Tags

21.0.1 (January 24, 2022)

Bug-fix release in the 21.0.x series.

This release re-enables reverse-PE EPI fieldmaps, i.e. EPIs acquired with the
opposite phase-encoding direction to a BOLD series.
Additionally, the ``--use-syn-sdc`` option will now error by default if no
``PhaseEncodingDirection`` can be found for a BOLD series. To reduce this to
a warning, use ``--use-syn-sdc warn``. SyN-SDC will NOT be run, but the workflow
will proceed.

* FIX: Create single fmap_select_std node for use with all ANAT estimators (#2692)
* FIX: Re-enable reverse-PE EPI fieldmaps (#2684)
* FIX: Pass boolean use_syn_sdc to find_estimators (#2685)
* FIX: Ensure AROMA inputs are uncompressed if --low-mem (#2657)
* ENH: Add ``--topup-max-vols`` flag to control TOPUP runtime (#2688)
* ENH: Allow ``--use-syn-sdc`` to take a "warn" option to avoid exiting when PE dir is unavailable (#2680)
* RF: Add extension field to differentiate from upcoming templates (#2613)
* WRAPPER: Map ``--bids-filter-file``\s into Docker container (#2691)
* MNT: Silence warning from pybids; list packaging as dependency (#2689)
* MNT: Add netbase to Docker image to ensure correct datalad operation (#2682)
* MNT: Restore nitime to requirements, necessary for DVARS (#2678)

20.2.7 (January 24, 2022)

Bug-fix release in the 20.2.x LTS series.

  * FIX: Clarify phase encoding direction, rather than axis (#2690)
  * FIX: Ensure AROMA inputs are uncompressed if --low-mem (#2657)
  * FIX: Add ``-basescale 1`` parameter to avoid ``flirt`` scaling (#2624)
  * WRAPPER: Map ``--bids-filter-file``\s into Docker container (#2691)
  * MNT: Add netbase to Docker image to ensure correct datalad operation (#2682)

21.0.0 (December 13, 2021)
==========================
A new series is finally here!

Some highlights of this version's new features include a substantial rework of fMRIPrep's
susceptibility distortion correction (including the addition of FSL's `topup` as the new
default PEPOLAR correction technique), improved flexibility for multiecho scans, and
dependency version upgrades within the Docker environment.

.. note::

  To follow BIDS Derivatives more closely, *fMRIPrep*'s default output layout has changed.
  To enable the legacy layout, use the `--output-layout legacy` flag.
  For more information, please see https://fmriprep.org/en/latest/outputs.html#layout

.. caution::

    As with all minor version increments, working directories
    from previous versions **should not be reused**.

Thank you for using *fMRIPrep*!
If you encounter any issues with this release, please let us know
by posting an issue on our GitHub page!

A full list of changes can be found below.

