Diﬀusion Tensor Imaging (DTI) Mode

5.22 Diﬀusion Tensor Imaging (DTI) Mode

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Functionality is available in the Pro edition
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Tractography results cannot be used for establishing a diagnosis

The DICOM Viewer in the MPR reconstruction and Volume reconstruction tabs allows you to show the result of the ﬁber tractography for the series of Diﬀusion MRI. Fig. 5.29 shows tracks which are the result of brain tractography.

Figure 5.29: Result of brain tractography

The tracks which are the result of tractography are refered to as ﬁbers in the DICOM Viewer interface and in the User Manual.

5.22.1 Open series in DTI Mode

The tractography will be performed automatically for the series made in the DTI mode when you open it in the MPR reconstruction or Volume reconstruction tabs. To display ﬁbers over the images not made in the DTI mode (for the same study):

Open the series not made in the DTI mode.
Click the DTI button on the toolbar.

In the DTI Series dialog that appears, select the series made in the DTI mode.

The DTI Series window doesn’t show the current series, the DTI series added before, or the series that cannot be used for construction of a 3D model.

Click SELECT to display ﬁbers over the images or CANCEL to cancel.
To superimpose an image of ﬁbers from another DTI series on an open series, repeat steps 2 — 4.

The images of ﬁbers from each DTI series are added to the Fibers panel.

To delete an image of ﬁbers contained in a superimposed DTI series, click the Remove DTI series button on the Fibers panel.

5.22.2 Opening a Fused Series in the DTI Mode

An image of ﬁbers can be superimposed on a fused series of one or several non-DTI studies. To do this, proceed as follows:

Open the fused series in the MPR reconstruction or Volume reconstruction tab (see Sections 4.1 and 4.2).
Open the segmentation panel by clicking the Segmented structure panel button.
Select one of the layers of the fused series on the segmentation panel.
Click the DTI button on the toolbar.

In the DTI Series window that pops up, select a DTI series and click SELECT.

The DTI Series window doesn’t show the current series, the DTI series added before, other layers series, fused series, or the series that cannot be used for construction of a 3D model.

For the second and subsequent layers, repeat steps 3 — 5.

The images of ﬁbers from each DTI series are added to the Fibers panel.

To delete an image of ﬁbers contained in a superimposed DTI series, click the Remove DTI series button on the Fibers panel.

5.22.3 Fibers Panel

To open the Fibers panel in the MPR reconstruction or Volume reconstruction tab, click the Segmented structure panel button on the toolbar.

The Fibers panel for the MPR reconstruction tab is shown in Fig. 5.30, for the Volume reconstruction tab — in Fig. 5.31. On the panel for the Volume reconstruction tab, there are no ROI tools or their visualization elements.

The actions performed with groups of ﬁbers are duplicated on the Fibers panel in the MPR reconstruction and Volume reconstruction tabs.

Figure 5.30: The Fibers panel it in the MPR reconstruction tab

Figure 5.31: The Fibers panel it in the Volume reconstruction tab

Tools and buttons on the Fibers panel:

	ROI ... tools (Rectangle , Ellipse , Polygon ). The shape of the button changes depending on the tool chosen.
	Polygon cut tool.
	Inverse polygon cut tool.
	The Undo cut button cancels the previous cutting operation.
	The Redo cut button repeats the last undone cutting operation.
	The New ﬁbers group button adds a new group.
	The Remove ﬁbers group/Remove ROI/Remove DTI series button deletes a selected group of ﬁbers, a ROI within a group or a superimposed DTI series.
	The DTI parameters button calls up a dialog box to enable saving .spj ﬁles in the format compatible with the previous DICOM Viewer versions up to and including version 2.17 (see Section 5.22.9).
	The Voxelize tracks button is used to build a voxel model for the selected group of ﬁbers (see Section 5.22.8).
	The Convert tracks to polygonal mesh button is used to build a polygonal surface for the selected group of ﬁbers (see Section 5.22.7).

5.22.4 Select Visible Fibers

If you want to make only some ﬁbers visible, specify the areas through which the ﬁbers pass as visible or invisible. Use the ROI tools from the Fibers panel. The operation of these tools is similar to using ROI from the toolbar at the top of the window (see Section 2.19.7). Note that you cannot use the ROI tools from the top toolbar to adjust the visibility of the ﬁbers.

