registration of filamentous structures

[drchrisch]

Hi elastix users,

I would like to register (ITKElastix) two images containing very thin filamentous structures.
There exist some suggestions as to use AdvancedKappaStatistic or AdvancedMattesMutualInformation as Metric and starting from binary input or distance transformed images. So far, I run into trouble having a "too many samples map outside" error. I could not come around this error using a mask. Does anybody have a working solution to this question? Is elastix really the best way to go?