Skip to content

Latest commit

 

History

History
1441 lines (1206 loc) · 73.5 KB

CHANGES.rst

File metadata and controls

1441 lines (1206 loc) · 73.5 KB
Raw

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. 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.

Long-Term Support (LTS)

fMRIPrep 20.2 LTS introduces the long-term support program. This LTS version will be kindly steered and maintained by the group of Dr. Basile Pinsard and Prof. Pierre Bellec at CRIUGM, (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)

Author list for papers based on fMRIPrep 20.2 LTS series

As described in the Contributor Guidelines, 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. 1; Goncalves, Mathias 1; DuPre, Elizabeth 2; Kent, James D. 3; Salo, Taylor 4; Ciric, Rastko 1; Pinsard, Basile 5; Finc, Karolina 6; de la Vega, Alejandro 7; Feingold, Franklin 1; Tooley, Ursula A. 8; Benson, Noah C. 9; Urchs, Sebastian 2; Blair, Ross W. 1; Erramuzpe, Asier 10; Lurie, Daniel J. 11; Heinsfeld, Anibal S. 12; Jacoby, Nir 13; Jamison, Keith W. 14; Frederick, Blaise B. 15, 16; Valabregue, Romain 17; Sneve, Markus H. 18; Liem, Franz 19; Adebimpe, Azeez 20; Velasco, Pablo 21; Wexler, Joseph B. 1; Groen, Iris I. A. 22; Ma, Feilong 23; Amlien, Inge K. 18; Bellec, Pierre 5; Cieslak, Matthew 20; Devenyi, Grabriel A. 24; Ghosh, Satrajit S. 25, 26; Gomez, Daniel E. P. 27; Halchenko, Yaroslav O. 23; Isik, Ayse Ilkay 28; Moodie, Craig A. 1; Naveau, Mikaël 29; Rivera-Dompenciel, Adriana 3; Satterthwaite, Theodore D. 20; Sitek, Kevin R. 30; Stojić, Hrvoje 31; Thompson, William H. 1; Wright, Jessey 1; Ye, Zhifang 32; Gorgolewski, Krzysztof J. 1; Poldrack, Russell A. 1; Esteban, Oscar 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 (September 15, 2020)

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.

20.1.2 (September 04, 2020)

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)

20.1.0 (May 27, 2020)

The second minor release series of 2020 is finally here!

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.

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 or the preprint.

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)

Author list for papers based on fMRIPrep v20.1.x series

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

20.0.x series (February 2020)

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

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.

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.

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).

20.0.3 (March 12, 2020)

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.

  • FIX: Remedy fsLR surface resampling (#2032)

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)

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)

20.0.0 (February 24, 2020)

The major release of 2020 is here!

fMRIPrep is transitioning to a calendar version system (#1912). The CalVer system reflects fMRIPrep's nature as an evolving workflow and does not impose any artificial incentive for "big-change" releases. It also permits to quickly see how out-of-date someone's version is. As of now, the default version increment is the minor release number. Hence, when the minor release number changes the work directory of fMRIPrep will presumably break. Micro releases only include bug-fixes that can reuse exiting working directories.

The major highlight of this release entails CIFTI generation to match :abbr:`HCP (Human Connectome Project)` grayordinates. In addition, the new fMRIPrep 20.0.0 has gone through a major overhaul in the handling of standard spaces (spatial normalizations, fusion of prior knowledge from corresponding atlases) and imaging outputs. In particular, the new series almost completely implements the new syntax for --output-spaces to describe the (non)standard spatial references that shall be used for generating outputs (#1604).

This release includes contributions from Azeez Adebimpe and Basile Pinsard - very much appreciated.

  • ENH: Warn when existing output version does not match current pipeline version (#1967)
  • ENH: Add --clean-workdir argument (#1966)
  • ENH: Refactor of how spatial normalization targets and --output-spaces are maintained (#1955) (#1983)
  • ENH: Add --bids-filter-file argument for more controlled data querying (#1770)
  • FIX: Ensure subject ID is used when selecting BIDS data (#1982)
  • FIX: Display a log message when processing completes successfully (#1977)
  • DOC: Clean up surface outputs (#1993)
  • DOC: Integrate intersphinx, drop external module wrapping (#1989)
  • DOC: Improve custom template usage description (#1969)
  • MAINT: Use local docker registry (#1990)
  • MAINT: Pin connectome-workbench 1.3.2, add to documented dependencies (#1958)
  • MAINT: Pin NiBabel, NiWorkflows, sMRIPrep (#1971)
  • MAINT: CI build error fixes (#1976)

Author list for papers based on fMRIPrep v20.0.0

As described in the Contributor Guidelines, 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.1; DuPre, Elizabeth2; Goncalves, Mathias1; Kent, James D.3; Ciric, Rastko1; Salo, Taylor4; de la Vega, Alejandro5; Finc, Karolina6; Feingold, Franklin1; Urchs, Sebastian2; Blair, Ross W.1; Erramuzpe, Asier7; Valabregue, Romain8; Jacoby, Nir9; Lurie, Daniel J.10; Heinsfeld, Anibal S.11; Halchenko, Yaroslav O.12; Sneve, Markus H.13; Devenyi, Grabriel A.14; Liem, Franz15; Gomez, Daniel E. P.16; Adebimpe, Azeez17; Velasco, Pablo18; Groen, Iris I. A.19; Ma, Feilong12; Rivera-Dompenciel, Adriana3; Amlien, Inge K.13; Cieslak, Matthew17; Ghosh, Satrajit S.20, 21; Isik, Ayse Ilkay22; Moodie, Craig A.1; Naveau, Mikaël23; Satterthwaite, Theodore D.17; Sitek, Kevin R.24; Stojić, Hrvoje25; Thompson, William H1; Tooley, Ursula A.26; Wright, Jessey1; Ye, Zhifang27; Gorgolewski, Krzysztof J.1; Poldrack, Russell A.1; Esteban, Oscar1.

