That’s actually really hard to say, you were using the old viewer with no indication of the projection you were using. All I could say is that the results were essentially the same in terms of orientation. For all I know, the problem might have been exactly the same.
Just the grad encoding file.
Use the force.
Kidding aside, it does take a bit of experience. But it’s basically geometry, you have to imagine what directions the fibres might be running in if you were to invert the X or the Y or Z component, etc. and see if that would be a better fit to what you expect to see given the anatomy…
Probably easiest in Matlab, or you could write a python script, or you could use awk if you’re a command-line die-hard like I am:
$ cat encoding.b | awk '{ print $1, $2, -$3, $4; }'
Not sure about ‘proper’ - but your ADC, FA, RD & AD values should be unaffected. But in general, it’s really important to get this right, it will come back to bite you eventually…