Fmriprep

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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)

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* ENH: Increased support for partial field-of-view BOLD datasets (659)
* FIX: Slice time correction is now being applied to output data (not only to intermediate file used for motion estimation - 662)
* FIX: Fieldmap unwarping is now being applied to MNI space outputs (not only to T1w space outputs - 662)

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* ENH: Include ICA-AROMA confounds in report (646)
* ENH: Save non-aggressively denoised BOLD series (648)
* ENH: Improved logging messages (621)
* ENH: Improved resource management (622, 629, 640, 641)
* ENH: Improved confound header names (634)
* FIX: Ensure multi-T1w image datasets have RAS-oriented template (637)
* FIX: More informative errors for conflicting options (632)
* DOC: Improved report summaries (647)

0.x series (July 2017)
======================

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With thanks to Yaroslav Halchenko and Ilkay Isik for contributions.

* ENH: Set threshold on up-sampling ratio in conformation, report results (601)
* ENH: Censor non-steady-state volumes prior to CompCor (603)
* FIX: Conformation failure in thick-slice, oblique T1w datasets (601)
* FIX: Crash/report failure of phase-difference SDC pipeline (602, 604)
* FIX: Prevent AFNI NIfTI extensions from crashing reference EPI estimation (619)
* DOC: Save logs to output directory (605)
* ENH: Upgrade to ICA-AROMA 0.4.1-beta (611)

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* DOC: Improved report summaries describing steps taken (584)
* ENH: Uniformize command-line argument style (592)