Alignment of two images in physical space prior to landmark registration


I am very new to Slicer and would like to register a phantom to a patient image (same image dimensions) using the Landmark Registration module. However, they are not in the same orientation: the patient image is in the axial plane, while the phantom image is at an arbitrary angle.

To align the images prior to registration, I have tried the following:

  • Automatic Initialization (Geometry Align) in the General Registration (BRAINs) module
  • Apply that transform to phantom image using ResampleScalarVectorDWIVolume module

My transformed phantom image is now in the axial plane as desired, but appears to cut off at certain slices.

Is this the right procedure to align two images prior to registration? If so, how can I prevent the transformed image from being “cut off”?

Thank you.

If the input images are far from each other then you can prealign them before automatic registration using semi-automatic registration methods. You need to harden the transforms on the images before starting automatic registration.

For automatic registration only the physical location of the volumes matter. Orientation of the voxel array axes is irrelevant (volumes are always shifted and rotated during registration anyway).

Just to confirm, are you registering 3D volumes to each other? You can do 2D/2D, 2D/3D, and multi-slice 2D/3D registration, too, but those are very different problems from 3D/3D registration.

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