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Fixes+new features: Union of 3 PRs

Tom Nichols requested to merge (removed):Fixes+NewFeat into master

Since I discovered that my 3 branches can't cleanly all merge, here is one unified PR if that's easier to deal with.

I.e., this is the union of PRs https://git.fmrib.ox.ac.uk/falmagro/fsl_deface/merge_requests/1, https://git.fmrib.ox.ac.uk/falmagro/fsl_deface/merge_requests/2 & https://git.fmrib.ox.ac.uk/falmagro/fsl_deface/merge_requests/3.

Edited by Tom Nichols

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