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. Computational Neuroimaging Lab, BioCruces Health Research Institute
  8. 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
  9. Department of Psychology, Columbia University
  10. Department of Psychology, University of California, Berkeley
  11. Child Mind Institute
  12. Dartmouth College: Hanover, NH, United States
  13. Center for Lifespan Changes in Brain and Cognition, University of Oslo
  14. Department of Psychiatry, McGill University
  15. URPP Dynamics of Healthy Aging, University of Zurich
  16. Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen
  17. Perelman School of Medicine, University of Pennsylvania, PA, USA
  18. Center for Brain Imaging, New York University
  19. Department of Psychology, New York University, NY, USA
  20. McGovern Institute for Brain Research, MIT, MA, USA
  21. Department of Otolaryngology, Harvard Medical School, MA, USA
  22. Max Planck Institute for Empirical Aesthetics
  23. Cyceron, UMS 3408 (CNRS - UCBN), France
  24. Speech & Hearing Bioscience & Technology Program, Harvard University
  25. Max Planck UCL Centre for Computational Psychiatry and Ageing Research, University College London
  26. Department of Neuroscience, University of Pennsylvania, PA, USA
  27. State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University

1.5.x series (September 2019)

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.

1.5.9 (February 14, 2020)

Bug-fix release in the 1.5.x series.

This release fixes a bug for some phase maps generated by Philips. A full fix with better handling of all phase maps will be available in an upcoming minor release (20.0 or 20.1), but this should permit users who are processing with 1.5.x to resolve this issue in a way that does not affect phase maps unaffected by the bug.

  • FIX: Center phase maps around central mode, avoiding FoV-related outliers (nipreps/sdcflows#89)

1.5.8 (January 28, 2020)

Bug-fix release in the 1.5.x series.

  • FIX: SyN SDC logic failing in --force-syn cases (#1951)

1.5.7 (January 23, 2020)

Bug-fix release in the 1.5.x series.

This release fixes a bug specifically for T1w images with dimensions ≤256 voxels but a field-of-view >256mm.

1.5.6 (January 22, 2020)

Bug-fix release in the 1.5.x series.

  • FIX: Include all functional runs in reports, establish consistent ordering (#1937)
  • FIX: Use SyN-SDC if --use-syn-sdc and --ignore fieldmaps are used (#1942)

1.5.5 (January 14, 2020)

Bug-fix release in the 1.5.x series.

  • FIX: Correctly select volumetric spaces for carpetplot (#1932) @effigies
  • FIX: Constrain setuptools for Python 2.7 installs of fmriprep-docker (#1933) @effigies

1.5.4 (December 18, 2019)

Bug-fix release in the 1.5.x series.

1.5.3 (December 12, 2019)

The last patch release of the 1.5.x series containing features. As of 1.5.4, patch releases will only contain bug fixes, maintenance tasks and minor documentation revisions.

  • FIX: Do not run STC if SliceTiming metadata is set but empty (#1854) @oesteban
  • FIX: Link to EPINorm issue in README (#1903) @adelavega
  • FIX: Respect --dummy-scans 0 (#1908) @jdkent
  • ENH: Upgrade SDCFlows to new API (1.0.0) (#1886) @oesteban
  • ENH: Add --fs-subjects-dir flag (#1901) @effigies
  • DOC: Improving accessibility of confounds description (#1877) @kfinc
  • MAINT: Ensure data is packaged in sdist (#1902) @effigies
  • MAINT: Remove deprecated command-line arguments (#1909) @mgxd

1.5.2 (December 2, 2019)

Bug-fix release in the 1.5.x series.

1.5.1 (November 26, 2019)

After an arduous walk through release-candidates, release 1.5.1 includes a new release of Nipype which addresses the problems related to results files many users have been experiencing.

With thanks to Marc Bue, Alejandro De La Vega, Tailor Salo, Asier Erramuzpe and Soichi Hayashi.

