registration with mask does not work

[jslalu]

I tried to use a binary mask as the fixed mask to guide the registration, but the log said fMask was unspecified. What Should I do to make the mask work?

[ViktorvdValk]

Did you have a look at the example notebooks yet?
In case of masks, example 3 might be helpful.

[jslalu]

Did you have a look at the example notebooks yet?
In case of masks, example 3 might be helpful.

I did refer to example 3, but the log still said both fMask and mMask were unspecified. Here's my code.

elastix_object = itk.ElastixRegistrationMethod.New(fixed_image, moving_image)
elastix_object.SetFixedMask(mask)
elastix_object.SetMovingMask(mask)
elastix_object.SetParameterObject(parameter_object)
elastix_object.SetLogToConsole(True)
elastix_object.UpdateLargestPossibleRegion()
result_image = elastix_object.GetOutput()
result_transform_parameters = elastix_object.GetTransformParameterObject()

[ViktorvdValk]

Can you also show the part of the code that loads the mask?
And why would you want to use the same mask for both the fixed and the moving mask?

[ntatsisk]

The empty BufferedRegion seems to be caused by not setting WriteResultImage to True (as reported in #157).

However, I am not sure if the masks are not read. Indeed, the log indicates:

ELASTIX version: 5.1.0
Command line options from ElastixBase:
-fMask unspecified, so no fixed mask used
-mMask unspecified, so no moving mask used

but later it also reports:

Setting the fixed masks took: 0 ms.
Setting the moving masks took: 1 ms.

So, I assume the masks are being used.. cc. @N-Dekker