3.1 General

3.1.1 Incorrect color coding FA maps

FA color coding is incorrect. Why? Because co-ordinate system of scanner and BrainVoyager is different. This is not a BV problem, since co-ordinate systems are not standardized.

Normal color coding:

Left-Right vv (= X direction)
Anterior-Posterior vv (= Y direction)
Inferior-Superior vv (= Z direction)

An example of abnormal color coding:


Example: Original colorProposed change
Ant-Post = blue X: direction = Inf-Sup
Inf-Sup = red Y: direction = Left-Right
Left-Right = green Z: direction = Ant-Post

Procedure to correct:
go to DTI -> Diffusion Weighted Data Analysis -> VDW Properties -> Gradients. Change x, y and z to what you think is correct. This is a mathematical operation and has nothing to do with orientation in the brain. Next, click the OK button.


Re-calculate the tensors by clicking the Estimate button. In the Calculations tab, create the color coded FA maps and check them for the right colors.


Then, Go to DTI -> Tensor visualisation and check for tensor directions. I always use the splenium of the corpus callosum to check for correct orientation.

(a) incorrect tensors
(b) correct tensors

Figure 3.1: Splenium of the corpus callosum, view from the top