* DOC: Remove mention to ``epidewarp.fsl`` from ``NOTICE`` (#2629)
* DOC: Update description of output layout, add discussion of legacy mode (#2646)
* DOC: ME | Add missing output to documentation, improve boilerplate (#2608)
* DOC: Add --index-metadata to `pybids layout` faq (#2546)
* DOC: Add warning about slice timing correction in output documentation. (#2502)
* DOC: Update sample report (#2519)
* DOC: Refactor README and citing information (#2474)
* DOC: Point documentation at *SDCFlows* and remove SDC section (#2470)\
* DOC: Transfer duplicated documentation to www.nipreps.org (#2469)
* DOC: Better explanation on how spike regressors are generated (#2465)
* DOC: Clarify that ``res-2`` entity does not mean 2mm (#2466)
* DOC: adds --mem metavar (#2378)
* DOC: skull stripping is forced by default (#2345)
* DOCKER: Shrink Docker image size (#2551)
* DOCKER: Strip ABI tag from libQt5Core.so.5 to prevent Singularity failures (#2535)
* ENH: Make bids the default output layout option (#2555)
* ENH: Mask multi-echo data with reference mask instead of echo-specific masks (#2349)
* ENH: Replace initial FLIRT with mri_coreg, use -basescale 1 for FLIRT-BBR (#2625)
* ENH: Add flag for STC reference time and set in all cases (#2520)
* ENH: Use ``BIDSLayoutIndexer`` and do not index unnecessary modalities (#2494)
* ENH: Allow users to download templateflow templates to directory (#2482)
* ENH: Detect 3D & too-short BOLD series, warn and skip run's workflow building (#2461)
* ENH: Modernize Dockerfile (#2409) (#2270)
* ENH: Leverage SDCFlows 2.x API (#2392)
* ENH: Tedana-friendly ME derivatives (#2575)
* ENH: Better integration of *SDCFlows*' unwarping (#2576)
* ENH: Refactor workflow to adopt *SDCFlows*' new correction workflow (#2547)
* FIX: Threshold boldref resampled values to be non-negative (#2630)
* FIX: Restore SyN-SDC (#2530)
* FIX: Confusing I/O field ``bold_mask`` in bold-to-bold resampling workflow (#2611)
* FIX: ME | Revise SDC compute graph (#2610)
* FIX: Propagate the SDC warp to resampling node also with ME (#2609)
* FIX: Optimize build job on CircleCI (#2605)
* FIX: Minor multiecho issues (#2574)
* FIX: Missing numpy import (#2533)
* FIX: Avoid eager imports from *NiWorkflows* causing API breaks (#2495)
* FIX: Split aCompCor into aCompCor, cCompCor, wCompCor (#2523)
* FIX: Avoid unnecessary connections based on branching logic (#2508)
* FIX: Permit missing TR to show PyBIDS error at workflow construction time (#2513)
* FIX: Simplify STC logic for too short BOLD series (#2489)
* FIX: Catch FreeSurfer error related to FIPS being enabled (#2490)
* FIX: ``DerivativesDataSink`` nondeterministic checksums fixed with ``niworkflows=~1.3.4`` (#2458)
* FIX: Address dependency incompatibilities by pinning specific packages (#2463)
* FIX: Unprotected import of ``sentry_sdk``, which is not a dependency (#2460)
* FIX: Clarify phase encoding direction, rather than axis (#2302)
* MAINT: Reduce redundant processing of ds005 (#2649)
* MAINT: Finalize the work we started with the refactor of the Docker image (#2601)
* MAINT: Run full workflows on tags (#2593)
* MAINT: Stage Python environment of Docker image from nipreps/miniconda (#2581)
* MAINT: Stop NeuroDebian dependency in Dockerfile (#2578)
* MAINT: Run pytest through GitHub actions (#2529)
* MAINT: Relicense +20.3.x - BSD-3-Clause -> Apache License 2.0 (#2325)
* MAINT: Add missing OASIS30 WM/BS probsegs (#2471)
* MAINT: Update BIDS validator to 1.8.0 (#2443)
* MAINT: Address the problems of a sloppy merge (#2468)
* MAINT: Containers - remove ``/root/.npm`` (#2464)
* MAINT: Remove traces of Xenial base (#2459)
* MAINT: Revise CircleCI's cache tags to avoid mixups between builds (#2457)
* MAINT: Back port CircleCI configuration from dev branch (#2456)
* MAINT: Increase minimum tedana version (#2366)
* MAINT: Docker hub has disabled password authentication (#2448)
* MAINT: Add Lea Waller to ``contributors.json`` (#2304)
* MAINT: Move away from nearly deprecated images (#2295)
* MAINT: Migrate from poldracklab to nipreps orgs (#2290)
* MAINT: Ease CI packaging tests (#2472)
* RF/FIX: Iterate over echo indices, not filenames, simplifying iteration logic (#2651)

21.0.0rc2 (November 18, 2021)
-----------------------------
* DOC: ME | Add missing output to documentation, improve boilerplate (#2608)
* ENH: Tedana-friendly ME derivatives (#2575)
* ENH: Better integration of *SDCFlows*' unwarping (#2576)
* ENH: Refactor workflow to adopt *SDCFlows*' new correction workflow (#2547)
* FIX: Restore SyN-SDC (#2530)
* FIX: Confusing I/O field ``bold_mask`` in bold-to-bold resampling workflow (#2611)
* FIX: ME | Revise SDC compute graph (#2610)
* FIX: Propagate the SDC warp to resampling node also with ME (#2609)
* FIX: Optimize build job on CircleCI (#2605)
* FIX: Minor multiecho issues (#2574)
* MAINT: Finalize the work we started with the refactor of the Docker image (#2601)
* MAINT: Run full workflows on tags (#2593)
* MAINT: Stage Python environment of Docker image from nipreps/miniconda (#2581)
* MAINT: Stop NeuroDebian dependency in Dockerfile (#2578)

20.2.6 (October 27, 2021)
=========================
Patch release in the 20.2.x LTS series.

This release includes an updated runtime environment for Docker/Singularity users.
This environment includes a newer release of `indexed_gzip`, fixing `CrcError`s previously encountered.

  * CI: Run full workflows on tags (#2593)
  * RF: Add extension field to differentiate from upcoming templates (#2613)

20.2.5 (October 12, 2021)

Bug-fix release in the 20.2.x LTS series.

