Mdt

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A small maintenance release for cleaning up some unused or outdated features.

Changed
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- Removed the used_protocol.prtcl from the output folder. Since with the extra_protocol the input has become more convoluted, the used protocol no longer reflects the actual used inputs.
- Removed the cascade_subdir from the model fit arguments. This behaviour was easily replicated by providing another output directory.
- Removed the save_user_script_info from the fit model parameters. It was hardly used and not a primary function of MDT.
- Renamed the post-processing switch covariance to covariances and added the switch for variances. Both must be set to False to disable computation of the FIM. If only one of them is False, the FIM will be computed and only the elements desired will be returned.

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Added
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- Adds support for gradient deviations per volume.
- Adds spherical proposal transformations to the theta and phi parameters. This ensures valid proposals around the [0, pi] range for both theta and phi.

Changed
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- Simplified the implementation of the NODDI_IC compartment model by removing support for cylindrical diffusion.
This simplifies the requirements of the model by removing the need to supply 'delta', 'Delta' and 'G'.
NODDI results are unaltered since the cylindrical diffusion was not used anyway.

Other
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- Removed the (previously) deprecated static map parameters.
- Renamed the DMRICompositeModelTemplate to CompositeModelTemplate.
- Removed some deprecated attributes from the compartment models.

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Fixed
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- Fixed small issue found by Dr. Luke Edwards. The legendre polynomial in the NODDI_IC compartment was not computed correctly. This only subtly changes the results.

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This version removes support for Python version <= 2.7. Now only Python > 3 is supported.

Added
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- Adds the CHARMED_r1 model using the van Gelderen model of diffusion.
- Adds scientific articles section to the docs.
- Adds Ubuntu 18.04 release target.
- Adds a convenience function for generating a brain mask.

Changed
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- Updates default protocol save name.
- Removed Python2.7 support.

Other
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- Mac compatibility change.
- Slightly changed the masking algorithms with a different median filter.

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Fixed
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- Fixes issue with the JohnsonNoise model in the model builder.

Other
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- Renamed some of the command line commands from generate to create.

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The most important update is a bugfix in the CHARMED models. Unfortunately the CHARMED reference paper (Assaf, 2004) contains
a small omission in the formula for the Neuman cylindrical diffusion model (a ``2`` is missing).
Correcting this mistake slightly changes the CHARMED results.

Furthermore, the static maps and static parameters have been merged with the protocol parameters.
This allows, or will allow in the future, overloading protocol parameters with 3d/4d volumes.

Added
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- Added functionality for nesting templates. This allows adding components that can only be used in the context of another component.
- Adds EPI relaxometry models.
- Adds functionality for unique names in a cascade.
- Adds the Van Gelderen cylinder model and renamed the Von Neumann cylinder model. Corrected the CHARMEDRestricted equation.

Other
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- Redefined the kappa parameter of the NODDI model to be between 0 and 64.
- Removed the static map parameters and merged these with the protocol parameters.
- Merged the model builder with the composite model.