Fmriprep

-------------------------
Bug-fix release in the 1.5.x series.

* FIX: Integrate fix for nipreps/sdcflows77 (pin niworkflows-1.0.3, sdcflows-1.0.3) oesteban

-------------------------
The last patch release of the 1.5.x series containing features.
As of 1.5.4, patch releases will only contain bug fixes, maintenance
tasks and minor documentation revisions.

* FIX: Do not run STC if SliceTiming metadata is set but empty (1854) oesteban
* FIX: Link to EPINorm issue in README (1903) adelavega
* FIX: Respect ``--dummy-scans 0`` (1908) jdkent
* ENH: Upgrade SDCFlows to new API (1.0.0) (1886) oesteban
* ENH: Add ``--fs-subjects-dir`` flag (1901) effigies
* DOC: Improving accessibility of confounds description (1877) kfinc
* MAINT: Ensure data is packaged in sdist (1902) effigies
* MAINT: Remove deprecated command-line arguments (1909) mgxd

------------------------
Bug-fix release in the 1.5.x series.

* FIX: Ensure data type of masked image matches T1.mgz (nipreps/niworkflows430) effigies

-------------------------
After an arduous walk through release-candidates, release 1.5.1 includes a new release of
Nipype which addresses the problems related to *results* files many users have been experiencing.

With thanks to Marc Bue, Alejandro De La Vega, Tailor Salo, Asier Erramuzpe and Soichi Hayashi.

* FIX: Treat missing field maps as empty list instead of ``None`` (1820) tsalo
* FIX: Raise error if ``work_dir`` is a child of ``bids_dir`` (1860) adelavega
* FIX: Change ICA-AROMA filenames to fit current naming scheme (1861) jdkent
* FIX: Update code-server in the Dockerfile_devel (1852) erramuzpe
* FIX: Do not generate ``desc-smoothAROMAnonaggr_bold`` conversions on standard spaces (1838) oesteban
* FIX: Skip plotting step of ICA-AROMA (1834) oesteban
* FIX: Error during version check trying to access read-only file systems (1830) oesteban
* FIX: Bad results files loads; PIN: nipy/nipype master (1806) effigies
* FIX: Adding comma to outputnode in init_func_preproc_wf (1795) marcbue
* FIX: Ignore sourcedata and derivatives when fetching data (1788) effigies
* ENH: Added skip_citation_process flag to skip processing ``citation.md`` (1876) soichih
* ENH: Restore ``space-MNI152NLin6Asym`` for AROMA denoised outputs (1839) oesteban
* ENH: Confounds metadata (1708) rciric
* DOC: Remove OpenNeuro badge (1862) adelavega
* DOC: Improve documentation about TemplateFlow and Containers (1802) oesteban
* DOC: Add ``VERSION`` argument to docker build instructions (1797) effigies
* DOC: Revise docstrings of workflows for correct parsing with napoleon 1882 (oesteban)
* CI: Use recent Python image to build packages (1790) effigies
* MAINT: Update to the new API of *sMRIPrep* (1879) adelavega
* MAINT: Update ``CONTRIBUTING.md`` inspired by *dMRIPrep*'s (1853) oesteban
* MAINT: Enable circleci-artifacts-redirector (1857) effigies
* MAINT: Cleaning up dependencies (1832) oesteban
* MAINT: Pin Python 3.7.4 in CircleCI's ``build_docs`` (1836) oesteban
* MAINT: Purge Cython and depend on SDCflows (1792) effigies
* MAINT: Container images - cleanup ``$HOME`` in docker build (1768) oesteban

off from *fMRIPrep* codebase.
*PyBIDS* 0.9.x has a better handling of the indexed dataset that will permit some
optimizations to *fMRIPrep*'s memory fingerprint.
*SDCflows* now are found at `nipreps/sdcflows <https://github.com/nipreps/sdcflows>`__,
and have been split to allow a more granular and thorough testing in collaboration
with M. Cieslak, A. Adebimpe, and T. Satterthwaite.
Some other bugfixes, improvements to the documentation and minor features are also
shipped with the new release.
With thanks to Ursula Tooley, Sebastian Urchs and Gabriel A. Devenyi for contributions.

* FIX: Minor improvements for templateflow installation in Docker images (1764) oesteban
* FIX: Passing surface template keywords into carpetplot workflow (1755) oesteban
* FIX: Postpone ``pandoc`` conversion of boilerplate after workflow has fully run (1710) oesteban
* FIX: Use MNI152NLin2009cAsym for SDC if no templates are specified (1703) effigies
* FIX: Correct BOLD-T1w registration description if DoF != 9 (1701) effigies
* ENH: Set up code-server docker recipe for interactive development (1730) jdkent
* ENH: Make fmriprep print defaults for arguments with help (1735) gdevenyi
* ENH: Add check for updates and check whether version has been flagged. (1715) oesteban
* ENH: Add TaskName metadata to BOLD outputs (1714) effigies
* REF: Separate *SDCflows* from *fMRIPrep* (1670) oesteban
* DOC: Adding *fMRIPrep* benchmark info to FAQs (1759) surchs
* DOC: Update ``.zenodo.json`` (1732) utooley
* DOC: Add link to documentation in help of ``--output-spaces`` argument (1722) oesteban
* DOC: adding recon-all issue to faq (1622) franklin-feingold
* DOC: Add copyright waiver to boilerplate and reviewer note to docs (1691) effigies
* MAINT: niworkflows and nipype to use latest ``N4BiasFieldCorrection`` (1752) oesteban
* MAINT: Bump pybids and nipype dependencies (1744) effigies
* MAINT: Move regression tests of EPI masks over to Niworkflows (1716) oesteban
* MAINT: Remove old ``extensions`` entity selector for PyBIDS queries (1707) oesteban
* MAINT: Use PyBIDS 0.9.x via niworkflows/smriprep PRs (1695) effigies

1.4.x series (May 2019)
=======================

--------------------
As of 1.4.1, the new infant and pediatric templates added to TemplateFlow are available to
brain extraction and spatial normalization.
Containers do not set the ``TEMPLATEFLOW_HOME`` environment variable anymore, allowing
increased flexibility when running them (especially Singularity, for which the filesystem
is generally set read-only).
Additionally, BOLD files in native space can be generated and a minor bug related to the
handling of FreeSurfer outputs have been included.

* FIX: Finalizing support for new templates and their command line modifiers (1671) oesteban
* FIX: Do not set ``TEMPLATEFLOW_HOME`` (1669) oesteban
* FIX: FreeSurfer failed without adding some ``fs*`` to ``--output-spaces`` (1643) oesteban
* ENH: Show informative warning for phase1/2 type of fieldmaps (1689) oesteban
* ENH: Allow template modifiers (a la ``--output-spaces``) in skull-stripping (1666) oesteban
* ENH: Write outputs in native-BOLD space (1646) oesteban
* DOC: Add WHT to Zenodo (1683) wiheto