This release includes a fix to `--slice-time-ref` parsing. Also, some
issues in anatomical processing are resolved, including poorly-interpolated
labels in aseg segmentations, and probabilistic segmentations have reverted
to FAST.

  * FIX: --slice-time-ref option parsing (#2573)
  * CI: Add style checks (missing since Travis got throttled) (#2570)

20.2.4 (October 04, 2021)

Bug-fix release in the 20.2.x LTS series.

This release includes some fixes to minor bugs, and includes enhancements
to allow the user to specify a different slice-timing-correction (STC) target.

Each BOLD series will contain ``SliceTimingCorrected`` metadata to indicate
whether STC was performed. If performed, the ``StartTime`` metadata field will
be set to indicate the onset time of the BOLD series.

  * FIX: Avoid unnecessary connections based on branching logic (#2508)
  * FIX: Permit missing TR to show PyBIDS error at workflow construction time (#2513)
  * [BACKPORT] FIX: Catch FreeSurfer error related to FIPS being enabled (#2490)
  * ENH: Use ``BIDSLayoutIndexer`` and do not index unnecessary modalities (#2494)
  * [BACKPORT] ENH: Slice-timing correction improvements (#2565)

21.0.0rc1 (September 21, 2021)
=============================
A new release candidate of the upcoming 21.0.x series.
Included are some vital bug fixes, a drastic decrease in Docker image size, and a change in the default output directory structure.

* DOC: Add --index-metadata to `pybids layout` faq (#2546)
* DOC: Add warning about slice timing correction in output documentation. (#2502)
* ENH: Make bids the default output layout option (#2555)
* ENH: Mask multi-echo data with reference mask instead of echo-specific masks (#2349)
* FIX: Missing numpy import (#2533)
* DOCKER: Shrink Docker image size (#2551)
* DOCKER: Strip ABI tag from libQt5Core.so.5 to prevent Singularity failures (#2535)
* MAINT: Run pytest through GitHub actions (#2529)

21.0.0rc0 (September 2, 2021)
=============================
The first release candidate for a new major version of fMRIPrep!

Changes:
  * DOC: Update sample report (#2519)
  * DOC: Refactor README and citing information (#2474)
  * DOC: Point documentation at *SDCFlows* and remove SDC section (#2470)\
  * DOC: Transfer duplicated documentation to www.nipreps.org (#2469)
  * DOC: Better explanation on how spike regressors are generated (#2465)
  * DOC: Clarify that ``res-2`` entity does not mean 2mm (#2466)
  * DOC: adds --mem metavar (#2378)
  * DOC: skull stripping is forced by default (#2345)
  * ENH: Add flag for STC reference time and set in all cases (#2520)
  * ENH: Use ``BIDSLayoutIndexer`` and do not index unnecessary modalities (#2494)
  * ENH: Allow users to download templateflow templates to directory (#2482)
  * ENH: Detect 3D & too-short BOLD series, warn and skip run's workflow building (#2461)
  * ENH: Modernize Dockerfile (#2409) (#2270)
  * ENH: Leverage SDCFlows 2.x API (#2392)
  * FIX: Avoid eager imports from *NiWorkflows* causing API breaks (#2495)
  * FIX: Split aCompCor into aCompCor, cCompCor, wCompCor (#2523)
  * FIX: Avoid unnecessary connections based on branching logic (#2508)
  * FIX: Permit missing TR to show PyBIDS error at workflow construction time (#2513)
  * FIX: Simplify STC logic for too short BOLD series (#2489)
  * FIX: Catch FreeSurfer error related to FIPS being enabled (#2490)
  * FIX: ``DerivativesDataSink`` nondeterministic checksums fixed with ``niworkflows=~1.3.4`` (#2458)
  * FIX: Address dependency incompatibilities by pinning specific packages (#2463)
  * FIX: Unprotected import of ``sentry_sdk``, which is not a dependency (#2460)
  * FIX: Clarify phase encoding direction, rather than axis (#2302)
  * MAINT: Relicense +20.3.x - BSD-3-Clause -> Apache License 2.0 (#2325)
  * MAINT: Add missing OASIS30 WM/BS probsegs (#2471)
  * MAINT: Update BIDS validator to 1.8.0 (#2443)
  * MAINT: Address the problems of a sloppy merge (#2468)
  * MAINT: Containers - remove ``/root/.npm`` (#2464)
  * MAINT: Remove traces of Xenial base (#2459)
  * MAINT: Revise CircleCI's cache tags to avoid mixups between builds (#2457)
  * MAINT: Back port CircleCI configuration from dev branch (#2456)
  * MAINT: Increase minimum tedana version (#2366)
  * MAINT: Docker hub has disabled password authentication (#2448)
  * MAINT: Add Lea Waller to ``contributors.json`` (#2304)
  * MAINT: Move away from nearly deprecated images (#2295)
  * MAINT: Migrate from poldracklab to nipreps orgs (#2290)
  * MAINT: Ease CI packaging tests (#2472)

20.2.3

Patch release in the 20.2.x LTS series.
Addresses minimal problems in some edge-cases, overall improves the documentation and infrastructure.
Exercises some maintenance operations addressing problems surfaced when the previous tag 20.2.2 was released.

