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Releases: nipreps/fmriprep

20.1.0

28 May 03:42
@oesteban oesteban
20.1.0
ea35110
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20.1.0

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The second minor release series of 2020 is finally here!

Release Notes

fMRIPrep 20.1.0 introduces a magnitude of new features and improvements. Originally nominated to become the first LTS (long-term support) version of fMRIPrep, this release has been supercharged with many new features and bug-fixes. To ensure long-term stability, we have postponed the LTS nomination to 20.2 to allow us unlocking the 20.1 earlier, and a more extensive stress testing of the series before jumping into a longer support commitment. Some key additions in this release include:

  • A centralized configuration module keeping track of fMRIPrep's many options and run-time and environmental circumstances and settings. The new config module, which has been also propagated to other NiPreps dMRIPrep, MRIQC), comes to robustify the run-to-run replicability of fMRIPrep (e.g., tracking random seeds), make the option handling more modular but consistent (e.g., setting the ground for a command-line interface built off of the config module), and ease troubleshooting and telemetry.
  • The anatomical preprocessing fast-track: a new experimental command-line option (--anat-derivatives <PATH>) checks that all necessary anatomical derivatives required by fMRIPrep are present under <PATH>, and skips the anatomical processing in full if fMRIPrep's expectations are met. Because now functional processing of many sessions and runs can be efficiently split into more digestible computational units (i.e., cluster job) while guaranteeing the exact same anatomical results are being used, this can significantly speed up longitudinal study preprocessing, and it is a fundamental optimization to process databases of densely scanned individuals such as My Connectome. This option is not recommended for single-session processing.
  • A change in output CIFTI2 subcortical volume orientation to be compatible with HCP Pipeline tools and data.

Thanks

With thanks to Basile Pinsard, Joe B. Wexler, Noah Benson, and Marc Bue for contributions.

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!

CHANGES

  • FIX: MultiLabel interpolations should not use float=True (#2147)
  • FIX: Generate proper LTA transform prior BOLD sampling on surfaces (#2146)
  • FIX: Temporary config file in work directory gets clobbered in parallel jobs (#2138)
  • FIX: Dismiss echo entity on several derivatives and figures outputs (#2133)
  • FIX: Correct summary report when using previously run recon-all (#2124)
  • FIX: Ensure correct WM and CSF masks are picked in confounds workflow (#2128)
  • FIX: Explicitly add default native resolution to volumetric outputs (nipreps/niworkflows#494)
  • ENH: Finish the upstreaming of NiTransforms interfaces to NiWorkflows (#2132)
  • ENH: Enable filtering for ANY or NONE in --bids-filter-file (#2123)
  • ENH: Use new DerivativesDataSink from NiWorkflows 1.2.0 (#2114)
  • ENH: Config module (#2018)
  • ENH: Add option to ignore T2w / FLAIR images (#2015)
  • ENH: Ensure subcortical volume in CIFTI is in LAS orientation (nipreps/niworkflows#484)
  • ENH: Add option to skip brain extraction (#2039)
  • ENH: Use CIFTI sampling for carpetplot when available (#2055)
  • MAINT: Stop printing full boilerplate, black fmriprep/cli (#2119)
  • MAINT: Ensure YAML loader is specified (#2125)
  • MAINT: PIN tedana version (#2117)
  • MAINT: Bump minimum Python to 3.7 (#2017)
  • MAINT: Remove unused console scripts (#2048)
  • MAINT: Reduce the overall size of outputs (nipreps/niworkflows#492)
  • DOC: Update parallel subject neurostars link in FAQ (#2104)
  • DOC: Add FAQ about reusing work directory (#2045)
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20.1.0rc4

28 May 03:35
@oesteban oesteban
20.1.0rc4
3276875
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20.1.0rc4 Pre-release
Pre-release 
*fMRIPrep* 20.1.0 introduces a magnitude of new features and improvements.
Originally nominated to become the first LTS (long-term support) version of *fMRIPrep*, this release has been supercharged with many new features and bug-fixes.
To ensure long-term stability, we have postponed the LTS nomination to 20.2 to allow us unlocking the 20.1 earlier, and a more extensive stress testing of the series before jumping into a longer support commitment.
Some key additions in this release include:

