How to write a recursive script to crop volumes with ROI?

[jenaflex]

1. How to write recursive script to run ‘crop volume’ (like attached screenshot) on all 3D volumes (3D volumes extracted from 4D nifti)? I have ‘UtBox.acsv’ ROI file already.

2. (Am I supposed to, OR, ) how to make function call ‘slicer.modules.cropvolume’ in built-in Python console to crop 3D volumes with ROI (instead of using GUI).
   The documentation seems to be very limited.
   

   

Thanks!

[jenaflex]

Up. Please help. Thanks!

[pieper (Steve Pieper (Isomics, Inc.))]

You could start by looking at the SlicerCaseIterator. Once you can iterate through your volumes you could add some code to do the cropping. I agree it’s not well documented but the building blocks are there and you can see example scripts.

[jenaflex]

Thanks!
I think I should be able to figure out iteration method.
My main concern is how to call cropvolume function with input ROI being UtBox ROI file (like the screenshot).

[simonoxen (Simon Oxenford)]

Hi, this is a part of a script I used to call cropvolume from a python script:

parameters = slicer.vtkMRMLCropVolumeParametersNode()
slicer.mrmlScene.AddNode(parameters)

parameters.SetInputVolumeNodeID(input.GetID())
parameters.SetOutputVolumeNodeID(output.GetID())
parameters.SetROINodeID(roiNode.GetID())
slicer.modules.cropvolume.logic().Apply(parameters)