  * FIX: Address the problems of a sloppy merge (#2468)
  * FIX: ``DerivativesDataSink`` nondeterministic checksums fixed with ``niworkflows=~1.3.4`` (#2458)
  * FIX: Address dependency incompatibilities by pinning specific packages (#2463)
  * FIX: Unprotected import of ``sentry_sdk``, which is not a dependency (#2460)
  * ENH: Detect 3D & too-short BOLD series, warn and skip run's workflow building (#2461)
  * DOC: Transfer duplicated documentation to www.nipreps.org (#2469)
  * DOC: Better explanation on how spike regressors are generated (#2465)
  * DOC: Clarify that ``res-2`` entity does not mean 2mm (#2466)
  * MAINT: Containers - remove ``/root/.npm`` (#2464)
  * MAINT: Back port CircleCI configuration from dev branch (#2456)

20.1.4

Hotfix release addressing a bug on *fMRIPrep*'s resampling to standard spaces.
This release also includes some maintenance changes handling old versions of software.

  * FIX: Feed *NiTransforms* with LTAs of type RAS2RAS (#2444)
  * MAINT: Pin ``svgutils==0.3.1`` for the 20.1.x series (#2450)
  * MAINT: Keep pip and setuptools with support for Python 3.5 (#2449)
  * MAINT: Some dependencies cannot be left unpinned (#2446)

20.2.2

Hot-fix release in the 20.2.x LTS series.
Addressing a bug on *fMRIPrep*'s resampling to standard spaces (#2444).
In addition, some other relevant bug-fixes and performance improvements are built in this patch.

* FIX: Feed *NiTransforms* with LTAs of type RAS2RAS (#2444)
* FIX: Add some clarity to ``BrokenProcessPool`` failures (#2436)
* FIX: Fall-back to initializing workflow in main process (#2435)
* FIX: Raise informative error when duplicate subworkflows are added (#2434)
* FIX: Non-existing path or JSON syntax error for ``--bids-filter-file`` should raise on error (#2331)
* FIX: Ignore SBRef files if ``--ignore sbref`` is passed (#2370)
* ENH: Relax requirement for *PyBIDS* databases to exist (#2429)
* ENH: Improve ``_get_series_len`` performance (#2406)
* ENH: Set and track NumPy's random seed (#2400)
* DOC: Skull-stripping is forced by default (#2430)
* MAINT: Pin ``nilearn==0.6.2`` (#2427)
* MAINT: Pin ``tedana==0.0.9a1`` for LTS branch (#2403)
* MAINT: Failing CI (#2401)

20.2.1 (November 06, 2020)

Bug-fix release in the 20.2.x LTS series.

This release adds missing metadata to GIFTI and CIFTI-2 derivatives and fixes a logging
bug affecting a small number of datasets.

Additionally the ``--output-layout bids`` flag will now output fMRIPrep derivatives directly
into the output directory, nesting FreeSurfer derivatives by default in
``<output>/sourcedata/freesurfer``. This layout allows the output root to be a valid BIDS
Derivatives dataset, simplifying data management and provenance tracking with content tracking
tools, such as `DataLad <https://handbook.datalad.org/>`__. This layout will likely become the
default in future release series.

  * ENH: Output TaskName and timing metadata for all resampled BOLD series (#2320)
  * ENH: Add --output-layout CLI option to enable BIDS (YODA) mode (#2303)
  * ENH: Add Docker authentication to increase pull rate limit (#2316)
  * FIX: Specify logger for warning (#2298)

20.2.0 (September 28, 2020)

With this third minor release series of 2020,
the first *fMRIPrep LTS* (*long-term support*) is finally here!

This release contains a number of bug-fixes and enhancements mostly
related to easing the maintenance, anticipating patch-release breaking
changes to ensure a longstanding LTS, and addressing some run-to-run
repeatability problems of the CompCor implementation.

Thank you for using *fMRIPrep*!
If you encounter any issues with this release, please let us know
by posting an issue on our GitHub page!

A full list of changes can be found below.

