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20.2.0
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)
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20.2.0rc2
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
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
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.
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20.2.0rc0
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)
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20.1.2
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)
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20.1.1
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)
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20.1.0
20.1.0 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 <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 <https://fmriprep.readthedocs.io/en/latest/usage.html#the-anatomical-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. 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) .. _`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 .. admonition:: Author list for papers based on *fMRIPrep* v20.1.x series As described in the `Contributor Guidelines <https://github.com/poldracklab/fmriprep/blob/e3d3bc51dbf03215e3e4d2746d8aaacdd9afb84d/CONTRIBUTING.md#publications>`__, anyone listed as developer or contributor may write and submit manuscripts regarding *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`\ ; Ciric, Rastko \ :sup:`1`\ ; Salo, Taylor \ :sup:`4`\ ; de la Vega, Alejandro \ :sup:`5`\ ; Finc, Karolina \ :sup:`6`\ ; Feingold, Franklin \ :sup:`1`\ ; Tooley, Ursula A. \ :sup:`7`\ ; Benson, Noah C. \ :sup:`8`\ ; Urchs, Sebastian \ :sup:`2`\ ; Blair, Ross W. \ :sup:`1`\ ; Erramuzpe, Asier \ :sup:`9`\ ; Lurie, Daniel J. \ :sup:`10`\ ; Basile Pinsard \ :sup:`11`\ ; Heinsfeld, Anibal S. \ :sup:`12`\ ; Jacoby, Nir \ :sup:`13`\ ; Frederick, Blaise B. \ :sup:`14, 15`\ ; Valabregue, Romain \ :sup:`16`\ ; Sneve, Markus H. \ :sup:`17`\ ; Liem, Franz \ :sup:`18`\ ; Adebimpe, Azeez \ :sup:`19`\ ; Velasco, Pablo \ :sup:`20`\ ; Wexler, Joseph B. \ :sup:`1`\ ; Groen, Iris I. A. \ :sup:`21`\ ; Ma, Feilong \ :sup:`22`\ ; Rivera-Dompenciel, Adriana \ :sup:`3`\ ; Amlien, Inge K. \ :sup:`17`\ ; Cieslak, Matthew \ :sup:`19`\ ; Devenyi, Grabriel A. \ :sup:`23`\ ; Ghosh, Satrajit S. \ :sup:`24, 25`\ ; Gomez, Daniel E. P. \ :sup:`26`\ ; Halchenko, Yaroslav O. \ :sup:`22`\ ; Isik, Ayse Ilkay \ :sup:`27`\ ; Moodie, Craig A. \ :sup:`1`\ ; Naveau, Mikaël \ :sup:`28`\ ; Satterthwaite, Theodore D. \ :sup:`19`\ ; Sitek, Kevin R. \ :sup:`29`\ ; Stojić, Hrvoje \ :sup:`30`\ ; Thompson, William H. \ :sup:`1`\ ; Wright, Jessey \ :sup:`1`\ ; Ye, Zhifang \ :sup:`31`\ ; Gorgolewski, Krzysztof J. \ :sup:`1`\ ; Poldrack, Russell A. \ :sup:`1`\ ; Esteban, Oscar \ :sup:`1`\ . 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. University of Texas at Austin 6. Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń 7. Department of Neuroscience, University of Pennsylvania, PA, USA 8. Department of Psychology, New York University 9. Computational Neuroimaging Lab, BioCruces Health Research Institute 10. Department of Psychology, Columbia University 11. Department of Psychology, University of California, Berkeley 12. SIMEXP Lab, CRIUGM, University of Montréal, Montréal, Canada 13. Child Mind Institute 14. 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 15. McLean Hospital Brain Imaging Center, MA, USA 16. Consolidated Department of Psychiatry, Harvard Medical School, MA, USA 17. Center for Lifespan Changes in Brain and Cognition, University of Oslo 18. URPP Dynamics of Healthy Aging, University of Zurich 19. Perelman School of Medicine, University of Pennsylvania, PA, USA 20. Center for Brain Imaging, New York University 21. Department of Psychology, New York University, NY, USA 22. Dartmouth College: Hanover, NH, United States 23. Department of Psychiatry, McGill University 24. McGovern Institute for Brain Research, MIT, MA, USA 25. Department of Otolaryngology, Harvard Medical School, MA, USA 26. Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen 27. Max Planck Institute for Empirical Aesthetics 28. Cyceron, UMS 3408 (CNRS - UCBN), France 29. Speech & Hearing Bioscience & Technology Program, Harvard University 30. Max Planck UCL Centre for Computational Psychiatry and Ageing Research, University College London 31. State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University -
