I just discovered this flag in the [eddy_output_base].eddy_values_of_all_input_parameters file generated when running eddy_cuda from version 6.0.1 (there are a bunch of other useful flags documented in there that don't appear in the UsersGuide!):
# Do not mask output to include only voxels present for all volumes (default false)
--dont_mask_output=True
If one sets this flag to True it seems to prevent the cropping from happening.
See also my reply to a similar post here: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1909&L=FSL&O=D&X=EDC8A1D4AC7D52F2F5&Y=mheyne%40bu.edu&P=281940
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