How to merge several volumes?

Dear community,

Currently I am trying to merge several volumes into one large volume. This is what I have so far:

-Several volumes loaded into Slicer. The volumes were taken from one patient and show slightly different regions (e.g. volume 1 shows the segments of the liver right to the vena cava, volume 2 the segments left to the vena cava).
-The volumes do include overlapping areas which shall be used in order to register the volumes and merge them into one large volume
-As the volumes were taken at slightly different times, the registration has to balance not only translational and rotational differences between the volumes but also warping that results from altered tissue configuration (i.e. due to heartbeat and breathing).

What would be the best way to do this?
Thank you very much in advance!!!

This all sounds very doable.

  • Choose one of the volume as “reference” and align/warp the images to each other using any of the manual or automatic registration methods that supports non-linear warping.
  • Expand the reference volume to a cover the entire region that you are interested in using Crop volume module
  • Resample all the volumes using this expanded reference volume as “reference”
  • Combine the volumes, probably quickest to do it with a few numpy commands

Stitching of volumes has come up a few times on this forum, so you can find more detailed instructions for each step by searching here, but if anything is not clear then let us know.

If you need to do this regularly then it is probably worth creating a script (or module) for this that automates most of the steps.