  • FIX: Treat missing field maps as empty list instead of None (#1820) @tsalo
  • FIX: Raise error if work_dir is a child of bids_dir (#1860) @adelavega
  • FIX: Change ICA-AROMA filenames to fit current naming scheme (#1861) @jdkent
  • FIX: Update code-server in the Dockerfile_devel (#1852) @erramuzpe
  • FIX: Do not generate desc-smoothAROMAnonaggr_bold conversions on standard spaces (#1838) @oesteban
  • FIX: Skip plotting step of ICA-AROMA (#1834) @oesteban
  • FIX: Error during version check trying to access read-only file systems (#1830) @oesteban
  • FIX: Bad results files loads; PIN: nipy/nipype master (#1806) @effigies
  • FIX: Adding comma to outputnode in init_func_preproc_wf (#1795) @marcbue
  • FIX: Ignore sourcedata and derivatives when fetching data (#1788) @effigies
  • ENH: Added skip_citation_process flag to skip processing citation.md (#1876) @soichih
  • ENH: Restore space-MNI152NLin6Asym for AROMA denoised outputs (#1839) @oesteban
  • ENH: Confounds metadata (#1708) @rciric
  • DOC: Remove OpenNeuro badge (#1862) @adelavega
  • DOC: Improve documentation about TemplateFlow and Containers (#1802) @oesteban
  • DOC: Add VERSION argument to docker build instructions (#1797) @effigies
  • DOC: Revise docstrings of workflows for correct parsing with napoleon #1882 (@oesteban)
  • CI: Use recent Python image to build packages (#1790) @effigies
  • MAINT: Update to the new API of sMRIPrep (#1879) @adelavega
  • MAINT: Update CONTRIBUTING.md inspired by dMRIPrep's (#1853) @oesteban
  • MAINT: Enable circleci-artifacts-redirector (#1857) @effigies
  • MAINT: Cleaning up dependencies (#1832) @oesteban
  • MAINT: Pin Python 3.7.4 in CircleCI's build_docs (#1836) @oesteban
  • MAINT: Purge Cython and depend on SDCflows (#1792) @effigies
  • MAINT: Container images - cleanup $HOME in docker build (#1768) @oesteban

1.5.0 (September 9, 2019)

Two hallmark changes conducive to a new minor release line have been included in version 1.5.0: the upgrade of PyBIDS to the 0.9 series and the split of SDCflows off from fMRIPrep codebase. PyBIDS 0.9.x has a better handling of the indexed dataset that will permit some optimizations to fMRIPrep's memory fingerprint. SDCflows now are found at nipreps/sdcflows, and have been split to allow a more granular and thorough testing in collaboration with M. Cieslak, A. Adebimpe, and T. Satterthwaite. Some other bugfixes, improvements to the documentation and minor features are also shipped with the new release. With thanks to Ursula Tooley, Sebastian Urchs and Gabriel A. Devenyi for contributions.

  • FIX: Minor improvements for templateflow installation in Docker images (#1764) @oesteban
  • FIX: Passing surface template keywords into carpetplot workflow (#1755) @oesteban
  • FIX: Postpone pandoc conversion of boilerplate after workflow has fully run (#1710) @oesteban
  • FIX: Use MNI152NLin2009cAsym for SDC if no templates are specified (#1703) @effigies
  • FIX: Correct BOLD-T1w registration description if DoF != 9 (#1701) @effigies
  • ENH: Set up code-server docker recipe for interactive development (#1730) @jdkent
  • ENH: Make fmriprep print defaults for arguments with help (#1735) @gdevenyi
  • ENH: Add check for updates and check whether version has been flagged. (#1715) @oesteban
  • ENH: Add TaskName metadata to BOLD outputs (#1714) @effigies
  • REF: Separate SDCflows from fMRIPrep (#1670) @oesteban
  • DOC: Adding fMRIPrep benchmark info to FAQs (#1759) @surchs
  • DOC: Update .zenodo.json (#1732) @utooley
  • DOC: Add link to documentation in help of --output-spaces argument (#1722) @oesteban
  • DOC: adding recon-all issue to faq (#1622) @franklin-feingold
  • DOC: Add copyright waiver to boilerplate and reviewer note to docs (#1691) @effigies
  • MAINT: niworkflows and nipype to use latest N4BiasFieldCorrection (#1752) @oesteban
  • MAINT: Bump pybids and nipype dependencies (#1744) @effigies
  • MAINT: Move regression tests of EPI masks over to Niworkflows (#1716) @oesteban
  • MAINT: Remove old extensions entity selector for PyBIDS queries (#1707) @oesteban
  • MAINT: Use PyBIDS 0.9.x via niworkflows/smriprep PRs (#1695) @effigies

1.4.x series (May 2019)

1.4.1 (July 9, 2019)

As of 1.4.1, the new infant and pediatric templates added to TemplateFlow are available to brain extraction and spatial normalization. Containers do not set the TEMPLATEFLOW_HOME environment variable anymore, allowing increased flexibility when running them (especially Singularity, for which the filesystem is generally set read-only). Additionally, BOLD files in native space can be generated and a minor bug related to the handling of FreeSurfer outputs have been included.

  • FIX: Finalizing support for new templates and their command line modifiers (#1671) @oesteban
  • FIX: Do not set TEMPLATEFLOW_HOME (#1669) @oesteban
  • FIX: FreeSurfer failed without adding some fs* to --output-spaces (#1643) @oesteban
  • ENH: Show informative warning for phase1/2 type of fieldmaps (#1689) @oesteban
  • ENH: Allow template modifiers (a la --output-spaces) in skull-stripping (#1666) @oesteban
  • ENH: Write outputs in native-BOLD space (#1646) @oesteban
  • DOC: Add WHT to Zenodo (#1683) @wiheto

1.4.0 (May 15, 2019)

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)

1.3.2 (March 18, 2019)

A new release providing better support for BIDS-Derivatives, an wrapping-up all the developments around TemplateFlow and stability of singularity images. With thanks to @sarenseeley for contributions.

  • ENH: Write derivatives metadata (#1546) @oesteban
  • DOC: Indicate that interpolation is NN above the EPI-to-T1w reportlet (#1542) @sarenseeley

1.3.1.post2 (March 13, 2019)

A hotfix release addressing issues related to TemplateFlow for Singularity users, via pinning templateflow>=0.1.2.

1.3.1.post1 (March 11, 2019)

A hotfix release addressing issues related to TemplateFlow for Singularity users.

