Fmriprep

------------------------
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

--------------------------
Several bug fixes. With thanks to Elizabeth Dupre and Romain Vala for
contributions.

* FIX: Revert FreeSurfer download URL (1280) chrisfilo
* FIX: Default to 6 DoF for BOLD-T1w registration (1286) effigies
* FIX: Only grab sbref images, not metadata (1285) effigies
* FIX: QwarpPlusMinus renamed source_file to in_file (1289) effigies
* FIX: Remove long paths from all LTA output files (1274) romainVala
* ENH: Use single-band reference images when available (1270) effigies
* DOC: Note GIFTI surface alignment (1288) effigies
* RF: Split BOLD-T1w registration into calculation/application workflows (1278) emdupre
* MAINT: Pin pybids and grabbit in Docker build (1281) chrisfilo

--------------------------
Hotfix release.

* FIX: Typo in plugin config loading.

--------------------------
Improved documentation and minor bug fixes. With thanks to Jarod Roland and
Taylor Salo for contributions.

* DOC: Replace ``--clearenv`` with correct ``--cleanenv`` flag (1237) jarodroland
* DOC: De-indent to remove text from code block (1238) effigies
* TST: Add enhance-and-skullstrip regression tests (1074) effigies
* DOC: Clearly indicate that fMRIPrep requires Python 3.5+ (1249) oesteban
* MAINT: Update PR template (1239) effigies
* DOC: Set appropriate version in Zenodo citation (1250) oesteban
* DOC: Updating long description (1230) oesteban
* DOC: Add ME workflow description (1253) tsalo
* FIX: Add memory annotation to ROIPlot interface (1256) jdkent
* ENH: Write derivatives ``dataset_description.json`` (1247) effigies
* DOC: Enable table text wrap and link docstrings to code on GitHub (1258) tsalo
* DOC: Clarify language describing T1w image merging (1269) chrisfilo
* FIX: Accommodate new template formats (1273) effigies
* FIX: Permit overriding plugin config with CLI options (1272) effigies

-----------------------
A hotfix release for `1235
<https://github.com/nipreps/fmriprep/issues/1235>`_. Additionally,
notebooks have been synced with the latest version of that repository.

* FIX: Verify first word of ``_cmd`` in dependency check (1236)
* DOC: Add two missing references (1234)
* ENH: Allow turning off random seeding for ANTs brain extraction (919)