13. ROI

This section describes the commands under the main menu’s ROI tab, which act on ROI layers or create ROI layers as results.

13.1. Morphology (group)

13.1.1. Peel (all timepoints)

Requires a 3D or 4D ROI. Opens dialog (Peel ROI, Fig. 13.1). Removes a shell ofspecified width (Radius, by default in voxels, or in millimeters, byuser choice) from the outer boundary of the active ROI. Checking All Layers box removes this shell from all ROI layers, visible and invisible (unchecked by default). Checking 3D Mode results in voxels removed across slices. This operation writes results to the original layers and does not create new layers. To retain the original ROI layers, use Duplicate to create a copy and apply the Peel command to the copy instead. If the ROI is 4D, the Peel operation is applied to all dynamic frames.

Peel ROI panel

Fig. 13.1 Peel ROI panel.

13.1.2. Grow (all timepoints)

Requires a 3D or 4D ROI. Opens dialog (Grow ROI). Inverse operation to Peel operation. Adds a shell of specified width (Radius, by default in voxels, or in millimeters, by user choice) from the outer boundary of the active ROI. Options are the same as for Peel.

13.1.3. Skeleton (current timepoint)

Requires a 3D or 4D ROI. No parameters. Creates a new layer. ADD DETAILS.

13.1.4. Medial Axis Transform

ADD DETAILS.

13.1.5. Average Depth (internal thickness)

Requires a 3D ROI. No parameters. Returns the average depth of the ROI in millimeters.

13.1.6. Unclump perceived Connected Components to Layers

Requires a 3D ROI. Opens dialog (Specify Peel (mm)). Removes the original layer and creates one or more ROI layers instead, obtained by peeling a user-specified width from the ROI boundary.

13.1.7. Unclump perceived Connected Components to Atlas

Requires a 3D ROI. Opens dialog (Specify Peel (mm)). Creates a new, integer layer, labeled base, with voxel values of 1 inside the ROI and 0 values outside. The original ROI layer is retained.

13.1.8. Peel\Grow External Surface only

Requires a 3D ROI. Opens dialog (Specify PeelGrow). Removes or adds a shell of user-specified thickness (in millimeters) from the outside surface of the ROI. Returns the result to the original layer.

13.1.9. Current Slice Structure Graph

Requires a 3D ROI. Opens dialog (Specify Triangle size threshold). Creates a graph (vector object, made of 3 vertices and connecting vectors), on the current slice. Triangles of size above user-specified threshold are marked.

13.1.10. Close broken contours and fill 2D

Requires a 3D ROI. Opens dialog with options to specify maximum distance between ROI edges to be closed and the number of steps. Adds voxels to ROI edges in a user-specified number and up to maximum distance.

13.1.11. Extract Connected Components

Requires a 3D ROI. No parameters. Removes the original ROI and creates a new ROI layer with connected components.

13.1.12. Fill 2D Contours and Morph Convex

Requires a 3D ROI. Acts on current layer and returns results to the same layer. Fills 2D contours and extends convex areas across slices. Can be used to speed up segmentation: contours can be drawn selected slices (e.g., on every 5th slice) and Fill and Morph command will fill the contours and extend the ROI to every slice.

13.1.13. Morph Convex

Requires a 3D ROI. Acts on current layer and returns results to the same layer. Extends filled areas across slices. Does not fill contours.

13.1.14. Fill 2D Contours and Morph Arc

Requires a 3D ROI. Acts on current layer and returns results to the same layer. Fills 2D contours and extends filled areas across slices.

13.6. Fill 2D Contours

Requires an ROI layer. Fills voxels within ROI contours with ROI color. Contours are filled separately on each slice, but not across slices (unlike in Morph command).

13.7. Extract Atlas ROIs

Extracts Atlas ROIs for region indices from the range of signal intensities. Creates a new ROI layer for each region, named atlas region [number].

13.8. Threshold to ROI by Signal interval

Requires an image layer. Creates a new ROI layer with values of 1 where image voxels have signal inside the range between the low and high threshold, which the user can enter in a dialog panel (Specify signal range, Fig. 13.2). Voxels outside the range are transparent (VOID). The threshold values are entered as numerical values into the panel, so the user needs to determine them beforehand.

