Fmriprep

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With thanks to Feilong Ma for contributions.

* ENH: Option to provide a custom reference grid image (``--output-grid-reference``) for determining the field of view and resolution of output images (480)
* ENH: Improved EPI skull stripping and tissue contrast enhancements (519)
* ENH: Improve resource use estimates in FreeSurfer workflow (506)
* ENH: Moved missing values in the DVARS* and FramewiseDisplacement columns of the _confounds.tsv from last row to the first row (523)
* ENH: More robust initialization of the normalization procedure (529)

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* ENH: ``--output-space template`` targets template specified by ``--template`` flag (``MNI152NLin2009cAsym`` supported) (498)
* FIX: Fix a bug causing small numerical discrepancies in input data voxel size to lead to different FOV of the output files (513)

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* ENH: Use robust template generation for multiple T1w images (481)
* ENH: Anatomical MNI outputs respect ``--output-space`` selection (490)
* ENH: Added support for distortion correction using opposite phase encoding direction EPI images (493)
* ENH: Switched to FSL BET for skullstripping of EPI images (493)
* ENH: ``--omp-nthreads`` controls maximum per-process thread count; replaces ``--ants-nthreads`` (500)

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* Hotfix release (dependencies and deployment system)

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* ENH: Added an option to choose the degrees of freedom used when doing BOLD to T1w coregistration (``--bold2t1w_dof``). Set default to 9 to account for field inhomogeneities and coils heating up (448)
* ENH: Added support for phase difference and GE style fieldmaps (448)
* ENH: Generate GrayWhite, Pial, MidThickness and inflated surfaces (398)
* ENH: Memory and performance improvements for calculating the EPI reference (436)
* ENH: Sample functional series to subject and ``fsaverage`` surfaces (391)
* ENH: Output spaces for functional data may be selected with ``--output-space`` option (447)
* ENH: ``--skip-native`` functionality replaced by ``--output-space`` (447)
* ENH: ``fmriprep-docker`` wrapper script simplifies running in a Docker environment (317)

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With thanks to Asier Erramuzpe for contributions.

* ENH: Added optional slice time correction (415)
* ENH: Removed redundant motion parameter conversion step using avscale (415)
* ENH: FreeSurfer submillimeter reconstruction may be disabled with ``--no-submm-recon`` (422)
* ENH: Switch bbregister init from ``fsl`` to ``coreg`` (FreeSurfer native 423)
* ENH: Motion estimation now uses a smart reference image that takes advantage of T1 saturation (421)
* FIX: Fix report generation with ``--reports-only`` (427)