- A centralized `configuration module
  <https://fmriprep.readthedocs.io/en/latest/api.html#module-fmriprep.config>`__
  keeping track of *fMRIPrep*'s many options and run-time and environmental
  circumstances and settings.
  The new config module, which has been also propagated to other *NiPreps*
  (`dMRIPrep <https://nipreps.org/dmriprep>`__,
  `MRIQC <https://mriqc.readthedocs.io/>`__),
  comes to robustify the run-to-run replicability of *fMRIPrep* (e.g., tracking random seeds),
  make the option handling more modular but consistent (e.g., setting the ground for a
  command-line interface built off of the config module),
  and ease troubleshooting and telemetry.
- The *anatomical preprocessing fast-track*: a new experimental command-line option
  ``--anat-derivatives <PATH>`` checks that all necessary anatomical derivatives
  required by *fMRIPrep* are present under ``<PATH>``, and skips the anatomical
  processing in full if *fMRIPrep*'s expectations are met.
  Because now functional processing of many sessions and runs can be efficiently
  split into more digestible computational units (i.e., cluster job) while guaranteeing the
  exact same anatomical results are being used, this can significantly speed up
  longitudinal study preprocessing, and it is a fundamental optimization to process
  databases of densely scanned individuals such as `My Connectome
  <https://openneuro.org/datasets/ds000031>`__.
  This option is not recommended for single-session processing.
- A change in output CIFTI2 subcortical volume orientation to be compatible with HCP Pipeline tools and data.

.. admonition:: Thanks

    With thanks to Basile Pinsard, Joe B. Wexler, Noah Benson, and Marc Bue for contributions.

.. admonition:: New Paper!

    This release comes after our latest protocol paper "*Analysis of task-based
    functional MRI data preprocessed with fMRIPrep*" has been accepted.
    The protocol describes how to use *fMRIPrep* on high-performance
    clusters to preprocess fMRI data for task-based analyses.
    Please check out `the latest version on Nature Protocols
    <https://doi.org/10.1038/s41596-020-0327-3>`__ or `the preprint
    <https://doi.org/10.1101/694364>`__.

.. 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: ``MultiLabel`` interpolations should not use ``float=True`` (#2147)
* FIX: Generate proper LTA transform prior BOLD sampling on surfaces (#2146)
* FIX: Temporary config file in work directory gets clobbered in parallel jobs (#2138)
* FIX: Dismiss ``echo`` entity on several derivatives and figures outputs (#2133)
* FIX: Correct summary report when using previously run ``recon-all`` (#2124)
* FIX: Ensure correct WM and CSF masks are picked in confounds workflow (#2128)
* FIX: Explicitly add default ``native`` resolution to volumetric outputs (`nipreps/niworkflows#494`_)
* ENH: Finish the upstreaming of *NiTransforms* interfaces to *NiWorkflows* (#2132)
* ENH: Enable filtering for ``ANY`` or ``NONE`` in ``--bids-filter-file`` (#2123)
* ENH: Use new ``DerivativesDataSink`` from *NiWorkflows* 1.2.0 (#2114)
* ENH: Config module (#2018)
* ENH: Add option to ignore T2w / FLAIR images (#2015)
* ENH: Ensure subcortical volume in CIFTI is in LAS orientation (`nipreps/niworkflows#484`_)
* ENH: Add option to skip brain extraction (#2039)
* ENH: Use CIFTI sampling for carpetplot when available (#2055)
* MAINT: Stop printing full boilerplate, ``black fmriprep/cli`` (#2119)
* MAINT: Ensure YAML loader is specified (#2125)
* MAINT: PIN *tedana* version (#2117)
* MAINT: Bump minimum Python to 3.7 (#2017)
* MAINT: Remove unused console scripts (#2048)
* MAINT: Reduce the overall size of outputs (`nipreps/niworkflows#492`_)
* DOC: Update parallel subject neurostars link in FAQ (#2104)
* DOC: Add FAQ about reusing work directory (#2045)

.. _`nipreps/niworkflows#484`: https://github.com/nipreps/niworkflows/pull/484
.. _`nipreps/niworkflows#494`: https://github.com/nipreps/niworkflows/pull/494
.. _`nipreps/niworkflows#492`: https://github.com/nipreps/niworkflows/pull/492
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20.1.0rc3

