Tensor estimation represents the pre-processing step before fiber tracking. It also allows
you to visualize scalar maps such as Fractional Anisotropy (FA) or Apparent Diffusion
Coefficient (ADC). You can perform this estimation by clicking the ``Estimate Tensors''
button. This will not display anything on screens. To display tensors as ellipsoids please
see the next chapter concerning the Tensor Viewer Module. Once the estimation is done, you
can display scalar maps to evaluate your results (see Sec. 3.4.2).
You have the possibility to save the tensors independently (apart from the
DTI-study). They are saved in a home made format called Inrimage and are compressed to
save memory (extension .inr.gz).
You will be able to load these tensors afterward, and use them to track fibers
apart from any study or in another one.
Fig. 2.8 shows a part of the Processing panel
where you can set some parameters for processing estimation. The Background Removal
Threshold is the MRI signal threshold underwhich tensors will not be estimated (based on
the B image). For instance you may move the slider down if the FA map (see
Sec. 3.4.2) seems to contain too many empty pixels.
For noisy data, you may need to use the smoothing filter. It provides anisotropic tensor
smoothing. For that you have to click ``Use Smoothing'' (see Fig. 2.8) and choose
between the three different noise levels of the data (``High'' means highly noisy
data). Then perform tensor estimation. You have to note that when using the smoothing
filter, tensor estimation is very time consuming. Hence you may not choose this option
when time is a limiting factor. Once the estimation is done, you should save the tensor
field separatly (or with the study) for future use.