Need Help: ITK ERROR: ElastixRegistrationMethod(00000187F232D140) about itkelastix HOT 4 OPEN

Thank you so much for your comment @NHPatterson

My issue was exactly running the registration in the Jupyter Notebook and not having anything printed. Copied the content to a .py file and managed to have a detailed description of what was happening in the terminal (problems with the parameters).

Maybe a suggestion for the authors to write a quick comment in the example notebooks (maybe the first one) saying that setting console logging to True won't work in the Jupyter Notebooks.

from itkelastix.

The python traceback doesn't tell us your error. If you turn on elastix_object.SetLogToConsole(True )or SetLogToFileOn(True) you will get a more informative error message.

from itkelastix.

I'm having the exact same issue. Even if I set the SetLogToConsole to True, it doesn't return any information. It just breaks at line where elastix_object.UpdateLargestPossibleRegion() and it just says what's in the screenshots above: Internal elastix error.

from itkelastix.

If you are using a jupyter notebook, you may not be seeing everything that is printed to console. It may be better to run your code as a command line script by placing the python bits into a .py file and running from the terminal:

conda activate myenv
python mycode.py

Here is a reproducible example script creating a registration as a command line script that both prints to console and writes the console log to file:

if __name__ == "__main__":
    import itk
    import numpy as np

    im = np.random.randint(0, 255, (1024, 1024), dtype=np.uint8).astype(np.float32)

    im = itk.GetImageFromArray(im)

    itk.elastix_registration_method(im, im)

    parameter_object = itk.ParameterObject.New()
    default_rigid_parameter_map = parameter_object.GetDefaultParameterMap('rigid')
    parameter_object.AddParameterMap(default_rigid_parameter_map)

    result_image, result_transform_parameters = itk.elastix_registration_method(
        im, im,
        parameter_object=parameter_object,
        log_to_console=True,
        output_directory="/Users/nhp/Documents",
        log_to_file=True)

If you add log_to_file=True and output_dir=/my/cool/dir (changing to a directory that is easy for you to navigate to) to your registration, it will create a file called 'elastix.log' in that directory. This will contain what would normally be printed to console. Open it and scroll to the bottom and you may find a more informative error.

from itkelastix.