25 May 17:38
@oesteban oesteban
20.1.0rc3
f571626
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20.1.0rc3 Pre-release
Pre-release 
*fMRIPrep* 20.1.0 introduces a magnitude of new features and improvements.
Originally nominated to become the first LTS (long-term support) version of *fMRIPrep*, this release has been supercharged with many new features and bug-fixes.
To ensure long-term stability, we have postponed the LTS nomination to 20.2 to allow us unlocking the 20.1 earlier, and a more extensive stress testing of the series before jumping into a longer support commitment.
Some key additions in this release include:

- A centralized `configuration module
  <https://fmriprep.readthedocs.io/en/latest/api.html#module-fmriprep.config>`__
  keeping track of *fMRIPrep*'s many options and run-time and environmental
  circumstances and settings.
  The new config module, which has been also propagated to other *NiPreps*
  (`dMRIPrep <https://nipreps.org/dmriprep>`__,
  `MRIQC <https://mriqc.readthedocs.io/>`__),
  comes to robustify the run-to-run replicability of *fMRIPrep* (e.g., tracking random seeds),
  make the option handling more modular but consistent (e.g., setting the ground for a
  command-line interface built off of the config module),
  and ease troubleshooting and telemetry.
- The *anatomical preprocessing fast-track*: a new command-line option
  ``--anat-derivatives <PATH>`` checks that all necessary anatomical derivatives
  required by *fMRIPrep* are present under ``<PATH>``, and skips the anatomical
  processing in full if *fMRIPrep*'s expectations are met.
  Because now functional processing of many sessions and runs can be efficiently
  split into more digestible computational units (i.e., cluster job) while guaranteeing the
  exact same anatomical results are being used, this can significantly speed up
  longitudinal study preprocessing, and it is a fundamental optimization to process
  databases of densely scanned individuals such as `My Connectome
  <https://openneuro.org/datasets/ds000031>`__.
- A change in output CIFTI2 subcortical volume orientation to be compatible with HCP Pipeline tools and data.

.. admonition:: Thanks

    With thanks to Basile Pinsard, Joe B. Wexler, Noah Benson, and Marc Bue for contributions.

.. admonition:: New Paper!

    This release comes after our latest protocol paper "*Analysis of task-based
    functional MRI data preprocessed with fMRIPrep*" has been accepted.
    The protocol describes how to use *fMRIPrep* on high-performance
    clusters to preprocess fMRI data for task-based analyses.
    Please check out `the latest version on Nature Protocols
    <https://doi.org/10.1038/s41596-020-0327-3>`__ or `the preprint
    <https://doi.org/10.1101/694364>`__.

.. 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: Temporary config file in work directory gets clobbered in parallel jobs (#2138)
* FIX: Dismiss ``echo`` entity on several derivatives and figures outputs (#2133)
* FIX: Correct summary report when using previously run ``recon-all`` (#2124)
* FIX: Ensure correct WM and CSF masks are picked in confounds workflow (#2128)
* FIX: Explicitly add default ``native`` resolution to volumetric outputs (`nipreps/niworkflows#494`_)
* ENH: Finish the upstreaming of *NiTransforms* interfaces to *NiWorkflows* (#2132)
* ENH: Enable filtering for ``ANY`` or ``NONE`` in ``--bids-filter-file`` (#2123)
* ENH: Use new ``DerivativesDataSink`` from *NiWorkflows* 1.2.0 (#2114)
* ENH: Config module (#2018)
* ENH: Add option to ignore T2w / FLAIR images (#2015)
* ENH: Ensure subcortical volume in CIFTI is in LAS orientation (`nipreps/niworkflows#484`_)
* ENH: Add option to skip brain extraction (#2039)
* ENH: Use CIFTI sampling for carpetplot when available (#2055)
* MAINT: Stop printing full boilerplate, ``black fmriprep/cli`` (#2119)
* MAINT: Ensure YAML loader is specified (#2125)
* MAINT: PIN *tedana* version (#2117)
* MAINT: Bump minimum Python to 3.7 (#2017)
* MAINT: Remove unused console scripts (#2048)
* MAINT: Reduce the overall size of outputs (`nipreps/niworkflows#492`_)
* DOC: Update parallel subject neurostars link in FAQ (#2104)
* DOC: Add FAQ about reusing work directory (#2045)