To make some ﬁbers visible:

Open the series made in the DTI mode or display ﬁbers over the series not made in the DTI mode.
Select the plane and the image in which you want to specify the area through which the target ﬁbers pass.
Open the Segmented Structure panel by clicking the Segmented structure panel button. The Fibers panel will be located at the bottom.
Specify the desired area using the ROI tools (Rectangle , Ellipse , Polygon ) on the Fibers panel. After making the ROI, only the ﬁbers passing through the region speciﬁed by the ROI will be visible. A new group appears on the Fibers panel. This group includes the new ROI.
Each ROI tool can be activated with the left, right, or middle mouse button. To continue work with the same tool, use the button with which the tool was activated. For details on tool management, see Section 1.14.
If you want external ﬁbers beyond a ROI to be visible, click the Set outer ﬁbers button for this ROI. If you want internal ﬁbers within a ROI to be visible, click the Set inner ﬁbers button for this ROI.
Make new ROIs until you see only the target ﬁbers. Only the ﬁbers which pass through all the ROIs are visible (or invisible if you check the outer ﬁbers box).

The Polygon cut and Inverse polygon cut tools can be used to edit groups of ﬁbers on orthogonal sections in the MPR reconstruction tab and on 3D models in the Volume reconstruction tab. To open a series in the 3D view window, in the MPR reconstruction tab, click 3D button on the toolbar. The 3D view window that pops up will show the 3D model. For details on customizing the section windows arrangement in the MPR reconstruction tab, see Section 5.2.1.

To hide all the ROIs, click the Hide ROI button in the line with the name of the series on the Fibers panel. To show all the ROI, click the Show ROI button. In the same way, you can hide or display the ROI for each group or for a certain ROI within each group. The visibility of the ROI does not aﬀect the visibility of the ﬁbers.

To hide ﬁbers for the whole series, a Base ﬁbers group, or a ROI group, click the Hide button in the respective line. To show ﬁbers, click the Show button. This button does not aﬀect the visibility of ﬁbers, it only allows you to temporarily hide them, for example, to adjust the visibility of other ﬁber groups.

To rename a group or ROI, double-click the left mouse button on the group or ROI name, enter the new name, and press the Enter key on the keyboard.

To delete ROI select it and click the Remove ﬁbers group/Remove ROI button on the Fibers panel.

To make other ﬁbers visible without changing the visibility of the ﬁbers previously made visible:

If necessary, hide the previously displayed ﬁbers by clicking the Hide button in the row with the ﬁber group name.
Show the base ﬁbers by clicking the Show button in the row with the Base ﬁbers group.
Add a new group by clicking the New ﬁbers group on the Fibers panel.
Add a new ROI to make only the target ﬁbers visible. To ensure that the ROI is in the right group, this group must be selected before making a ROI.
If necessary, show some other ﬁbers by clicking the Show button in the rows with their names.

To show the image containing a certain ROI, click the Find ROI button on the Fibers panel.

Figure 5.32: Edited groups of brain nerve ﬁbers

5.22.5 Fiber Color

By default, ﬁbers are colored in accordance with the DEC (Direction Encoded Color) scheme. It means that the color of a ﬁber depends on its direction. You can set color for each group manually.

On the Fibers panel, the button for selection of the color for a group of ﬁbers is shown as a color spectrum in the DEC mode and as the selected color in the manual mode.

To choose the color for a selected group of ﬁbers in the manual mode, check the box on the right-hand side of the color selection button. Then left-click on the color selection button and in the dialog box that pops up, select the color required or keep the default color.

To switch back to the DEC mode, uncheck the box on the right-hand side of the color selection button showing the selected color.

5.22.6 Scalar Maps

The DTI maps panel is only shown in the MPR reconstruction tab.

The DICOM Viewer allows to display scalar maps for series made in the DTI mode. The following types of maps are available:

Fractional Anisotropy (FA);
Mean Diﬀusivity (MD);
Axial Diﬀusivity (AD);
Radial Diﬀusivity (RD).

By default, the maps are not displayed. To display the map, select the target map on the drop-down list Scalar map type (Fig. 5.33). To hide the map, select an empty value from the list.

On the CLUT drop-down list, select the CLUT for the map spectrum. In the Value range ﬁelds, specify the minimum and the maximum values for the selected map visible range.

To restore the default range values for the selected map type, click the Restore default value range button on the maps panel. If the minimum and the maximum values for the visible range of the selected map type are the same as the default values, the Restore default value range button will be unavailable.