  • FIX: Make sure --cifti-output requires at least one of fsaverage{5,6} (#1514) @oesteban
  • FIX: Avoid using $HOME for storing templates (#1529) @chrisfilo

1.3.1 (March 6, 2019)

Updated ecosystem's versions (TemplateFlow 0.1.x, Niworkflows 0.8.x, and sMRIPrep 0.1.x) to include latest improvements (bugfixes from niworkflows and the new pybids interface of templateflow). TemplateFlow 0.1.0 does not require datalad anymore. With thanks to @franklin-feingold for contributions.

  • UX: Reduce warning levels (#1513) @effigies
  • DOC: fmriprep-docker documentation (#1515) @franklin-feingold
  • REL: 1.3.1 (#1527) @oesteban

1.3.0.post3 (March 1, 2019)

Hotfix release intended for Docker users, smoothing the experience of TemplateFlow when using the -u UID flag is necessary.

  • FIX: Orientation problem with niworkflows<0.7.2 (nipreps/niworkflows#312) @effigies
  • ENH: TemplateFlow + docker run -u ... (#1525) @oesteban
  • ENH: Include repetition time in functional summary (#1508) @wiheto
  • FIX: Do not crash if all aroma components are classified as noise (#1467) @jdkent

1.3.0.post2 (February 14, 2019)

Hotfix release intended for Singularity users, amending the previous iteration that didn't fix the problem (#1510) @effigies.

1.3.0.post1 (February 8, 2019)

Hotfix release intended for Singularity users. For further detail, please see #1500.

1.3.0 (February 7, 2019)

We start the 1.3.x series including a few bugfixes, housekeeping duty and a refactors to leverage sMRIPrep (which is a fork of fMRIPrep's anatomical workflow), pybids>=0.7 for querying dataset, and TemplateFlow for handling standard spaces.

  • FIX: Bad fsnative replacement in CIfTI workflow (#1476) @oesteban
  • FIX: Avoid warning when generating boilerplate (#1464) @oesteban
  • MAINT: resolves #1485 : patch fmriprep-docker automount for use with Python 3.7 (#1486) @rciric
  • RF: Use anatomical workflows from sMRIPrep (#1482) @oesteban
  • MAINT: Update sentry-sdk (#1490) @chrisfilo
  • ENH: Remaining TemplateFlow integrations (#1494) @oesteban
  • MAINT: Update to keep up with nipreps/niworkflows#299 (#1496) @oesteban
  • FIX: Updating bids-validator to 1.1.3 (#1498) @chrisfilo

1.2.x series (January 2019)

1.2.6-1 (January 24, 2019)

Hotfix release of version 1.2.6, pinning niworkflows to a release version (instead of the development branch, since #1459) and including to bugfixes.

  • PIN: NiWorkflows 0.5.2.post7 (1bf4a21).
  • FIX: Bad fsnative replacement in CIfTI workflow (#1476) @oesteban
  • FIX: Avoid warning when generating boilerplate (#1464) @oesteban

1.2.6 (January 17, 2019)

This is a bug fix release in the 1.2 series. Probably the most noticeable improvement is the restoration of auto-generated content in the documentation.

Additionally, FreeSurfer aparc/aseg segmentations are now sampled to all output spaces.

For any users importing fMRIPrep interfaces, many of these have been moved to the niworkflows package.

With thanks to Nir Jacoby and Hrvoje Stojic for contributions.

  • FIX: Use keyword arguments for Sentry breadcrumb reporting (#1441) @chrisfilo
  • FIX: Verify proc file exists before reading (#1454) @effigies
  • ENH: Only report participants with errors (#1437) @effigies
  • ENH: Resample aparc/aseg into specified output spaces (#1401) @nirjacoby
  • ENH: Copy BibTeX file to log directory for LaTeX users (#1446) @hstojic
  • RF: Use niworkflows upstreamed interfaces and utilities (#1438) @oesteban
  • DOC: Fix documentation build (#1451) @oesteban
  • DOC: Fix ReadTheDocs builds (#1459) @effigies
  • MAINT/DOC: Clean-up __about__, update with Nat Meth (#1445) @oesteban
  • MAINT: Make sure Python 3.7.1 is installed (#1452) @oesteban
  • MAINT: Dev status to beta, bump copyright year (#1468) @effigies

1.2.5 (December 4, 2018)

Hotfix release.

  • FIX: Breadcrumb reporting (#1435) @chrisfilo

1.2.4 (December 3, 2018)

Bugfixes, an additional iteration over Sentry reporting and some relevant ME-EPI updates (with thanks to @emdupre).

  • ENH: Update ME-EPI workflow to create optimal combination (#1263) @emdupre
  • MAINT: Merge master into multiecho (#1324) @effigies
  • ENH: Add echo-idx flag (#1355) @emdupre
  • FIX: Always run FreeSurfer interfaces that sink outside working directory (#1397) @effigies
  • ENH: Use Python 3.7 in Dockerfile (#1398) @effigies
  • DOC: Update contributing guide and add code of conduct (#1404) @emdupre
  • FIX: Calculate template transforms explicitly as RAS2RAS (#1399) @effigies
  • MAINT: Replace img.get_affine() -> img.affine (#1414) @oesteban
  • FIX: Truncating of sentry messages (#1417) @chrisfilo
  • ENH: Add fmriprep-docker execution environment (#1416) @chrisfilo
  • MAINT: Update indexed_gzip to handle small .nii.gz (#1421) @effigies
  • ENH: Group common issues with fingerprints (#1418) @chrisfilo
  • ENH: adding memory and cpu info to sentry logs (#1420) @chrisfilo
  • ENH: Use standard T2* map as coregistration target (#1383) @emdupre
  • ENH: Handle FreeSurfer subject directory preparation gracefully when run in parallel (#1413) @effigies
  • ENH: Make sure inputs are BIDS compliant before running fmriprep (#1419) @chrisfilo
  • ENH: Sentry event categorization propagation (#1422) @chrisfilo
  • MAINT: Require nipype >= 1.1.6 (#1426) @effigies
  • ENH: Omnibus multi-echo pull request (#1296) @effigies
  • ENH: Report memory overcommit policies (#1429) @effigies

