[Insight-users] Possible LevelSet Bug Due To Filters' Default UseDirectionOn?

[Chad Stanford]

Hello, 
I think have found a bug in many of the level set functions where the level set function derivatives could potentially not correspond with the advection derivatives and possibly other terms.  Essentially, many of the level set methods use derivative/gradient filters which take into account image direction by default to compute some of their terms e.g. advection.  The ComputeUpdate function in itkLevelSetFunction.hxx does not seem to take this into account when it computes the derivatives/gradients of the level set function.  In my case where the cosine direction matrix was diagonal and had -1 for the first 2 elements, the x and y advection gradient were off by a sign with respect to the sign of the level set function gradients.
Suggestion:  It'd be really great if the UseDirection option being set by default could be mentioned in the user guide because I was not aware of it until I'd spent a lot of time tracing a bug to one of the gradient filter's having that option set by default.  Also, the option is easy to miss because the user guide does not mention the direction matrix once (as far as I can tell), which would also be a nice addition, amongst other things.

While we're on the topic of the direction matrix, this problem has raised some questions I have about it.  Any answers or general insight would be greatly appreciated:
1.) I just want to verify that the direction matrix does not need to be diagonal or have unit elements and is fine as long as it's orthogonal?
2.) What coordinate system is the direction matrix rotating the image-coordinate system to? Basically I'm wondering where it comes from, not how it's made, as I understand given another coordinate system how to generate it.
Thanks!- Chad 		 	   		  
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