Fmriprep

--------------------------
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)

---------------------
This release comes with many updates to the documentation, a more lightweight
``SignalExtraction``, a new dynamic boilerplate and some new features from
Nipype.

* ENH: Use upstream ``afni.TShift`` improvements (1160)
* PIN: Nipype 1.1.1 (65078c9)
* ENH: Dynamic citation boilerplate (1024)
* ENH: Check Command Line dependencies before running (1044)
* ENH: Reimplement ``SignalExtraction`` (1170)
* DOC: Update copyright year to 2018 (1224)
* ENH: Enable ``-u`` (docker user/userid) flag in wrapper (1223)
* FIX: Corrects Dockerfile ``WORKDIR``. (1218)
* ENH: More specific errors for missing echo times (1221)
* ENH: Change ``WORKDIR`` of Docker image (1204)
* DOC: Update documentation related to contributions (1187)
* DOC: Additions to include before responding to reviews of the pre-print (1195)
* DOC: Improving documentation on using Singularity (1063)
* DOC: Add OHBM 2018 poster, presentation (1198)
* ENH: Replace ``InvertT1w`` with upstream ``Rescale(invert=True)`` (1161)

--------------------
This release incorporates Nipype improvements that should reduce the
chance of hanging if tasks are killed for excessive resource consumption.

Thanks to Elizabeth DuPre for documentation updates.

* DOC: Clarify how to reuse FreeSurfer derivatives (1189)
* DOC: Improve command line option documentation (1186, 1080)
* MAINT: Update core dependencies (1179, 1180)