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:
An example of abnormal color coding:
Example: Original color | Proposed 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.