RuntimeError: If input is a dictionary, a value for "include" must be specified when instantiating the transform

Hi @fepegar, I get the following error when I am trying to apply the CropOrPad Transform on my Subject Object.

RuntimeError: If input is a dictionary, a value for "include" must be specified when instantiating the transform

I am instantiating my transform as follows:

transform = torchio.CropOrPad(roi_shape, mask_name='roi_mask')
transformed = transform(subject)

I searched the documentation for the CropOrPad transform, but I do not seem to find the include parameter anywhere.

My Subject is a dictionary with the following keys: ['1', '2', '3', 'label', 'path_to_metadata', 'roi_mask']

Please do let me know if I am missing something. Thanks for your help, Megh

[fepegar]

Thanks, @meghbhalerao.

[meghbhalerao]

Sure! Here is the way to use the include parameter while using CropOrPad function:

subject_dict['1'] = tio.ScalarImage("path/to/image")
subject_dict['roi_mask'] = torchio.LabelMap("path/to/roi")
subject_dict['path_to_metadata'] = "path/to/metadata"
subject = torchio.Subject(subject_dict)
roi_shape = subject['roi_mask']['data'][0].shape
transform = torchio.CropOrPad(roi_shape, mask_name='roi_mask',include=['1','roi_mask'])
transformed = transform(subject)