1.2.3 (November 16, 2018)

Refactor of Sentry reporting, bug fixes and added tests. With thanks to @sebnaze for contributions.

  • TST: Utility functions for skipping/re-inserting non-steady-state volumes (#1382) @jdkent
  • FIX: Correctly populate right-hemisphere time series in CIFTI derivatives (#1378) @sebnaze
  • FIX: Restore original contour colors in reports (#1385) @oesteban
  • ENH: New sentry SDK (#1381) @chrisfilo
  • ENH: Sentry refinement (#1394) @chrisfilo

1.2.2 (November 9, 2018)

Several bug fixes. With thanks to Franz Liem, Nir Jacoby and Markus Handal Sneve for contributions.

  • FIX: Do not show --debug deprecation warning unless used (#1361) @effigies
  • FIX: Select consistent parcellation for producing aparcaseg derivatives (#1369) @nirjacoby
  • FIX: Count non-steady-state volumes even if sbref is passed (#1373) @effigies
  • ENH: Respect SliceEncodingDirection metadata (#1350) @fliem
  • ENH: Set maximum MELODIC components to 200 by default (#1366) @markushs
  • TST: Verify LegacyMultiProc functionality (#1368) @effigies

1.2.1 (November 1, 2018)

Hotfix release (deployment system)

1.2.0 (October 31, 2018)

This release marks a substantial renaming of derivatives to conform to the BIDS Derivatives specification [release candidate](https://docs.google.com/document/d/17ebopupQxuRwp7U7TFvS6BH03ALJOgGHufxK8ToAvyI/).

The most significant additional change is a substantial revision of BOLD skull-stripping, using a BOLD template constructed from many open datasets. Building off the work of Zhifang Ye (see #1050), the skull-stripping is now much more resilient to intensity inhomogeneity.

With many thanks to Ali Cohen, James Kent, Inge Amlien, Sebastian Urchs, and Zhifang Ye for contributions.

  • FIX: Missing BOLD reports (#1326) @oesteban
  • FIX: Ensure encoding when reading boilerplate (#1322) @alioco
  • FIX: Reportlets - bbregister vs flirtbbr (continues #1326) (#1328) @oesteban
  • FIX: Quick update to new template structure (#1330) @oesteban
  • FIX: Explicitly pass bold mask to AROMA (#1332) @jdkent
  • FIX: Missing report output - #1339 (#1346) @kasbohm
  • FIX: Remove non-steady-state volumes prior to ICA-AROMA (#1335) @jdkent
  • ENH: Store BOLD reference images (#1306) @oesteban
  • ENH: Deprecate --debug with --sloppy (#1347) @effigies
  • ENH: Conform confound regressor names to Derivatives RC2 (#1343) @effigies
  • ENH: Do not set KEEP_FILE_OPEN_DEFAULT (#1356) @effigies
  • ENH: Template-based masking of EPI boldrefs (#1321) @oesteban
  • DOC: Update BIDS-validator link (#1320) @surchs
  • DOC: add --bind method to singularity patch documentation (#1340) @jdkent
  • RF: Update anatomical derivatives for RC1 (#1325) @effigies
  • RF: Update functional derivatives for RC1 (#1333) @effigies
  • TST: Add heavily-nonuniform boldrefs for regression tests (#1329) @oesteban
  • TST: Fix expectations for CIFTI outputs & ds005 (#1344) @oesteban
  • MAINT: Ignore project settings files from popular python/code editors (#1336) @jdkent
  • CI: Deploy nipreps/fmriprep:unstable tracking master (#1307) @effigies

1.1.x series (October 2018)

1.1.8 (October 4, 2018)

Several bug fixes. This release is intended to be the last before start adopting BIDS-Derivatives RC1 (which will trigger 1.2.x versions).

  • DOC: Switch to orig graph for init_bold_t2s_wf (#1298) @effigies
  • FIX: Enhance T2 contrast enhance_t2 in reference estimate (#1299) @effigies
  • FIX: Create template from one usable T1w image (#1305) @effigies
  • MAINT: Pin grabbit and pybids in setup.py (#1284) @oesteban

1.1.7 (September 25, 2018)

Several bug fixes. With thanks to Elizabeth Dupre and Romain Vala for contributions.

  • FIX: Revert FreeSurfer download URL (#1280) @chrisfilo
  • FIX: Default to 6 DoF for BOLD-T1w registration (#1286) @effigies
  • FIX: Only grab sbref images, not metadata (#1285) @effigies
  • FIX: QwarpPlusMinus renamed source_file to in_file (#1289) @effigies
  • FIX: Remove long paths from all LTA output files (#1274) @romainVala
  • ENH: Use single-band reference images when available (#1270) @effigies
  • DOC: Note GIFTI surface alignment (#1288) @effigies
  • RF: Split BOLD-T1w registration into calculation/application workflows (#1278) @emdupre
  • MAINT: Pin pybids and grabbit in Docker build (#1281) @chrisfilo

1.1.6 (September 10, 2018)

Hotfix release.