Specify signal range

Fig. 13.2 Specify signal range.

13.9. Threshold to ROI by Signal-to-Gradient ratio

Requires an image layer. Creates a new ROI layer with filled voxels where signal-to-gradient (ratio) exceeds a user-specified threshold value.

13.10. Local Otsu Threshold to ROI

Moved from Volume > Adaptive Threshold and fully revised.

The function works for integer and real volumes. Creates a new ROI layer with a binary mask generated by signal thresholding.

For every voxel (x,y,z), the command performs Otsu thresholding within the vicinity of a user-specified radius R (in voxels). The operation creates a mask (ROI) layer and sets the value of the mask at voxel (x,y,z) to 1 if the signal at this voxel exceeds the threshold and 0 otherwise.

Note: March 2022 - Currently only a 2D version is available (i.e., only 2D vicinity is analyzed). The 3D code is working but computationally expensive.

13.11. Split ROI with Threshold (group)

Requires an image layer. Creates two new ROI layers with values based on the image intensity: ROI A (low intensity) with filled voxels where image intensity is below the threshold value and ROI B (high intensity) with filled voxels where image intensities are above the threshold value. Opens a panel allowing the user to adjust the threshold based on visual inspection of the ROIs (Fig. 13.3). Pressing Cancel closes the panel and removes newly created layers.

Split with Threshold

Fig. 13.3 Split with Threshold panel for manual threshold selection.

Panel Elements:

B=…, A=… – Volumes of ROI A and B (in cm3 and as percent total volume) and ratio of B/A.

Slider – The horizontal slider can be moved with the mouse to adjust the threshold intensity. The minimum, threshold, and maximum values are shown under the slider. The resulting ROIs A and B are updated in real time. The transparency of the ROI layers can be adjusted with the vertical slider on the right hand side (up – more transparent, down – less transparent).

Specify – Enter a threshold value. The slider is placed at this value.

The two submenu options differ by the choice of the default threshold value.

13.11.1. Using initial threshold

Default threshold is the minimum intensity.

13.11.2. Using low portion

Default threshold is the midpoint of the intensity range.

13.12. Normalize by ROI

Requires an image and a single visible 3D ROI. Creates a new real-valued layer. Opens Volume Normalization panel to select the options: 1) Division by Coefficient – New voxel values are equal to the original intensities divided by the average value within the ROI, 2) Z-score – (SI-avgROI)/stdevROI – New voxel values are original intensities shifted by the average ROI values and normalized by the standard deviation of the ROI.

13.13. Make Convex 2D

Requires an image layer and a 3D ROI. Fills voxels within a 2D convex shape that can be drawn around existing ROI areas (e.g., if three points are drawn on the ROI layer, the command fills a triangle created by them).

13.14. Clip Volume by ROI

Requires an image layer and a visible 3D ROI. Removes image voxels outside the visible ROI (not just active) and replaces them with user-selected values. The user is prompted to enter a clip value (replacement): -1 (or any negative value) for transparent voxels (signal value VOID), or 0 (or any non-negative value) for black voxels (signal value 10). The image values within the ROI are retained. The image dimensions are preserved. No new layers or document windows are created, the result is written to the same image layer. Therefore if users want to retain the original image, they should duplicate this image layer of it and apply the Clip command to the copy.

Other ROIs are unaffected. More than one ROI layer may be present. If there are two or more visible ROIs and one of them is active, the active ROI will be used. If there are two or more visible ROIs, but none of them is active, FireVoxel will show a warning about an ambiguous layer configuration and the command will not be executed.

13.15. Crop Volume by ROI

Requires an image layer and a visible 3D ROI. Crops a 3D image around the ROI in the active layer. A single visible ROI layer is required; if there are two or more ROIs, FireVoxel shows a warning about ambiguous layer configuration, and the command is not executed. The cropped image is placed into a new document window named the same as the original window with _cropped suffix. The cropped region is sized to accommodate the maximum dimensions of the ROI in all dimensions. If there are other ROI layers in the original document, they are retained in the cropped document.