* FIX: Pin *NiWorkflows* 1.3.1 and *sMRIPrep* 0.7.0rc2, including bugfix for INU-correction failures (nipreps/niworkflows#567)
* FIX: Get missing ``probseg`` file from MNI152NLin2009cAsym (#2271)
* FIX: Restore ``--ignore t2w/flair`` options (#2260)
* FIX: Revise the reproducibility of *CompCor* masks (#2130)
* FIX: Simplify transform aggregation in resampling, pass identity transforms for multi-echo cases (#2239)
* FIX: Skip the T1w check if ``--anat-derivatives`` is provided. (#2201)
* FIX: Storing ``--bids-filters`` within config file (#2177)
* FIX: Revise multi-echo reference generation, permitting using SBRefs too (#1803)
* FIX: *FreeSurfer* license manipulation & canary
* ENH: Output CompCor masks if ``--debug compcor`` is passed (#2248)
* ENH: Conform to BIDS Derivatives as of BIDS 1.4.0 (#2223)
* ENH: Reuse config (#2240)
* ENH: Save BOLD-anatomical transforms to derivatives folder (#2233)
* ENH: Leverage BIDSLayout's ``database_path`` (#2203)
* ENH: Add ``--no-tty`` option to ``fmriprep-docker.py`` (#2204)
* ENH: Report number of echoes in BOLD summary. (#2184)
* ENH: Ensure *NiPype* telemetry is just pinged once (#2168)
* DOC: Add FAQ entry for using pre-indexed layouts (#2256)
* DOC: Update reference in "Refinement of Brain Mask" description (#2215)
* DOC: List *TemplateFlow* templates that need to be prefetched (#2196)
* DOC: Update references to https://github.com/nipreps (#2191)
* DOC: Pin *NiPype* with new Sphinx extension syntax (#2092)
* MAINT: Upgrade ANTs to 2.3.3 in ``Dockerfile`` (9512086)
* MAINT: Track #2269 and #2269, bug-fixes on the 20.1.x series
* MAINT: Remove derivatives from layout index ignores (#2258)
* MAINT: Track #2252 from 20.1.x series (#2253)
* MAINT: Silence *PyBIDS* warning by setting extension mode (#2250)
* MAINT: Drop CircleCI docs build (#2247)
* MAINT: Pin latest *NiPreps* (#2244)
* MAINT: Update ``setup.cfg`` (flake8 and pytest) (#2183)
* MAINT: Delete release-drafter (#2169)
* MAINT: Track bug-fix release on the 20.1.x series (#2165)
* MAINT: Remove auto-comment bot (#2166)
* MAINT: Improve the questions on the bug-report template (#2158)

20.2.0rc2

With this third minor release series of 2020,
the first *fMRIPrep LTS* (*long-term support*) is finally here!

This release contains a number of bug-fixes and enhancements mostly
related to easing the maintenance, anticipating patch-release breaking
changes to ensure a longstanding LTS, and addressing some run-to-run
repeatability problems of the CompCor implementation.

.. admonition:: Long-Term Support (LTS)

    *fMRIPrep* 20.2 LTS introduces the `long-term support program
    <https://www.nipreps.org/devs/releases/#long-term-support-series>`__.
    This LTS version will be kindly steered and maintained by
    the group of Dr. Basile Pinsard and Prof. Pierre Bellec at
    `CRIUGM <http://www.criugm.qc.ca/>`__, (Université de Montréal).
    The LTS is planned for a window of 4 years of support (i.e., until
    September 2024).

.. caution::

    As with all minor version increments, working directories
    from previous versions **should not be reused**.

Thank you for using *fMRIPrep*!
If you encounter any issues with this release, please let us know
by posting an issue on our GitHub page!

A full list of changes can be found below.

