[Insight-users] Histoligical images registration

[delphine.ribes at epfl.ch]

Dear all,

I am doing Image registration of histological images. My goal is to align brain
mice in the same space coordinate to compare them. To do so I am using a
reference volume.
During the sectioning, some part of the brain is lost which create holes. To
align volume, I am using 4 following registration : land mark, rigid, affine
and a non rigid one which is Bspline. the last one is used to align internal
organs. The alignment is good. But if the external border is cut, artifacts
appear.

Do you know if there is a way to mask the hole to avoid those artifacts ?

I read in the itk book that you can pass the mask to the metric, but as far as I
understand it, it helps to improve computational cost ( as the metric is
focusing on pixel mask).  But I might misunderstood it...

Thanks a lot
Delphine