Hi Andras, with those methods related on the previous comment we didn´t achieve any results… If we focus on the first one:
- When we straight the volume around one centerline, we also use the straightening transform to straight the model of the segmentation that we have.
- In this procedure, the model becomes straight over the centerline and the rest is usually distorted.
- Then, we use this model to create a new segmentation (if we don’t do this proccess segmentation → model → segmentation, the results are even worse). In this segmentation we obtain the volume using the tool Mask Volume from Segment Editor module.
- The mask is used out of slicer.
With this method, which we consider is more solid and useful, we found some technical issues:
• The quality of the segmentation made from the model is poor (see image below) on critical zones.
Blue: straighten model
Pink: straighten segment obtained by converting the model to a segment
Although this zone is bad reconstructed, the “easy” zones are well reconstructed (see image below). However, we need to be very precise in all the segmentation.
Blue: straighten model
Pink: straighten segment obtained by converting the model to a segment
What we expected is that all pixel inside the blue model would be part of the pink segmentation, but it is not the case.
• Also, we want to know if is possible, starting from a segmentation we have, select only the part that corresponds to a specific centerline and work with this cut-out instead with the original segmentation.
Finally, one more question: Slicer is awesome when it works with geometries ([x,y,z] world), because we can clearly straight a geometry and nothing bad happens, but is slicer able to, given a volume (made of mask images), come through the transform an recover the original segmentation with enough quality?
We lose information becoming from the model to the segmentation.
That´s all, we hope the procedure is clearly enough.
Thanks a lot 
.