  • FIX: Typo in plugin config loading.

1.1.5 (September 06, 2018)

Improved documentation and minor bug fixes. With thanks to Jarod Roland and Taylor Salo for contributions.

  • DOC: Replace --clearenv with correct --cleanenv flag (#1237) @jarodroland
  • DOC: De-indent to remove text from code block (#1238) @effigies
  • TST: Add enhance-and-skullstrip regression tests (#1074) @effigies
  • DOC: Clearly indicate that fMRIPrep requires Python 3.5+ (#1249) @oesteban
  • MAINT: Update PR template (#1239) @effigies
  • DOC: Set appropriate version in Zenodo citation (#1250) @oesteban
  • DOC: Updating long description (#1230) @oesteban
  • DOC: Add ME workflow description (#1253) @tsalo
  • FIX: Add memory annotation to ROIPlot interface (#1256) @jdkent
  • ENH: Write derivatives dataset_description.json (#1247) @effigies
  • DOC: Enable table text wrap and link docstrings to code on GitHub (#1258) @tsalo
  • DOC: Clarify language describing T1w image merging (#1269) @chrisfilo
  • FIX: Accommodate new template formats (#1273) @effigies
  • FIX: Permit overriding plugin config with CLI options (#1272) @effigies

1.1.4 (August 06, 2018)

A hotfix release for #1235. Additionally, notebooks have been synced with the latest version of that repository.

  • FIX: Verify first word of _cmd in dependency check (#1236)
  • DOC: Add two missing references (#1234)
  • ENH: Allow turning off random seeding for ANTs brain extraction (#919)

1.1.3 (July 30, 2018)

This release comes with many updates to the documentation, a more lightweight SignalExtraction, a new dynamic boilerplate and some new features from Nipype.

  • ENH: Use upstream afni.TShift improvements (#1160)
  • PIN: Nipype 1.1.1 (65078c9)
  • ENH: Dynamic citation boilerplate (#1024)
  • ENH: Check Command Line dependencies before running (#1044)
  • ENH: Reimplement SignalExtraction (#1170)
  • DOC: Update copyright year to 2018 (#1224)
  • ENH: Enable -u (docker user/userid) flag in wrapper (#1223)
  • FIX: Corrects Dockerfile WORKDIR. (#1218)
  • ENH: More specific errors for missing echo times (#1221)
  • ENH: Change WORKDIR of Docker image (#1204)
  • DOC: Update documentation related to contributions (#1187)
  • DOC: Additions to include before responding to reviews of the pre-print (#1195)
  • DOC: Improving documentation on using Singularity (#1063)
  • DOC: Add OHBM 2018 poster, presentation (#1198)
  • ENH: Replace InvertT1w with upstream Rescale(invert=True) (#1161)

1.1.2 (July 6, 2018)

This release incorporates Nipype improvements that should reduce the chance of hanging if tasks are killed for excessive resource consumption.

Thanks to Elizabeth DuPre for documentation updates.

  • DOC: Clarify how to reuse FreeSurfer derivatives (#1189)
  • DOC: Improve command line option documentation (#1186, #1080)
  • MAINT: Update core dependencies (#1179, #1180)

1.1.1 (June 7, 2018)

  • ENH: Pre-cache DKT31 template in Docker image (#1159)
  • MAINT: Update core dependencies (#1163)

1.1.0 (June 4, 2018)

  • ENH: Use Reorient interface included upstream in nipype (#1153)
  • FIX: Refine BIDS queries to avoid indexing derivatives (#1141)
  • DOC: Clarify outlier columns (#1138)
  • PIN: Update to niworkflows 0.4.0 and nipype 1.0.4 (#1133)

1.0.x series (May 2018)

1.0.15 (May 17, 2018)

  • DOC: Add lesion masking during registration (#1113)
  • FIX: Patch boldbuffer for ME (#1134)

1.0.14 (May 15, 2018)

With thanks to @ZhifangYe for contributions

  • FIX: Non-invertible transforms bringing parcellation to BOLD (#1130)
  • FIX: Bad connection for --medial-surface-nan option (#1128)

1.0.13 (May 11, 2018)

With thanks to @danlurie for the outstanding contribution of #1106

  • ENH: Some nit picks on reports (#1123)
  • ENH: Carpetplot + confounds plot (#1114)
  • ENH: Add constrained cost-function masking to T1-MNI registration (#1106)
  • FIX: Circular dependency (#1104)
  • ENH: Set PYTHONNOUSERSITE in containers (#1103)

1.0.12 (May 03, 2018)