* FIX: Pin *NiWorkflows* 1.3.1 and *sMRIPrep* 0.7.0rc2, including bugfix for INU-correction failures (nipreps/niworkflows#567)
* FIX: Get missing ``probseg`` file from MNI152NLin2009cAsym (#2271)
* FIX: Restore ``--ignore t2w/flair`` options (#2260)
* FIX: Revise the reproducibility of *CompCor* masks (#2130)
* FIX: Simplify transform aggregation in resampling, pass identity transforms for multi-echo cases (#2239)
* FIX: Skip the T1w check if ``--anat-derivatives`` is provided. (#2201)
* FIX: Storing ``--bids-filters`` within config file (#2177)
* FIX: Revise multi-echo reference generation, permitting using SBRefs too (#1803)
* FIX: *FreeSurfer* license manipulation & canary
* ENH: Output CompCor masks if ``--debug compcor`` is passed (#2248)
* ENH: Conform to BIDS Derivatives as of BIDS 1.4.0 (#2223)
* ENH: Reuse config (#2240)
* ENH: Save BOLD-anatomical transforms to derivatives folder (#2233)
* ENH: Leverage BIDSLayout's ``database_path`` (#2203)
* ENH: Add ``--no-tty`` option to ``fmriprep-docker.py`` (#2204)
* ENH: Report number of echoes in BOLD summary. (#2184)
* ENH: Ensure *NiPype* telemetry is just pinged once (#2168)
* DOC: Add FAQ entry for using pre-indexed layouts (#2256)
* DOC: Update reference in "Refinement of Brain Mask" description (#2215)
* DOC: List *TemplateFlow* templates that need to be prefetched (#2196)
* DOC: Update references to https://github.com/nipreps (#2191)
* DOC: Pin *NiPype* with new Sphinx extension syntax (#2092)
* MAINT: Upgrade ANTs to 2.3.3 in ``Dockerfile`` (9512086)
* MAINT: Track #2269 and #2269, bug-fixes on the 20.1.x series
* MAINT: Remove derivatives from layout index ignores (#2258)
* MAINT: Track #2252 from 20.1.x series (#2253)
* MAINT: Silence *PyBIDS* warning by setting extension mode (#2250)
* MAINT: Drop CircleCI docs build (#2247)
* MAINT: Pin latest *NiPreps* (#2244)
* MAINT: Update ``setup.cfg`` (flake8 and pytest) (#2183)
* MAINT: Delete release-drafter (#2169)
* MAINT: Track bug-fix release on the 20.1.x series (#2165)
* MAINT: Remove auto-comment bot (#2166)
* MAINT: Improve the questions on the bug-report template (#2158)

20.2.0rc1

With this third minor release series of 2020,
the first *fMRIPrep LTS* (*long-term support*) is finally here!

This release contains a number of bug-fixes and enhancements mostly
related to easing the maintenance, anticipating patch-release breaking
changes to ensure a longstanding LTS, and addressing some run-to-run
repeatability problems of the CompCor implementation.

.. admonition:: Long-Term Support (LTS)

    *fMRIPrep* 20.2 LTS introduces the `long-term support program
    <https://www.nipreps.org/devs/releases/#long-term-support-series>`__.
    This LTS version will be kindly steered and maintained by
    the group of Dr. Basile Pinsard and Prof. Pierre Bellec at
    `CRIUGM <http://www.criugm.qc.ca/>`__, (Université de Montréal).
    The LTS is planned for a window of 4 years of support (i.e., until
    September 2024).

.. caution::

    As with all minor version increments, working directories
    from previous versions **should not be reused**.

Thank you for using *fMRIPrep*!
If you encounter any issues with this release, please let us know
by posting an issue on our GitHub page!

A full list of changes can be found below.

* FIX: Get missing ``probseg`` file from MNI152NLin2009cAsym (#2271)
* FIX: Restore ``--ignore t2w/flair`` options (#2260)
* FIX: Revise the reproducibility of *CompCor* masks (#2130)
* FIX: Simplify transform aggregation in resampling, pass identity transforms for multi-echo cases (#2239)
* FIX: Skip the T1w check if ``--anat-derivatives`` is provided. (#2201)
* FIX: Storing ``--bids-filters`` within config file (#2177)
* FIX: Revise multi-echo reference generation, permitting using SBRefs too (#1803)
* FIX: *FreeSurfer* license manipulation & canary
* ENH: Output CompCor masks if ``--debug compcor`` is passed (#2248)
* ENH: Conform to BIDS Derivatives as of BIDS 1.4.0 (#2223)
* ENH: Reuse config (#2240)
* ENH: Save BOLD-anatomical transforms to derivatives folder (#2233)
* ENH: Leverage BIDSLayout's ``database_path`` (#2203)
* ENH: Add ``--no-tty`` option to ``fmriprep-docker.py`` (#2204)
* ENH: Report number of echoes in BOLD summary. (#2184)
* ENH: Ensure *NiPype* telemetry is just pinged once (#2168)
* DOC: Add FAQ entry for using pre-indexed layouts (#2256)
* DOC: Update reference in "Refinement of Brain Mask" description (#2215)
* DOC: List *TemplateFlow* templates that need to be prefetched (#2196)
* DOC: Update references to https://github.com/nipreps (#2191)
* DOC: Pin *NiPype* with new Sphinx extension syntax (#2092)
* MAINT: Track #2269 and #2269, bug-fixes on the 20.1.x series
* MAINT: Remove derivatives from layout index ignores (#2258)
* MAINT: Track #2252 from 20.1.x series (#2253)
* MAINT: Silence *PyBIDS* warning by setting extension mode (#2250)
* MAINT: Drop CircleCI docs build (#2247)
* MAINT: Pin latest *NiPreps* (#2244)
* MAINT: Update ``setup.cfg`` (flake8 and pytest) (#2183)
* MAINT: Delete release-drafter (#2169)
* MAINT: Track bug-fix release on the 20.1.x series (#2165)
* MAINT: Remove auto-comment bot (#2166)
* MAINT: Improve the questions on the bug-report template (#2158)

