Fmriprep

------------------------
Bugfixes, an additional iteration over Sentry reporting and some relevant ME-EPI updates
(with thanks to emdupre).

* ENH: Update ME-EPI workflow to create optimal combination (1263) emdupre
* MAINT: Merge master into multiecho (1324) effigies
* ENH: Add echo-idx flag (1355) emdupre
* FIX: Always run FreeSurfer interfaces that sink outside working directory (1397) effigies
* ENH: Use Python 3.7 in Dockerfile (1398) effigies
* DOC: Update contributing guide and add code of conduct (1404) emdupre
* FIX: Calculate template transforms explicitly as RAS2RAS (1399) effigies
* MAINT: Replace ``img.get_affine()`` -> ``img.affine`` (1414) oesteban
* FIX: Truncating of sentry messages (1417) chrisfilo
* ENH: Add fmriprep-docker execution environment (1416) chrisfilo
* MAINT: Update indexed_gzip to handle small .nii.gz (1421) effigies
* ENH: Group common issues with fingerprints (1418) chrisfilo
* ENH: adding memory and cpu info to sentry logs (1420) chrisfilo
* ENH: Use standard T2* map as coregistration target (1383) emdupre
* ENH: Handle FreeSurfer subject directory preparation gracefully when run in parallel (1413) effigies
* ENH: Make sure inputs are BIDS compliant before running fmriprep (1419) chrisfilo
* ENH: Sentry event categorization propagation (1422) chrisfilo
* MAINT: Require nipype >= 1.1.6 (1426) effigies
* ENH: Omnibus multi-echo pull request (1296) effigies
* ENH: Report memory overcommit policies (1429) effigies

-------------------------
Refactor of Sentry reporting, bug fixes and added tests. With thanks to sebnaze for contributions.

* TST: Utility functions for skipping/re-inserting non-steady-state volumes (1382) jdkent
* FIX: Correctly populate right-hemisphere time series in CIFTI derivatives (1378) sebnaze
* FIX: Restore original contour colors in reports (1385) oesteban
* ENH: New sentry SDK (1381) chrisfilo
* ENH: Sentry refinement (1394) chrisfilo

------------------------
Several bug fixes. With thanks to Franz Liem, Nir Jacoby and Markus Handal Sneve for contributions.

* FIX: Do not show --debug deprecation warning unless used (1361) effigies
* FIX: Select consistent parcellation for producing aparcaseg derivatives (1369) nirjacoby
* FIX: Count non-steady-state volumes even if sbref is passed (1373) effigies
* ENH: Respect SliceEncodingDirection metadata (1350) fliem
* ENH: Set maximum MELODIC components to 200 by default (1366) markushs
* TST: Verify LegacyMultiProc functionality (1368) effigies

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Hotfix release (deployment system)

------------------------
This release marks a substantial renaming of derivatives to conform to the BIDS Derivatives specification [release candidate](https://docs.google.com/document/d/17ebopupQxuRwp7U7TFvS6BH03ALJOgGHufxK8ToAvyI/).

The most significant additional change is a substantial revision of BOLD skull-stripping, using a BOLD template constructed from many open datasets. Building off the work of Zhifang Ye (see 1050), the skull-stripping is now much more resilient to intensity inhomogeneity.

With many thanks to Ali Cohen, James Kent, Inge Amlien, Sebastian Urchs, and Zhifang Ye for contributions.

* FIX: Missing BOLD reports (1326) oesteban
* FIX: Ensure encoding when reading boilerplate (1322) alioco
* FIX: Reportlets - bbregister vs flirtbbr (continues 1326) (1328) oesteban
* FIX: Quick update to new template structure (1330) oesteban
* FIX: Explicitly pass bold mask to AROMA (1332) jdkent
* FIX: Missing report output - 1339 (1346) kasbohm
* FIX: Remove non-steady-state volumes prior to ICA-AROMA (1335) jdkent
* ENH: Store BOLD reference images (1306) oesteban
* ENH: Deprecate --debug with --sloppy (1347) effigies
* ENH: Conform confound regressor names to Derivatives RC2 (1343) effigies
* ENH: Do not set KEEP_FILE_OPEN_DEFAULT (1356) effigies
* ENH: Template-based masking of EPI boldrefs (1321) oesteban
* DOC: Update BIDS-validator link (1320) surchs
* DOC: add --bind method to singularity patch documentation (1340) jdkent
* RF: Update anatomical derivatives for RC1 (1325) effigies
* RF: Update functional derivatives for RC1 (1333) effigies
* TST: Add heavily-nonuniform boldrefs for regression tests (1329) oesteban
* TST: Fix expectations for CIFTI outputs & ds005 (1344) oesteban
* MAINT: Ignore project settings files from popular python/code editors (1336) jdkent
* CI: Deploy nipreps/fmriprep:unstable tracking master (1307) effigies

1.1.x series (October 2018)
===========================

-----------------------
Several bug fixes. This release is intended to be the last before start
adopting BIDS-Derivatives RC1 (which will trigger 1.2.x versions).

* DOC: Switch to orig graph for ``init_bold_t2s_wf`` (1298) effigies
* FIX: Enhance T2 contrast ``enhance_t2`` in reference estimate (1299) effigies
* FIX: Create template from one usable T1w image (1305) effigies
* MAINT: Pin grabbit and pybids in ``setup.py`` (1284) oesteban