Calculating the Streamlines

When arriving at the TRACKING page, the image area shows a fusion of the Angio image (A) and the masked Angio image for highlighting areas with high flow. Also shown in the overlay are the VOIs.

Tracking Configuration

The area in the lower right serves for defining the tracking algorithm and its parameters. Three algorithms are supported and can be selected in the Method list:

FACT: Similar to the FACT algorithm proposed by Mori et al [1], this method follows the local fiber orientation in each voxel. No interpolation is used.
EULER: Tracking proceeds using a fixed step size along the local fiber orientation [2]. With nearest-neighbor interpolation, this method may be very similar to FACT, except that the step size is fixed, whereas FACT steps extend to the boundary of the next voxel (distance variable depending on the entry and exit points to the voxel).
RK4 - Fourth-order Runge-Kutta method [2]. The step size is fixed, however the eventual direction of the step is determined by taking and averaging a series of partial steps. Interpolation determines how the fiber direction is determined at a given point in space.

The Interpolation setting is not relevant for FACT. For EULER and RK4 the choices are

NN: Nearest-neighbor interpolation using the local voxel data directly.
NC: Probabilistic nearest-neighbor interpolation, similar to the method proposed by Behrens et al [3]. The data is not interpolated, but at each point one of the 8 voxels neighbors is randomly chosen. The probability of choosing a particular voxel is based on how close the point is to the center of that voxel.
TRILINEAR: Linear interpolation of the vector components using the 8 neighbors.

Further parameters and options determine how tracking proceeds and when it ends:

Step size	Distance between points on the streamlines. Not used for FACT as it does not apply interpolation.
Velocity	Track ends if the velocity amplitude drops below this threshold.
Min length	If checked, streamlines shorter than the minimal length specified are discarded.
Curvature	If checked, streamlines are terminated in case the curvature exceeds the specified angle within the length specified. If length = 0.0, the curvature is checked at each step.
Exclusion VOI entry	Defines the behavior, when a streamline enters an EXCLUDE VOI: DISCARD the whole track, or CLIP it at the entry point.
Colour by	The streamlines can be functionally colored as follows: SEED: Using the color of the SEED VOI. END VOI: Using the color of the END VOI. DIRECTION: Each segment of the track has a color combined from its direction cosines values: Red, Green, and Blue from direction cosines x, y and z respectively. VELOCITY: Using the velocity amplitude value along the track for coloring. Vorticity Amlitude: Absolute Helicity:

Streamline Masking

An additional means for restricting the generated streamlines is by checking the Mask streamlines box and defining a mask. The elements in

have the following functionality:

	Generate a mask from the ANGIO image by applying the specified threshold and include it in the image list B for viewing.
	Open the current mask in the VOI editor and convert it into a VOI. The VOI can be edited, and the mask finally updated from the VOI.
	Select an external mask file.

Note: Please first perform tracking without streamline masking, and only afterwards gradually increase masking, if necessary.

As tracking is relatively time-consuming, it can optionally be restricted to a certain section of the acquisition with the Frames selection

After configuring all tracking parameters, please proceed with the button. The streamlines are calculated and visualized on the 3D page.

References

[1] Mori S, Crain BJ, Chacko VP, van Zijl PC: Three-dimensional tracking of axonal projections in the brain by magnetic resonance imaging. Ann Neurol 1999, 45(2):265-269.

[2] Basser PJ, Pajevic S, Pierpaoli C, Duda J, Aldroubi A: In vivo fiber tractography using DT-MRI data. Magn Reson Med 2000, 44(4):625-632.

[3] Behrens TE, Woolrich MW, Jenkinson M, Johansen-Berg H, Nunes RG, Clare S, Matthews PM, Brady JM, Smith SM: Characterization and propagation of uncertainty in diffusion-weighted MR imaging. Magn Reson Med 2003, 50(5):1077-1088. DOI