FAQ

Installation

During installation the Platipy module failed to install

You may need to install the platipy module separately. This can be done using pip: pip install platipy . Detailed installation instructions are found here: https://pyplati.github.io/platipy/getting_started.html

Running the Code

Is there a code for modifying the elastix parameter files or do I have to do it manually?

In deformation.py there is a function ModifyElastixParameterFile which allows you to change parameters in the elastix file.

When running the main deformation script I get an error "JSONDecodeError: Invalid \escape"

This means that the json file is not formatted properly. Ensure all file paths have a forward slash '/' instead of a backward slash ''. All json items should have a comma after them, with the exception of the final item.

I get an error "Description: itk::ERROR: itk::ERROR: ElastixMain(0x55d536a90540): The following component could not be created: OpenCLResampler"

This error is because the elastix parameter file that is being used assumes the computer has access to a GPU. Either run on a computer with a GPU, or modify the elastix parameter that is being used (i.e. alter the "OpenCLResamplerUseOpenCL" and "Resampler" parameters). However this code has not been tested with alternate resamplers.

Code output

The output deformation is different to what I thought it should be

Assuming that the code has run correctly, the deformation is controlled by the elastix parameter file. Try experimenting with the parameters in this file. If the bony anatomy structure is not preserved you may need to increase the 'Metric1Weight' value or the 'LinearConditionWeight', 'OrthonormalityConditionWeight' or 'PropernessConditionWeight' values. If the deformation, particularly the structure deformation, is less than what it expected you may need to decrease the FinalGridSpacing or MaximumStepLength parameters.