Fmriprep

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* FIX: Allow missing magnitude2 in phasediff-type fieldmaps (802)
* FIX: Lower tolerance deciding t1_merge shapes (798)
* FIX: Be robust to 4D T1w images (797)
* ENH: Resource annotations (746)
* ENH: Use indexed_gzip with nibabel (788)
* FIX: Reduce FoV of outputs in T1w space (785)

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* ENH: Update pinned version of nipype to latest master
* ENH: Added rX permissions to make life easier on Singularity users (757)
* DOC: Citation boilerplate (779)
* FIX: Patch to remove long filenames after mri_concatenate_lta (778)
* FIX: Only use unbiased template with ``--longitudinal`` (771)
* FIX: Use t1_2_fsnative registration when sampling to surface (762)
* ENH: Remove ``--skull_strip_ants`` option (761)
* DOC: Add reference to beginners guide (763)

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* ENH: Add inverse normalization transform (MNI -> T1w) to derivatives (754)
* ENH: Fall back to initial registration if BBR fails (694)
* FIX: Header and affine transform updates to resolve intermittent
misalignments in reports (743)
* FIX: Register FreeSurfer template to FMRIPREP template, handling pre-run
FreeSurfer subjects more robustly, saving affine to derivatives (733)
* ENH: Add OpenFMRI participant sampler command-line tool (704)
* ENH: For SyN-SDC, assume phase-encoding direction of A-P unless specified
L-R (740, 744)
* ENH: Permit skull-stripping with NKI ANTs template (729)
* ENH: Erode aCompCor masks to target volume proportions, instead of fixed
distances (731, 732)
* DOC: Documentation updates (748)

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* FIX: Skip slice time correction on BOLD series < 5 volumes (711)
* FIX: Skip AFNI check for new versions (723)
* DOC: Documentation clarification and updates (698, 711)

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With thanks to Mathias Goncalves for contributions.

* ENH: Collapse ITK transforms of head-motion correction in only one file (695)
* FIX: Raise error when run.py is called directly (692)
* FIX: Parse crash files when they are stored as text (690)
* ENH: Replace medial wall values with NaNs (687)

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With thanks to Anibal Sólon for contributions.

* ENH: Add ``--low-mem`` option to reduce memory usage for large BOLD series (663)
* ENH: Parallelize anatomical conformation step (666)
* FIX: Handle missing functional data in SubjectSummary node (670)
* FIX: Disable ``--no-skull-strip-ants`` (AFNI skull-stripping) (674)
* FIX: Initialize SyN SDC more robustly (680)
* DOC: Add comprehensive documentation of workflow API (638)