ROI will remain unchanged. The cut tool is useful for eliminating undesired features in images, such as metal instrumentation that may appear in some CTs.

Show or Hide an ROI

To hide an ROI, Check the boxes in the H column. An ROI can also be hidden by selecting it and clicking on the Hide/Show button Hide ROI .

Copy or Paste the 3D ROI

Click the Copy/Paste ROI button Hide ROI to copy and/or paste ROIs between instances of VivoQuant.

Export ROIs into the Bed Removal Tool

Click the Export to Bed Removal button Hide ROI to export ROIs into VivoQuant’s Bed Removal tool.

Import Layers and ROIs with Overlapping Regions New Feature

Certain image formats, such as PMOD VOI and DICOM RTSTRUCT, support overlapping regions inherently. VivoQuant’s 3D ROI tool loaders have been updated to handle the overlap appropriately.

Note: Overlapping ROIs should be assigned to different layers.

Not only has the 3D ROI Tool been updated to be compatible with overlapping ROIs, but numerous pre-existing features also successfully operate on the active layer supporting overlapping ROIs. These include: Segmentation Algorithms, Painting in the slice views, Tooltip Pixel hovers, Reorientation Operator, Modeling Operator, Multi-view Visibility, VTK MIP, AutoRAD, MAS, Brain Atlas and Smoothing Operator.

Tip: The number of imported layers should not exceed the limit of 8. Number of layers should be efficient. Do not create one layer per region; but rather, collapse regions to the same layer where possible.

Painting Tools

There are several paintbrushes to choose from when creating an ROI. The sphere Sphere Paintbrush , cylinder Cylinder Paintbrush , 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 the painting tools can be used.

ROIs can be drawn freely on any of the three slice views. The view currently being drawn in will be denoted as 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 Edit 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 option is selected, 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 ROI selector.

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 ROI Drop-down Selector .

To perform the erosion or dilation, click the Checkmark button Perform Erosion/Dilation .

2D Drawing Tools

The 2D drawing tools match the options available within the Projection++ Tool.

Choose the desired tool from the drop-down menu to begin drawing. Use the Delete button to delete a contour (this will not delete the ROI). Use the Perform Erosion/Dilation button to add the voxels within a drawn contour to the currently selected ROI.

	Spline tool
	Bully tool
	Freehand tool
	2D Thresholding tool

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 by click on a middle point, or added by double clicking on a curve. Once a shape has been closed by clicking the right mouse button, it can be re-opened by hitting 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 left 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
	Apply Spline Path to ROI
	Clear Spline Path

Apply Spline Path to ROI and move to next slice.

This button creates a 2D ROI within the spline path and moves to next slice.

Apply Spline Path to ROI

This button creates a 2D ROI within the spline path.

Clear Spline Path

This button clears the spline path and all points.

3D Segmentation Tools

The 3D Segmentation Tools are located in the Segmentation Algorithms tab . They 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 the segmentation tools can be used.

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 Edit 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.

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 can be selected from the Segmentation Algorithm drop-down menu. After selecting a seed and thresholds as necessary, click ‘Apply’ to perform the segmentation. The thresholding operation may take about a minute to complete.

	Requires Seed?	Requires Thresholds?
Global Thresholding	No	Yes
Connected Thresholding	Yes	Yes
Neighborhood Thresholding	Yes	Yes
Otsu Thresholding	No	Yes
Confidence Connected	Yes	No
ROI Connected	Yes	No
ROI Max Size	No	No
Low-pass Smoothing	No	No
Bounding Cylinders	No	No
Interpolate Slices	No	No
Modal Smoothing	No	No
Connected Components	No	No
K-Means Clustering	Yes	No

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.

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.

Note: If there are any ROIs present prior to using this tool, they will be deleted.

Expert Settings

The Expert tab, presents the advanced settings of the 3D ROI Operator. For the typical user, these settings will not need to be changed.

Data Group

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 Import button Import ROI 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 Export 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 Segmentation fields to tune up the parameters of the segmentation methods. The Smoothing filter will use the Iterations and Time Step 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:

Open the Cropping operator from the Operators drop-down menu.
Use the red sliders to select the desired region of the image.
After you’ve selected the desired region, go back to the 3D ROI tool by selecting the 3D ROI operator from the Operators drop-down menu.
In the Expert tab of the 3D ROI Operator, mark the Crop Range checkbox. Dashed red lines will appear on the image, indicating the boundaries of the selected region.
When the desired thresholding method is performed (see Segmentation Tools to learn how to use the Segmentation panel of the 3D ROI Operator), only the region within the crop range will be segmented.

Undo/Redo Functionality

To undo/redo operations performed in the 3D ROI tool go to the View tab on ViviQuant’s main menu and click the Undo Undo or Redo Redo button. The operation to be undone or redone will be described in the drop-down menu.Keyboard shortcuts are also available for undoing or redoing an operation.

Note: The input ROI will be set to background whenever the undo function is applied.

The undo/redo functionalities are applicable to all functions performed on 3D ROI data itself. 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.

Note: To undo/redo filling a contour in the Spline Tool the user must navigate away from the spine tool window.