Fmriprep

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* FIX: Fixed 776 (aCompCor - numpy.linalg.linalg.LinAlgError: SVD did not converge) via 807.
* ENH: Added ``CSF`` column to ``_confounds.tsv`` (included in 807)
* DOC: Add more details on the outputs of FMRIPREP and minor fixes (811)
* ENH: Processing confounds in BOLD space (807)
* ENH: Updated niworkflows and nipype, including the new feature to close all file descriptors (810)
* RF: Refactored BOLD workflows module (805)
* ENH: Improved memory annotations (803, 807)

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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)