--------------------
The new 1.4 series include several new features, several maintenance patches,
and numerous bugfixes.
The largest change to *fMRIPrep*'s interface is the new ``--output-spaces``
argument that allows running spatial normalization to one or more standard
templates, and also to indicate that data preprocessed and resampled to the
individual's anatomical space should be generated.
The implementation of this option will be completed in future releases to include
new nonstandard spaces (e.g., this BOLD run's native space) and custom templates
providing a path.
For example, the following *fMRIPrep* options: ::
--template MNI152NLin6Asym --output-space template T1w fsaverage5 ----template-resampling-grid 2mm
now would be accomplished with: ::
--output-spaces MNI152NLin6Asym:res-2 anat fsaverage:den-10k
with the difference that more templates could be specified if needed, e.g., ::
--output-spaces MNI152NLin6Asym:res-2 anat fsaverage:den-10k MNI152NLin2009cAsym:native
Related anatomical preprocessing workflows from *sMRIPrep* have gone through
thorough revisions.
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 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 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, 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 ``--dummy-scans`` 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.x series (March 2019)
=========================