Fiber Tracking

We arrive now to the main purpose of DTI analysis : fiber tracking. White matter fiber bundles are tracked from the tensor field information. You can perform fiber tracking by clicking ``Track Fibers'' button. The reconstructed fibe are then displayed in the 3D view as lines colorized by their direction. As in the FAc map, red indicates a Left-Right orientation, green an Anterior-Posterior orientation and blue an Inferior-Superior orientation. In Fig. 3.9 you can see on the left a group of parameters you can set to optimize tracking. ``FA Threshold'' controls the FA value underwhich fiber tracking will stop (the value indicated on the slider has to be divided by 1000 to get the real FA value). ``Smoothness'' controls the smoothness of reconstructed fibers. The greater the slider value is, the smoother the fibers will be. The next parameter controls the minimum length of fibers to be valid (in mm). The last parameter is ``sampling''. If the set of reconstructed fiber tracts is too dense, you can set the sampling to a value greater than one. For instance if you set ``sampling'' to 4, fiber tracking will be performed onevoxel out of four. Consequently the process of fiber tracking will be 4 times faster. The next sections will explain you how to extract a fiber bundle from the set of reconstructed fibers.

Figure 3.9: On the left you see the parameters you can set to optimize fiber reconstruction. The ``FA Thresold'' controls the FA value underwhich the tracking will stop, the ``Smoothness'' slider controls the smoothness of the reconstructed fiber tracts. The next slider defines the minimum length autorized for a fiber bundle to be valid (in mm).''Sampling'' controls the result density, i.e. if ``Sampling'' is set to 4, a fiber will be tracked every voxel out of 4. On the right of the figure is shown an example of a set of reconstructed fiber tracts. Fibers are represented as colorized lines in the 3D view. The color characterize the direction of the fiber (see the color sphere).

On the Display panel you will see some parameters for fiber visualization (see Fig. 3.10). Here you can decide to show or hide the fibers and to show or hide the fiber cropping box (see Sec. 3.5.1). You also can choose between different visualization modes. Default ``polylines'' are simple lines. ``3D ribbons'' will represent each fiber as a ribbon. Finally you can choose ``3D tubes'' and set the tubes' radius (see Fig. 3.10). This last option takes a lot of resources and may slow down the graphic rendering. Note that these different modes are for visualization purpose and do not represent any anatomical reality.

Figure: Fiber visualization. On the left you can see some visualization parameters available in the Display panel. You can for example click on ``Crp. Box.'' to show or hide the fiber cropping box (see Sec. 3.5.1). On the right is shown a fiber bundle (Corpus Callosum) for different sets of parameters. On the upper-left figure is the default mode, fibers are represented as polylines. On the upper-right figure the cropping box has been switched off. On the bottom figuresare respectively shown the two other modes: 3D ribbons and 3D tubes. You can control the tubes' radius with the ``Radius slider'' parameter.