.. admonition:: Author list for papers based on *fMRIPrep* 20.2 LTS series

    As described in the `Contributor Guidelines
    <https://www.nipreps.org/community/CONTRIBUTING/#recognizing-contributions>`__,
    anyone listed as developer or contributor may write and submit manuscripts
    about *fMRIPrep*.
    To do so, please move the author(s) name(s) to the front of the following list:

    Markiewicz, Christopher J. \ :sup:`1`\ ; Goncalves, Mathias \ :sup:`1`\ ; DuPre, Elizabeth \ :sup:`2`\ ; Kent, James D. \ :sup:`3`\ ; Salo, Taylor \ :sup:`4`\ ; Ciric, Rastko \ :sup:`1`\ ; Pinsard, Basile \ :sup:`5`\ ; Finc, Karolina \ :sup:`6`\ ; de la Vega, Alejandro \ :sup:`7`\ ; Feingold, Franklin \ :sup:`1`\ ; Tooley, Ursula A. \ :sup:`8`\ ; Benson, Noah C. \ :sup:`9`\ ; Urchs, Sebastian \ :sup:`2`\ ; Blair, Ross W. \ :sup:`1`\ ; Erramuzpe, Asier \ :sup:`10`\ ; Lurie, Daniel J. \ :sup:`11`\ ; Heinsfeld, Anibal S. \ :sup:`12`\ ; Jacoby, Nir \ :sup:`13`\ ; Jamison, Keith W. \ :sup:`14`\ ; Frederick, Blaise B. \ :sup:`15, 16`\ ; Valabregue, Romain \ :sup:`17`\ ; Sneve, Markus H. \ :sup:`18`\ ; Liem, Franz \ :sup:`19`\ ; Adebimpe, Azeez \ :sup:`20`\ ; Velasco, Pablo \ :sup:`21`\ ; Wexler, Joseph B. \ :sup:`1`\ ; Groen, Iris I. A. \ :sup:`22`\ ; Ma, Feilong \ :sup:`23`\ ; Amlien, Inge K. \ :sup:`18`\ ; Bellec, Pierre \ :sup:`5`\ ; Cieslak, Matthew \ :sup:`20`\ ; Devenyi, Grabriel A. \ :sup:`24`\ ; Ghosh, Satrajit S. \ :sup:`25, 26`\ ; Gomez, Daniel E. P. \ :sup:`27`\ ; Halchenko, Yaroslav O. \ :sup:`23`\ ; Isik, Ayse Ilkay \ :sup:`28`\ ; Moodie, Craig A. \ :sup:`1`\ ; Naveau, Mikaël \ :sup:`29`\ ; Rivera-Dompenciel, Adriana \ :sup:`3`\ ; Satterthwaite, Theodore D. \ :sup:`20`\ ; Sitek, Kevin R. \ :sup:`30`\ ; Stojić, Hrvoje \ :sup:`31`\ ; Thompson, William H. \ :sup:`1`\ ; Wright, Jessey \ :sup:`1`\ ; Ye, Zhifang \ :sup:`32`\ ; Gorgolewski, Krzysztof J. \ :sup:`1`\ ; Poldrack, Russell A. \ :sup:`1`\ ; Esteban, Oscar \ :sup:`33`\ .

    Affiliations:

      1. Department of Psychology, Stanford University
      2. Montreal Neurological Institute, McGill University
      3. Neuroscience Program, University of Iowa
      4. Department of Psychology, Florida International University
      5. SIMEXP Lab, CRIUGM, University of Montréal, Montréal, Canada
      6. Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń
      7. University of Texas at Austin
      8. Department of Neuroscience, University of Pennsylvania, PA, USA
      9. Department of Psychology, New York University
      10. Computational Neuroimaging Lab, BioCruces Health Research Institute
      11. Department of Psychology, University of California, Berkeley
      12. Child Mind Institute
      13. Department of Psychology, Columbia University
      14. Department of Radiology, Weill Cornell Medicine
      15. McLean Hospital Brain Imaging Center, MA, USA
      16. Consolidated Department of Psychiatry, Harvard Medical School, MA, USA
      17. CENIR, INSERM U1127, CNRS UMR 7225, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
      18. Center for Lifespan Changes in Brain and Cognition, University of Oslo
      19. URPP Dynamics of Healthy Aging, University of Zurich
      20. Perelman School of Medicine, University of Pennsylvania, PA, USA
      21. Center for Brain Imaging, New York University
      22. Department of Psychology, New York University, NY, USA
      23. Dartmouth College: Hanover, NH, United States
      24. Department of Psychiatry, McGill University
      25. McGovern Institute for Brain Research, MIT, MA, USA
      26. Department of Otolaryngology, Harvard Medical School, MA, USA
      27. Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen
      28. Max Planck Institute for Empirical Aesthetics
      29. Cyceron, UMS 3408 (CNRS - UCBN), France
      30. Speech & Hearing Bioscience & Technology Program, Harvard University
      31. Max Planck UCL Centre for Computational Psychiatry and Ageing Research, University College London
      32. State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University
      33. Department of Radiology, CHUV, Université de Lausanne

20.1.3

Bug-fix release in the 20.1.x series.

* FIX: Dependency conflict between *NiWorkflows* and *TemplateFlow* (#2269)
* FIX: More targetted *TemplateFlow* queries to work with all later releases (#2268)
* MAINT: Update dependency pinnings including ``niworkflows~=1.2.9`` and three minimal bug-fixes.

20.2.0 RC0 (September 04, 2020)

With this third minor release series of 2020,
the first *fMRIPrep LTS* (*long-term support*) is finally here!

This release contains a number of bug-fixes and enhancements mostly
related to easing the maintenance, anticipating patch-release breaking
changes to ensure a longstanding LTS, and addressing some run-to-run
repeatability problems of the CompCor implementation.

Thank you for using *fMRIPrep*!
If you encounter any issues with this release, please let us know
by posting an issue on our GitHub page!

A full list of changes can be found below.

* FIX: Revise the reproducibility of CompCor masks (#2130)
* FIX: Simplify transform aggregation in resampling, pass identity transforms for multi-echo cases (#2239)
* FIX: Skip the T1w check if ``--anat-derivatives`` is provided. (#2201)
* FIX: Storing ``--bids-filters`` within config file (#2177)
* FIX: Revise multi-echo reference generation, permitting using SBRefs too (#1803)
* FIX: FreeSurfer license manipulation & canary
* ENH: Output CompCor masks if ``--debug compcor`` is passed (#2248)
* ENH: Conform to BIDS Derivatives as of BIDS 1.4.0 (#2223)
* ENH: Reuse config (#2240)
* ENH: Save BOLD-anatomical transforms to derivatives folder (#2233)
* ENH: Leverage BIDSLayout's ``database_path`` (#2203)
* ENH: Add ``--no-tty`` option to ``fmriprep-docker.py`` (#2204)
* ENH: Report number of echoes in BOLD summary. (#2184)
* ENH: Ensure NiPype telemetry is just pinged once (#2168)
* DOC: Update reference in "Refinement of Brain Mask" description (#2215)
* DOC: List *TemplateFlow* templates that need to be prefetched (#2196)
* DOC: Update references to https://github.com/nipreps (#2191)
* DOC: Pin NiPype with new Sphinx extension syntax (#2092)
* MAINT: Track #2252 from 20.1.x series (#2253)
* MAINT: Silence PyBIDS warning by setting extension mode (#2250)
* MAINT: Drop CircleCI docs build (#2247)
* MAINT: Pin latest *NiPreps* (#2244)
* MAINT: Update ``setup.cfg`` (flake8 and pytest) (#2183)
* MAINT: Delete release-drafter (#2169)
* MAINT: Track bug-fix release on the 20.1.x series (#2165)
* MAINT: Remove auto-comment bot (#2166)
* MAINT: Improve the questions on the bug-report template (#2158)

20.2.1

Bug-fix release in the 20.1.x series.

  * FIX: Revise confounds in confounds-correlation plots (#2252)
  * FIX: Coerce license path to pathlike (#2180)
  * DOC: Update new sMRIPrep location (#2211)

20.1.1 (June 04, 2020)
======================
Bug-fix release in the 20.1.x series.

* FIX: FreeSurfer license manipulation & canary (#2165)
* FIX: Dismiss ``echo`` entity from SDC reports (#2160)
* FIX: Ensure the command-line alias of ``--nprocs`` is respected (#2152)
* MAINT: Use legacy pip/setuptools for py2 checking (#2156)