To minimize the maps panel, click the Collapse button; to maximize the panel, click Expand .

Figure 5.33: DTI Maps Panel

There are three ways to measure intensity on scalar maps:

mouse over a selected point on the scalar map. The intensity value for the point indicated by the cursor is shown in the second line, in the bottom left corner of the viewer window where the cursor is placed. The intensity in the point indicated by the cursor is shown if the Show point value option has been activated (see Section 2.27);
measure the intensity value for a certain point on the scalar map with the Point value tool on the toolbar (see Section 2.19.6);
measure the average intensity value for a selected region on the scalar map with ROI ... tools (Rectangle , Ellipse , Polygon ) on the toolbar (see Section 2.19.7).

5.22.7 Building a Surface

DICOM Viewer allows for building ﬁber surfaces in the Multiplanar reconstruction window.

Select a group of ﬁbers or a ROI for the selected group of ﬁbers. A polygon surface is built for a group of ﬁbers. If you change the ROI visibility for the group of ﬁbers, it won’t have any impact on the surface to be built.

Each ﬁber is represented by a volumetric ﬁgure. The polygonal surface is constructed based on the ﬁber’s diameter and the number of points on its contour.

To set the parameters for the surface model surface, click the button Convert tracks to polygonal mesh on the Fibers panel. In the dialog box for the surface model parameters (Figure 5.34), provide the following parameters:

Fiber contour points, from 3 to 360. In most cases, six points are enough to ensure decent accuracy. The accuracy of the model, the time required for estimation and the memory space required increases with the number of points on the contour.
Fiber diameter, from 0.01 to 10 mm.

Figure 5.34: The dialog box for surface model options

Click OK to apply the settings or CANCEL to cancel.

A surface is created for the chosen group of ﬁbers and added to the list on the Segmented structure panel. The name of the surface, as well as the name of any structure without a volume model, is shown in italics. The name of the surface is copied from the name of the group on the Fibers panel.

You can view the built surface in the MPR reconstruction tab. To open a volume reconstruction, click the 3D button on the toolbar.

The 3D model will be shown in the 3D view window that pops up. For details on customizing the section windows arrangement in the MPR reconstruction tab, see Section 5.2.1.

The work with the structures from the segmented structure list is described in Section 6.4. The surfaces created can be exported or imported. For details on surface and structure export and import, see Section 6.7. The procedures of saving and opening segmentation projects and DTI projects are described in Section 6.11.

5.22.8 Creating a Voxel Model of Fibers

DICOM Viewer allows for building voxel models of ﬁbers in the Multiplanar reconstruction tab.

Select a group of ﬁbers or a ROI for the selected group of ﬁbers. A voxel model is built for a group of ﬁbers. If you change the ROI visibility for the group of ﬁbers, it won’t have any impact on the model to be built.

To build a voxel model, click the Voxelize tracks button on the Fibers panel.

A voxel model is created for the chosen group of ﬁbers and added to the list on the Segmented structure panel. The name of the structure is copied from the name of the group on the Fibers panel.

To create a voxel model based on all the ﬁbers, select the Base ﬁbers group and click the Voxelize tracks button on the Fibers panel.

The voxel model is created for the chosen group of ﬁbers (Base ﬁbers) and added to the list on the Segmented structure panel under the name DTI tracktography.

You can view the model built in the MPR reconstruction tab. To open a volume reconstruction, click the 3D button on the toolbar.

The 3D model will be shown in the 3D view window that pops up. For details on customizing the section windows arrangement in the MPR reconstruction tab, see Section 5.2.1.

The work with the structures from the segmented structure list is described in Section 6.4. The surfaces created can be exported or imported. For details on structure export and import, see Section 6.7. The procedures of saving and opening segmentation projects and DTI projects are described in Section 6.11.

5.22.9 Saving data in a ﬁle

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Functionality is available in a separate module which is activated in the Pro edition for an extra fee
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The DICOM Viewer provides an opportunity to save ROI and groups in ﬁles with .spj extension. The procedure for saving and opening ﬁles is described in Section 6.11. When a ﬁle is opened, the data contained in it is added to the data from the Fibers panel.

To save an .spj ﬁle in a format compatible with the previous DICOM Viewer Viewer versions (up to and including version 2.17), click the DTI parameters button on the Fibers panel. In the dialog box that pops up, enable the option Save the DTI ﬁbers data in a format compatible with legacy versions of the viewer. Click OK to apply the settings or CANCEL to cancel.

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