  • MAINT: fmriprep-docker: Ensure data/output/work paths are absolute (#1089)
  • ENH: Add usage tracking and centralized error reporting (#1088)
  • FIX: Ensure one motion IC index is loaded as list (#1096)
  • TST: Refactoring CircleCI setup (#1098)
  • FIX: Compression in DataSinks (#1095)
  • MAINT: fmriprep-docker: Support Python 2/3 without future or other helpers (#1082)
  • MAINT: Update npm to 10.x (#1087)
  • DOC: Prefer pre-print over Zenodo doi in boilerplate (#1086)
  • DOC: Stylistic fix (`'template'`) (#1083)
  • FIX: Run ICA-AROMA in MNI152Lin 2mm resampling grid (91x109x91 vox) (#1064)
  • MAINT: Remove cwebp to revert to png (#1081)
  • ENH: Allow changing the dimensionality of Melodic for AROMA. (#1052)
  • FIX: Derivatives datasink handling of compression (#1077)
  • FIX: Check for invalid sform matrices (#1072)
  • FIX: Check exit code from subprocess (#1073)
  • DOC: Add preprint fig. 1 to About (#1070)
  • FIX: Always strip session from T1w for derivative naming (#1071)
  • DOC: Add RRIDs in the citation boilerplate (#1061)
  • ENH: Generate CIFTI derivatives (#1001)

1.0.11 (April 16, 2018)

  • FIX: Do not detrend CSF/WhiteMatter/GlobalSignal (#1058)

1.0.10 (April 16, 2018)

  • TST: Re-run ds005 with only one BOLD run (#1048)
  • FIX: Patch subject_summary in reports (#1047)

1.0.9 (April 10, 2018)

With thanks to @danlurie for contributions.

  • FIX: Connect inputnode to SDC for pepolar images (#1046)
  • FIX: Pass ref_file to STC check (#1038)
  • DOC: Add BBR fallback to user docs. (#1036)
  • ENH: Revise resampling grid for template outputs (#1040)
  • MAINT: DataSinks within their workflows (#1021)
  • ENH: Add FLAIR pial refinement support (#829)
  • MAINT: Upgrade to pybids 0.5 (#1027)
  • MAINT: Refactor fieldmap heuristics (#1017)
  • FIX: Use metadata to select shortest echo as ref_file (#1018)
  • ENH: Adopt versioneer to compose version names (#1007)
  • ENH: Handle first echo separately for ME-EPI (#891)

1.0.8 (February 22, 2018)

With thanks to @mgxd and @naveau for contributions.

  • FIX: ROIs Plot and output brain masks consistency (#1002)
  • FIX: Init flirt with qform (#1003)
  • DOC: Prepopulate tag when posting neurostars questions. (#987)
  • FIX: Update fmap.py : import _get_pe_index in get_ees (#984)
  • FIX: Argparse action (#985)

1.0.7 (February 13, 2018)

  • ENH: Output aseg and aparc in T1w and BOLD spaces (#957)
  • FIX: Write latest BOLD mask out (space-T1w) (#978)
  • PIN: Updating niworkflows to 0.3.1 (#962)
  • FIX: Robuster BOLD mask (#966)

1.0.6 (29th of January 2018)

  • FIX: Bad connection in phasediff-fieldmap workflow (#950)
  • PIN: niworkflows-0.3.1-dev (including Nipype 1.0.0!)
  • ENH: Migrate to CircleCI 2.0 and workflows (#943)
  • ENH: Improvements to CLIs (native & wrapper) (#944)
  • FIX: Rerun tCompCor interface in case of MemoryError (#942)

1.0.5 (21st of January 2018)

  • PIN: niworkflows-0.2.8 to fix several execution issues.
  • ENH: Code cleanup (#938)

1.0.4 (15th of January 2018)

  • FIX: Pin niworkflows-0.2.6 to fix several MultiProc errors (nipy/nipype#2368)
  • DOC: Fix DOI in citation boilerplate (#933)
  • FIX: Heuristics to prevent memory errors during aCompCor (#930).
  • FIX: RuntimeWarning: divide by zero encountered in float_scalars (#931).
  • FIX: INU correction before merging several T1w (#925).

1.0.3 (3rd of January 2018)

  • FIX: Pin niworkflows-0.2.4 to fix (#868).
  • FIX: Roll back run/task groupings after BIDS query (#918). Groupings for the multi-echo extension will be reenabled soon.

1.0.2 (2nd of January 2018)

  • FIX: Grouping runs broke FMRIPREP on some datasets (#916) Thanks to @emdupre

1.0.1 (1st of January 2018)

With thanks to @emdupre for contributions.

  • PIN: Update required niworkflows version to 0.2.3
  • FIX: Refine antsBrainExtraction if recon-all is run (#912) With thanks to Arno Klein for his [helpful comments here](https://github.com/nipreps/fmriprep/issues/431#issuecomment-299583391)
  • FIX: Use thinner contours in reportlets (#910)
  • FIX: Robuster EPI mask (#911)
  • FIX: Set workflow return value before potential error (#887)
  • DOC: Documentation about FreeSurfer and --fs-no-reconall (#894)
  • DOC: Fix example in installation ants-nthreads -> omp-nthreads (#885) With thanks to @mvdoc.
  • ENH: Allow for multiecho data (#875)

1.0.0 (6th of December 2017)

  • ENH: Add --resource-monitor flag (#883)
  • FIX: Collision between Multi-T1w and --no-freesurfer (#880)
  • FIX: Setting use_compression on resampling workflows (#882)
  • ENH: Estimate motion parameters before STC (#876)
  • ENH: Add --stop-on-first-crash option (#865)
  • FIX: Correctly handling xforms (#874)
  • FIX: Combined ROI reportlets (#872)
  • ENH: Strip reportlets out of full report (#867)

1.0.0-rc13 (1st of December 2017)

  • FIX: Broken --fs-license-file argument (#869)

1.0.0-rc12 (29th of November 2017)

