Diffusion Tensor Tractography

Having computed the diffusion tensor, you can now go on to perform tractography. In the Diffusion Analysis tool, select the Tractography tab in the Diffusion Analysis tool, which will appear as below:

tractography_tab

You will use the diffusion tensor (DT) image produced by the tensor calculation, together with one or more regions of interest as seed points for the tracking. You can also optionally use a second set of regions of interest as a "target" for the tracking: only those tracts that pass through one of the target regions will be shown.

Select the diffusion tensor image that you have already created by the tensor calculation, either by clicking on the open icon, or by typing in the folder (directory) and file name of the image. The diffusion tensor image will have a suffix "DT":

tract_input

Next, select the ROI file that will be used to generate the tract seed points.

tract_seeds

Either click on the select_roi_file_button button, or type in the path to the ROI file name (and press return). The seed points will be selected from those pixels that are entirely contained within an ROI. If the ROI file contains Marker ROIs, each Marker location will be used as a seed point.

If you want to use target ROIs, make sure that the tract_target_check check-box is selected, and then select the ROI file that will be used as the tract target area(s).

tract_target

Either click on the select_roi_file_button button, or type in the path to the ROI file name (and press return). Only tracts that propagate from a seed point and pass through one of the regions defined in the tract target regions will be retained and displayed. Tracts which do not pass through at least one of the target regions will be discarded.

Now choose the other settings that will affect the way that tracts propagate.

tract_prop_panel

Now select how you would like the tracts to appear when displayed:

tract_appear_panel

The figures below show how tracts appear (zoomed in) with different combinations of the tract appearance settings.

Fibre tract appearance settings.
tract_line_uniform tract_line_fa
Uniform colour, line Coloured by FA, line
tract_tube_uniform tract_tube_fa
Uniform colour, tube Coloured by FA, tube
Note: each time you press the track_fibres_button, you will add new tracts to the display. You can set the appearance of the fibres you add between fibre tracking operations. However, once a set of fibre tracts has been added to the display, the appearance cannot be changed.

Gradient sign convention

You may already have corrected the gradient sign convention when calculating the diffusion tensor, in which case it does not need to be done again for tractography. However, if not, you now have the opportunity here to do so. If your computed tracts follow unexpected paths, with strange results, it may be that the gradient sign convention is wrong. The gradients specification, assumes that:

Performing tractography

You are now ready to generate some tracts and display them. You can either:

If you want to explicity remove all tracts from the display, click the remove_tracts_button button.

If you have already computed some tracts and saved them to disk (see below), you can load the tracts from disk without recomputing them by clicking the load_tracts_button button.

Now initiate tracking from the seed points by clicking the track_fibres_button button.

If you obtain satisfactory results, you can save the whole setup by clicking the save_settings_button button. Then, the next time you use perform tractography, the same settings will be retrieved. To revert to the default setting, click the set_defaults_button.

Saving tracts and tract statistics

You can save the tracts and tract statistics to disk file by selecting the save_tracts_check and/or save_tract_stats_check check-boxes in the tract output panel:

tract_output_panel

The format and contents of the files produced are detailed in the file formats chapter of this manual. The tract and tract statistics are computed with an adaptive step size propagation algorithm. However, once the tract is computed, its path and statistics along the path are output at regular steps, and you select the distance between steps using the tract_step_spinnerspinner. You can choose a value between 0.1 mm and 5.0 mm, in steps of 0.1 mm.

Set the base name of the tract and tract statistics file:

tracts_basename

The tracts and tract statistics files will be created in the same folder as the input image, and will have the following names.

See the file formats chapter for more detail.

If there is a pre-existing file with the same name, you can choose whether to append any existing tracts or tract statistics to that file by selecting the "Append" or "Overwrite" option.

Tract display

The Diffusion Analysis tool has an integrated 3-dimensional display to the left of the processing area. When you create fibre tracts, they will be automatically loaded and displayed there. However, you can of course, display any other 3-D objects that can be displayed on the regular 3-D display. Shown below is a screen shot showing orthogonal planes from a fractional anisotropy image as a backdrop, with two sets of tracts: the first was seeded from the motor tract and is coloured according to fractional anisotropy; the second was seeded from the genu of the corpus callosum has has a uniform colour.

tracts

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