.. _`nipreps/niworkflows#484`: https://github.com/nipreps/niworkflows/pull/484
.. _`nipreps/niworkflows#494`: https://github.com/nipreps/niworkflows/pull/494
.. _`nipreps/niworkflows#492`: https://github.com/nipreps/niworkflows/pull/492
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20.0.7

07 May 16:16
@mgxd mgxd
20.0.7
48517e0
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20.0.7

DOI

Release Notes

Bug-fix release in the 20.0.x series.

Changes

This release includes a new, portable version of the templateflow python client. This features an automatic check to fetch the most recent templateflow templates every time.

  • MAINT: Bump templateflow to auto-update template skeleton
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20.0.6

16 Apr 16:36
@effigies effigies
20.0.6
cb722ee
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20.0.6

DOI

Release Notes

Bug-fix release in the 20.0.x series.

This release fixes a bug for phase-difference fieldmaps that are not in RAS+ orientation.
The bug presented as an error if the orientation was reordered relative to RAS+ (for example,
AIL+) and the swapped dimensions were not of the same size.
Otherwise, the bug introduced a poor masking of the phase difference map, and could be quite subtle
if the original orientation was LAS+.
Runs of fMRIPrep that used other susceptibility distortion correction (SDC) methods are not
currently considered problematic.

This bug affects all earlier versions of fMRIPrep, except for 1.5.10 and any future releases in
the 1.5.x series.

Changes

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1.5.10

16 Apr 16:16
@effigies effigies
1.5.10
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effigies Chris Markiewicz
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1.5.10

DOI

Release Notes

Bug-fix release in the 1.5.x series.

This release fixes a bug for phase-difference fieldmaps that are not in RAS+ orientation.
The bug presented as an error if the orientation was reordered relative to RAS+ (for example,
AIL+) and the swapped dimensions were not of the same size.
Otherwise, the bug introduced a poor masking of the phase difference map, and could be quite subtle
if the original orientation was LAS+.
Runs of fMRIPrep that used other susceptibility distortion correction (SDC) methods are not
currently considered problematic.

This bug affects all previous versions of fMRIPrep, as well as versions 20.0.0-20.0.5.

Changes

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20.1.0rc1

23 Mar 17:03
@mgxd mgxd
20.1.0rc1
2c6141c
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20.1.0rc1 Pre-release
Pre-release

DOI

Release Notes

The first release candidate of the fMRIPrep 20.1.x series. This release introduces a configuration
file to easily distinguish which options were selected for each participant, along with other enhancements.

Changes

  • DOC: Add FAQ about reusing work directory (#2045)
  • ENH: Config module (#2018)
  • ENH: Add option to ignore T2w / FLAIR images (#2015)
  • ENH: Ensure subcortical volume in CIFTI is in LAS orientation (nipreps/niworkflows#484)
  • ENH: Add option to skip brain extraction (#2039)
  • MAINT: Bump minimum Python to 3.7 (#2017)
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20.0.5

23 Mar 14:50
@mgxd mgxd
20.0.5
2602ccc
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20.0.5

DOI

Release Notes

Bug-fix release in 20.0.x series.

With thanks to James Kent for the fix and Blaise Frederick for the report and testing.

Changes

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20.0.4

18 Mar 00:10
@mgxd mgxd
20.0.4
ab797a9
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20.0.4

DOI

Release Notes

A bug-fix release improving documentation for filtering BIDS files and standardizing CIFTI volume orientation.
☘️🌈💰

With thanks to Ursula Tooley for the contribution.

Changes

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20.0.3

12 Mar 21:07
@mgxd mgxd
20.0.3
ef4ccf4
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20.0.3

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Release Notes

A bug-fix release for CIFTI surfaces.

This release remedies a resampling error when generating fsLR surfaces that was producing erroneous CIFTI files.

We strongly recommend all users who have generated CIFTI output with previous 20.0.x releases to upgrade and rerun.

Changes

  • FIX: Remedy fsLR surface resampling (#2032)
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