13.16. Clear ROI slices (group)

Requires a 3D ROI. Erases the ROI voxels in user-selected slices. Opens parameter panel to enter slice numbers defining the interval [Z0, Z1] where the ROI will be erased (inside or outside this interval). The remaining ROI slices are unchanged.

13.16.1. Clear ROI slices outside [Z0, Z1]

Erases voxels in the active, visible ROI layer from slices between the first slice to slice number Z0-1 and from slice Z1+1 to the last slice. Edge slices Z0 and Z1 are not cleared. If the active ROI layer is invisible, the command is not executed.

13.16.2. Clear ROI slices inside [Z0, Z1]

Erases voxels in the active, visible ROI layer from slices starting with Z0 and ending with Z1. Edge slices Z0 and Z1 are cleared. If the active ROI layer is invisible, the command is not executed.

13.17. Average ROI layers

Create a new real-valued layer from visible ROI layers. Opens parameter panel. The user can select the values of background voxels (outside the ROIs): 0 for black (default) or -1 for transparent (VOID). The user can also select a normalization value by which the value inside the ROIs will be multiplied (e.g., 10 x avg value = 10).

13.18. Convert 3D to 4D

Requires a 4D image (dynamic series) and a 3D ROI. No parameters. Extends a 3D ROI to every frame of the 4D image.

13.19. Max Connected Component 3D

Requires a 3D ROI. Creates a new ROI layer. Finds and writes to the new layer an area of the maximum connected components in 3D.

13.20. Max Connected Component 2D

Requires a 3D ROI. Creates a new ROI layer. Finds and writes to the new layer an area of the maximum connected components in individual slices (2D).

13.21. Connected Component by Seed

Requires a 3D ROI and a VROI seed. Creates a new ROI layer. Finds connected component by seed growing based on the VROI seed and writes this area into the new layer.

13.22. Inside Surface Wave distance (in 0.01 mm)

Requires a 3D ROI. No parameters. Creates a new integer (grayscale) layer with the region inside ROI filled with values determined from ADD DETAILS.

13.23. Outside Surface Wave distance (in 0.01 mm)

Requires a 3D ROI. No parameters. Creates a new integer (grayscale) layer with the region outside ROI filled with values determined….

13.24. Layer Peel

Requires a 3D ROI. Opens parameter panel. The user specifies the number of layers to be created. Splits the original ROI into a specified number of layers by removing from the boundary of the original ROI a shell with the user-specified thickness (layer width). The innermost layer contains voxels that remain after peeling of the outer layers. The action is performed on all ROI layers (3D).

13.25. Smooth Shape

Requires a 3D ROI. Opens a parameter panel. Creates a new ROI layer. The new ROI is obtained from the original ROI by smoothing the ROI boundary with the specified radius.

13.26. Volumetric profile curve

Requires a 4D ROI. Displays info panel (4D ROI volume time profile, Fig. 13.4). Shows ROI volume on the vertical axis versus dynamic dimension on the horizontal axis. Can display multiple curves on the same plot. When the cursor is placed over a curve, displays ROI parameters: volume, MaxVol (cm3), FEV1 (cm3), FVC (cm3), FEV1/FVC. Copy Measures copies these values to clipboard. Copy Curves copies to clipboard ROI volumes as columns labeled by ROI name (only volumes are included, not the dynamic dimension). ADD DETAILS.

Volumetric profile curve

Fig. 13.4 Volumetric profile panel.

13.27. Concentric layers first order statistics

Requires a 3D ROI. Opens dialog panel (Specify Integer). Returns info panel (ROI concentric ring profiles, Fig. 13.5). Ring profiles shows plots of signal values versus the ring number from the outermost to the innermost. ADD DETAILS.

ROI concentric ring profiles panel

Fig. 13.5 ROI concentric ring profiles panel.

13.28. Zoom whole extent

Requires a 3D ROI (visible). Finds the slice with the largest ROI area and displays it at the maximum zoom that fits into the document window at its current size. If the active ROI is invisible, shows the visible ROI. If the active layer is invisible, but there are several visible ROIs, shows a warning about ambiguous layer configuration.