20.1.0rc4
20.1.0rc4 *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 -
20.1.0rc3
20.1.0rc3 *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 -
20.0.7
20.0.7 (May 5, 2020) ==================== Bug-fix release in the 20.0.x series. This release includes a new, portable version of the templateflow python client. This includes an automatic check to fetch the latest templateflow templates every time. * MAINT: Bump templateflow to auto-update template skeleton
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20.0.6cb722eeb · REL: 20.0.6 ·
20.0.6 (April 16, 2020) 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. * FIX: Do not reorient magnitude images nipreps/sdcflows#98
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1.5.10b529274b · REL: 1.5.10 ·
1.5.10 (April 16, 2020) 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. * FIX: Do not reorient magnitude images (nipreps/sdcflows#98)
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20.1.0rc2
20.1.0rc2 (April 9, 2020) ========================= The second release candidate of the *fMRIPrep* 20.1.x series. This release fixes numerous issues, as well as improves carpetplot visualizations when CIFTI output is used and reduces overall output size by downcasting the datatype precision of certain outputs. * ENH: Use CIFTI for carpetplot when available (#2055) * FIX: Explicitly add default native resolution to volumetric outputs (`nipreps/niworkflows#494`_) * MAINT: Remove unused console scripts (#2048) * MAINT: Reduce overall size of outputs (`nipreps/niworkflows#492`_) .. _`nipreps/niworkflows#494`: https://github.com/nipreps/niworkflows/pull/494 .. _`nipreps/niworkflows#492`: https://github.com/nipreps/niworkflows/pull/492
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20.1.0rc1
20.1.0rc1 (March 23, 2020) ========================== 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. * 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) .. _`nipreps/niworkflows#484`: https://github.com/nipreps/niworkflows/pull/484
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20.0.52602ccc6 · REL: 20.0.5 ·
20.0.5 (March 19, 2020) Bug-fix release in 20.0.x series. With thanks to James Kent for the fix and Blaise Frederick for the report and testing. * FIX: Add CE agent to output figure filename templates (nipreps/niworkflows#482)
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20.0.4
20.0.4 (March 17, 2020) ======================= A bug-fix release improving documentation for filtering BIDS files and standardizing CIFTI volume orientation. With thanks to Ursula Tooley for the contribution. * DOC: FAQ section for BIDS filter (#2028) * FIX: Ensure BOLD and label orientations are equal (`nipreps/niworkflows#477`_). .. _`nipreps/niworkflows#477`: https://github.com/nipreps/niworkflows/pull/477
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20.0.3
20.0.3 (March 12, 2020) ======================= A bug-fix release fixing 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**. * FIX: Remedy fsLR surface resampling (#2032)
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20.0.2
20.0.2 (March 6, 2020) ====================== A bug squashing release in the 20.0.x series. This release fixes the use of custom templates within the docker wrapper, remedies crashes when FreeSurfer HOME was not set, and improves the documentation for local installations. With thanks to Blaise Frederick for the contribution. * DOC: Update standalone installation requirements (#2009) * FIX: Crashes whenever FREESURFER_HOME is not set (#2014) * FIX: Local template mounting (wrapper) (#2020) * MAINT: Pin minor series of nipype, major series of nibabel (#2021)
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20.0.1fc842fd8 · REL: 20.0.1 ·
20.0.1 (February 27, 2020) Bug-fix release in 20.0.x series. This release includes fixes for rare images with invalid qform matrices and some minor improvements in report readability and inclusion of common templates in the Docker image. * FIX: Handle qforms with invalid quaternions (nipreps/niworkflows#466) * FIX: update niworkflows location (#2005) * ENH: Display errors as summary/details elements in reports (nipreps/niworkflows#464) * DOC: Add ``--fs-subjects-dir`` usage to slurm example (#2003) * CI: Test that Docker image can run a common set of output spaces without network access (#1997)