- Introduction
- 1. Loading the input images
- 2. Tracking
- 3. Fiber bundles
- 4. Statistics
- 5. Results
- 6. Display
Introduction
The fiber tracking program allows you to reconstruct fiber pathways from the diffusion tensor information. This program uses the streamline technique to integrate fiber bundles through the vector field comprising the principal direction of diffusion. It handles seeding the integration at individual points, entire regions of interest (ROIs), or via the landmark editor in the main viewer. It allows for arbitrary seed density, and provides flexible stopping criteria, including maximum fiber angle, fractional anisotropy and mean diffusivity values. In addition, the program calculates basic fiber bundle statistics. In order to invoke the fiber tracking tool, simply choose "Diffusion" menu, and select "Fiber Tracking". Below follows a sequence of steps explaining the use of the fiber tracking program.1. Loading the input images
First, you will need to load the tensor image, computed by the [ Tensor Utility ], as shown below. Second, load either the anatomical mask you created earlier or the ROI you would like to use for tracking in the Region of interest mask. Finally, load the auxiliary image, which could be any image in DTI space, for which fiber statistics can also be computed, in the Map for analysis box. Once all these input images are loaded, make sure that you have an image in the viewer (e.g. mask, or map for analysis) before you start tracking.
2. Tracking
Under the Tracking tab, you will find a series of options and parameters to control the fiber tracking procedure. To fiber track, you must 1) Select the appropriate seeding method; 2) Select parameters for tracking, such as transformation type, ranges for FA, or MD, and maximum angle; and finally 3) press Track!.Seed point selection
You may choose to seed the tracking using a single point, a region of interest, a volume, or points from the landmark control. In the case of a single point, the position of the cross-hairs in the main viewer will be used as coordinates for the point. In the case of a region of interest, you must specify the region number to start tracking from. All points from the ROI will be used as seeds. You can also increase the point density. For volume, a 3D window (subvolume) of size Width x Height x Depth is taken to initialize the tracking.
Integration parameters
The integration method used by the Fiber Tracking program is the well known Runge-Kutta method. You may specify second-order integration or fourth-order integration, which provides better accuracy. The step length (h) for integration represents the percentage of a voxel diagonal's length. Higher percentages will yield coarser results while smaller values will yield smoother fibers.
By default, the eigenvector field to be followed is the Primary, also known as the principal direction of diffusion. Note that the integration is performed both ways, at +h and -h, and final result will constitute a single fiber. The user is also allowed a set of simple transformations to the vector field when tracking: sign flips in the x, y and z directions. For more complex transformations, please see the [ Tensor Utility ] and [ Tensor Analysis ] tools.
Fiber filtering
Here you will see a series of stopping criteria options, ranging from minimum and maximum fractional anisotropy (FA), mean diffusivity (MD), fiber length, and maximum angle between steps. In addition, you may choose to track only fibers that cross a specific region. For that, enable the aforementioned option and choose the corresponding region number. By enabling Clip fibers, only fiber segments that end in the specified region are kept.
Once the relevant parameters are set, simply press the Track! button to start tracing.
You can save a bundle or a set of bundles by selecting them from the list and pressing the Save button. Note that you will be prompted for a directory name for saving. Bundles are saved according to their label names. To save a bundle with a different name, you must change its label first.
Important!
Fiber bundles are not immediately visible in the viewer, until you switch the viewer to 3D mode, and select "View fibers" under the Display tab, in the Fiber Tracking program (See item Display below)
Examples of fiber tracking by seeding a region of region of interest in the CC, shown with increasing fiber densities.
The integration method used by the Fiber Tracking program is the well known Runge-Kutta method. You may specify second-order integration or fourth-order integration, which provides better accuracy. The step length (h) for integration represents the percentage of a voxel diagonal's length. Higher percentages will yield coarser results while smaller values will yield smoother fibers.
By default, the eigenvector field to be followed is the Primary, also known as the principal direction of diffusion. Note that the integration is performed both ways, at +h and -h, and final result will constitute a single fiber. The user is also allowed a set of simple transformations to the vector field when tracking: sign flips in the x, y and z directions. For more complex transformations, please see the [ Tensor Utility ] and [ Tensor Analysis ] tools.
Fiber filtering
Here you will see a series of stopping criteria options, ranging from minimum and maximum fractional anisotropy (FA), mean diffusivity (MD), fiber length, and maximum angle between steps. In addition, you may choose to track only fibers that cross a specific region. For that, enable the aforementioned option and choose the corresponding region number. By enabling Clip fibers, only fiber segments that end in the specified region are kept.
Once the relevant parameters are set, simply press the Track! button to start tracing.
3. Fiber bundles
Once tracking is complete, you are
taken to the Fibers tab, in
which the tracing results will accumulate. Bundle names and colors can
be changed: simply select a bundle from the list and either change the
label or press the color button. They can also be made visible or
hidden by clicking the Display
checkbox.
You can save a bundle or a set of bundles by selecting them from the list and pressing the Save button. Note that you will be prompted for a directory name for saving. Bundles are saved according to their label names. To save a bundle with a different name, you must change its label first.
Important!
Fiber bundles are not immediately visible in the viewer, until you switch the viewer to 3D mode, and select "View fibers" under the Display tab, in the Fiber Tracking program (See item Display below)
Examples of fiber tracking by seeding a region of region of interest in the CC, shown with increasing fiber densities.
4. Statistics
Under the statistics pane, you will
find the basic statistics for every bundle that has been tracked. Both
fractional anisotropy (FA) and mean diffusivity (MD) as well as fiber
length and mean fiber angle measures are computed. In addition,
statistics on the auxiliary map, or input map, are also
provided. Press the Save
button to save the report as a text (ASCII) file which can be imported by
other software (spreadsheets, statistics, etc.).
5. Results
Under the Results pane, you will see a list of images generated by the tracking program. Currently, the only output from the tracking program is the fiber quantization mask, a binary mask representing the last tracked bundle in raster format. This mask can be saved as an Analyze image for use in BioImage Suite or other programs.
Example of fiber quantization result, delineation of the CC.
6. Display
As in the Tensor Analysis tool, under the Display tab you will find a set of visualization tools. Here you will be able to view the fibers, as well as color them according to various measures (FA, MD, etc.) and change their representation.
As mentioned earlier, fiber bundles will not be visible in the viewer until you switch the viewer to 3D only and then check the option View fibers to display them.
View colormap
If you would like to display the colormap in the main viewer, select this option.
Filter
Fibers are assigned to a solid color by default. Alternatively, you may choose to color them according to different indices, such as FA or MD. The Filter option lets you specify which measure should be used to color the fibers. To enable this option, please check the Apply colormap option. Fibers can also be displayed as a set of points, lines or tubes. The tube radius and point size can also be selected.
Examples of fiber tracings color according to fractional anisotropy (left) and region number (right).