How to crop and save a cropped volume as one file?


I have a really large DICOM dataset of a spine surgery patient, and I would like to crop it as well as save the cropped volume as a single mhd or nrrd file. When I try to do this, it produces a nrrd file for the first few slices, and each of them is massive (looks like a bug). I am trying to save in voxel format rather interpolating format… Is it possible to use Slicer that way to save a single volumetric file?

Btw, my problem with landmarks turns out to be that Slicer considers the orientation of the image axes while my deformable surface model program doesn’t (not an IJK vs RAS issue). I need to save it as a file format such as mhd that does not preserve the axes orientation, then acquire the landmarks with that volume.

Best wishes,


Is it a CT? What are the dimensions and voxel size?

Do you mean the slices are interpolated to a much finer resolution?

Yes. This is a very common task.

Axis direction is just as important as image origin and spacing. It must be taken into account when processing an image. MetaIO image (mhd, mha), nrrd, nifti,… all store axis directions.