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DOC: Changelog updates
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* Updates to release notes
* GitHub handles -> names
* Square brackets around PR tags
* Collate PRs into types
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effigies authored May 15, 2019
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Expand Up @@ -24,57 +24,58 @@ with the difference that more templates could be specified if needed, e.g., ::

Related anatomical preprocessing workflows from *sMRIPrep* have gone through
thorough revisions.
In particular, the brain extraction workflow now is implemented
in pure Nipype.
In particular, the brain extraction workflow now is implemented in pure Nipype.

Users will notice the addition of two new subsections in the reports generated by
*fMRIPrep*.
The first addition describes the accumulative variance explained by increasing numbers
of a/tComCor components.
The first addition describes the cumulative variance explained by successive a/tCompCor
components.
A second addition shows the correlations between the confounding regressors that
*fMRIPrep* writes to the corresponding file, and their correlation to the global signal.
Series 1.4 start with numerous improvements in the adoption of pyBIDS
to handle not only inputs, but also outputs and reportlets.

Series 1.4 increasingly relies on PyBIDS to handle not only inputs, but also outputs and
reporting.
The reports generation system has been deeply refactored to improve its generalizability
across BIDS-Apps and addressing some rendering problems (e.g., when resizing ICA-AROMA
components decompositions).
Finally, several maintenance activity and documentation updates complete a long
overdue series of changes to the codebase.

With thanks to @yarikoptic, @danlurie, @ariveradompenciel, @franklin-feingold,
@markushs, @anibalsolon, and @jdkent for contributions.

* FIX: Incorrect transforms being applied to aparc/asegs in standard space (#1636) @oesteban
* DOC: Improve appearance of parameter types in API docs (#1633) @anibalsolon
* ENH: add ``--skip-vols-num`` option (#1559) @jdkent
* FIX: Writing functional derivatives in standard spaces (#1632) @oesteban
* DOC: Confound enhancement documentation (#1625) @rciric
* FIX: Resampling of BOLD into standard spaces (#1627) @oesteban
* FIX: Re-enable correct versioning within container (#1623) @oesteban
* CI: Reduce pointless expenditures (#1614) @effigies
* DOC: Add FAQ, Tips, Tricks section to RTD (cont. #1601) (#1610) @franklin-feingold
* ENH: Reduce ``BSplineFieldmap`` memory usage (#1609) @effigies
* FIX: Update spline fitting distance for BOLD bias-field correction (#1603) @markushs
* CI: Use caches to pass data between jobs (#1608) @effigies
* MAINT: Consolidate build configuration in ``setup.cfg`` (#1607) @effigies
* DOC: Companion of #1596 + punctual improvements of docs (#1605) @oesteban
* ENH: Confound model enhancement (#1487, #1586) @rciric
* ENH: Allow multiple {non,}standard spaces (``--output-spaces``) (#1596) @oesteban
* CI: Build docs outside of container (#1606) @effigies
* ENH: Switch to the refactored report generation from NiWorkflows (#1599) @oesteban
* ENH: Force compression of derivative NIfTI volumes (#1600) @effigies
* FIX: Mount Nipype config file under new ``$HOME`` (#1602) @oesteban
* CI: Fix label on CI step "Skipping doc building job" (#1564) @ariveradompenciel
* ENH: Do not allow writing derivatives directly into the BIDS root folder (#1589) @oesteban
* MAINT: Progress bids-validator 1.2.3 (#1583) @yarikoptic
* PIN: ``nilearn!=0.5.0,!=0.5.1`` to avoid problems plotting mgz images (#1585) @oesteban
* FIX: Support 4D SBRefs when generating the bold reference (#1581) @oesteban
* DOC Add examples/clarify ``CONTRIBUTORS.md`` (#1566) @jdkent
* DOC: Add ``.bidsignore`` requirement to docs on lesion masks (#1574) @danlurie
* ENH: remove all prior existing citation files first (#1567) @yarikoptic
* DOC: Bump references of python3.6 to python3.7 (#1562) @jdkent
* FIX: Not having ``template`` as one ``--output-space`` crashes fMRIPrep (#1560) @oesteban
* MAINT: Group all 'finished running with errors' sentry messages (#1552) @chrisgorgo
* MAINT: Include hash of ``dataset_description.json`` in sentry metadata (#1553) @chrisgorgo
Finally, there were several updates to packaging, testing and documentation, which should
hopefully improve the experience for new users and contributors.

With thanks to Yaroslav Halchenko, Dan Lurie, Adriana Rivera-Dompenciel, Franklin Feingold,
Markus Sneve, Anibal Heinsfeld, and James Kent for contributions.

* [FIX] Incorrect transforms being applied to aparc/asegs in standard space (#1636) @oesteban
* [FIX] Writing functional derivatives in standard spaces (#1632) @oesteban
* [FIX] Resampling of BOLD into standard spaces (#1627) @oesteban
* [FIX] Re-enable correct versioning within container (#1623) @oesteban
* [FIX] Update spline fitting distance for BOLD bias-field correction (#1603) @markushs
* [FIX] Mount Nipype config file under new ``$HOME`` (#1602) @oesteban
* [FIX] Not having ``template`` as one ``--output-space`` crashes fMRIPrep (#1560) @oesteban
* [ENH] Add ``--skip-vols-num`` option (#1559) @jdkent
* [ENH] Reduce ``BSplineFieldmap`` memory usage (#1609) @effigies
* [ENH] Confound model enhancement (#1487, #1586) @rciric
* [ENH] Allow multiple {non,}standard spaces (``--output-spaces``) (#1596) @oesteban
* [ENH] Switch to the refactored report generation from NiWorkflows (#1599) @oesteban
* [ENH] Force compression of derivative NIfTI volumes (#1600) @effigies
* [ENH] Do not allow writing derivatives directly into the BIDS root folder (#1589) @oesteban
* [ENH] Support 4D SBRefs when generating the bold reference (#1581) @oesteban
* [ENH] Remove pre-existing citation files before running (#1567) @yarikoptic
* [DOC] Improve appearance of parameter types in API docs (#1633) @anibalsolon
* [DOC] Confound enhancement documentation (#1625) @rciric
* [DOC] Add FAQ, Tips, Tricks section to RTD (cont. #1601) (#1610) @franklin-feingold
* [DOC] Companion of #1596 + punctual improvements of docs (#1605) @oesteban
* [DOC] Add examples/clarify ``CONTRIBUTORS.md`` (#1566) @jdkent
* [DOC] Add ``.bidsignore`` requirement to docs on lesion masks (#1574) @danlurie
* [DOC] Bump references of python3.6 to python3.7 (#1562) @jdkent
* [MAINT] Consolidate build configuration in ``setup.cfg`` (#1607) @effigies
* [MAINT] Progress bids-validator 1.2.3 (#1583) @yarikoptic
* [MAINT] Pin ``nilearn!=0.5.0,!=0.5.1`` to avoid problems plotting mgz images (#1585) @oesteban
* [MAINT] Group all 'finished running with errors' sentry messages (#1552) @chrisgorgo
* [MAINT] Include hash of ``dataset_description.json`` in sentry metadata (#1553) @chrisgorgo
* [CI] Reduce pointless expenditures (#1614) @effigies
* [CI] Use caches to pass data between jobs (#1608) @effigies
* [CI] Build docs outside of container (#1606) @effigies
* [CI] Fix label on CI step "Skipping doc building job" (#1564) @ariveradompenciel


1.3.2 (March 18, 2019)
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