Changing orientation of slices in DICOM files

Operating system:win 10
Slicer version: 4.8
Expected behavior:
Actual behavior:

Can slicer change the orientation of the 3 cardinal views of the dicom data, IE say to change the orientation of the views? Say I want a view which changes the direction of the view of the orbit away from the normal?



Yes you can modify DICOM files using Slicer. Import the DICOM file, apply a transform, then export to DICOM.

Original metadata of the file is not preserved during this workflow. So, if you want to modify just a few tags while keeping all other metadata unchanged then you can use pydicom or DCMTK’s dcmodify tool instead.

thank you very much. The question is how do you apply the transform… I want to generate a plane and reformat the image along the new plane


For now, you can just apply a transform and adjust the angles using sliders. Later, if everything works well then you can tune how you define the new image orientation.

I am grateful for your help, but I don’t know how to apply a transform or generate one or use the sliders. Is there an article you can refer me to? What is a transformable node? I want to alter the slices to a 3point defined plane.

thank you


Transforms module documentation should help.

You can fit a plane to markup points as it is shown in this example in the script repository. You can modify the script to not set the slice plane but instead set the transform

What would you like to align? There is a module and code snippets available for brain AC-PC transformation.

Thanks, I’ll try that. I am just trying to align orbits to a plane.