  • ENH: Use Nipype MultiProc even for sequential execution (#856)
  • RF: More memory annotations and considerations (#816)
  • FIX: Controlling memory explosion (#854)
  • FIX: Mount nipype repositories as niworkflows submodule (#834)
  • FIX: Reduce image loads in local memory (#839)
  • ENH: Always sync qforms, refactor error messaging (#851)

1.0.0-rc11 (24th of November 2017)

  • ENH: Check for invalid qforms in validation (#847)
  • FIX: Update pybids to include latest bugfixes (#838)
  • FIX: MultiApplyTransforms failed with nthreads=1 (#835)

1.0.0-rc10 (9th of November 2017)

  • FIX: Adopt new FreeSurfer (v6.0.1) license mechanism (#787)
  • ENH: Output affine transforms from original T1w images to preprocessed anatomical (#726)
  • FIX: Correct headers in AFNI-generated NIfTI files (#818)
  • FIX: Normalize T1w image qform/sform matrices (#820)

1.0.0-rc9 (2nd of November 2017)

  • FIX: Fixed #776 (aCompCor - numpy.linalg.linalg.LinAlgError: SVD did not converge) via #807.
  • ENH: Added CSF column to _confounds.tsv (included in #807)
  • DOC: Add more details on the outputs of FMRIPREP and minor fixes (#811)
  • ENH: Processing confounds in BOLD space (#807)
  • ENH: Updated niworkflows and nipype, including the new feature to close all file descriptors (#810)
  • RF: Refactored BOLD workflows module (#805)
  • ENH: Improved memory annotations (#803, #807)

1.0.0-rc8 (27th of October 2017)

  • FIX: Allow missing magnitude2 in phasediff-type fieldmaps (#802)
  • FIX: Lower tolerance deciding t1_merge shapes (#798)
  • FIX: Be robust to 4D T1w images (#797)
  • ENH: Resource annotations (#746)
  • ENH: Use indexed_gzip with nibabel (#788)
  • FIX: Reduce FoV of outputs in T1w space (#785)

1.0.0-rc7 (20th of October 2017)

  • ENH: Update pinned version of nipype to latest master
  • ENH: Added rX permissions to make life easier on Singularity users (#757)
  • DOC: Citation boilerplate (#779)
  • FIX: Patch to remove long filenames after mri_concatenate_lta (#778)
  • FIX: Only use unbiased template with --longitudinal (#771)
  • FIX: Use t1_2_fsnative registration when sampling to surface (#762)
  • ENH: Remove --skull_strip_ants option (#761)
  • DOC: Add reference to beginners guide (#763)

1.0.0-rc6 (11th of October 2017)

  • ENH: Add inverse normalization transform (MNI -> T1w) to derivatives (#754)
  • ENH: Fall back to initial registration if BBR fails (#694)
  • FIX: Header and affine transform updates to resolve intermittent misalignments in reports (#743)
  • FIX: Register FreeSurfer template to FMRIPREP template, handling pre-run FreeSurfer subjects more robustly, saving affine to derivatives (#733)
  • ENH: Add OpenFMRI participant sampler command-line tool (#704)
  • ENH: For SyN-SDC, assume phase-encoding direction of A-P unless specified L-R (#740, #744)
  • ENH: Permit skull-stripping with NKI ANTs template (#729)
  • ENH: Erode aCompCor masks to target volume proportions, instead of fixed distances (#731, #732)
  • DOC: Documentation updates (#748)

1.0.0-rc5 (25th of September 2017)

  • FIX: Skip slice time correction on BOLD series < 5 volumes (#711)
  • FIX: Skip AFNI check for new versions (#723)
  • DOC: Documentation clarification and updates (#698, #711)

1.0.0-rc4 (12th of September 2017)

With thanks to Mathias Goncalves for contributions.

  • ENH: Collapse ITK transforms of head-motion correction in only one file (#695)
  • FIX: Raise error when run.py is called directly (#692)
  • FIX: Parse crash files when they are stored as text (#690)
  • ENH: Replace medial wall values with NaNs (#687)

1.0.0-rc3 (28th of August 2017)

With thanks to Anibal Sólon for contributions.

  • ENH: Add --low-mem option to reduce memory usage for large BOLD series (#663)
  • ENH: Parallelize anatomical conformation step (#666)
  • FIX: Handle missing functional data in SubjectSummary node (#670)
  • FIX: Disable --no-skull-strip-ants (AFNI skull-stripping) (#674)
  • FIX: Initialize SyN SDC more robustly (#680)
  • DOC: Add comprehensive documentation of workflow API (#638)

1.0.0-rc2 (12th of August 2017)

  • ENH: Increased support for partial field-of-view BOLD datasets (#659)
  • FIX: Slice time correction is now being applied to output data (not only to intermediate file used for motion estimation - #662)
  • FIX: Fieldmap unwarping is now being applied to MNI space outputs (not only to T1w space outputs - #662)

1.0.0-rc1 (8th of August 2017)

  • ENH: Include ICA-AROMA confounds in report (#646)
  • ENH: Save non-aggressively denoised BOLD series (#648)
  • ENH: Improved logging messages (#621)
  • ENH: Improved resource management (#622, #629, #640, #641)
  • ENH: Improved confound header names (#634)
  • FIX: Ensure multi-T1w image datasets have RAS-oriented template (#637)
  • FIX: More informative errors for conflicting options (#632)
  • DOC: Improved report summaries (#647)

0.x series (July 2017)

0.6.0 (31st of July 2017)

With thanks to Yaroslav Halchenko and Ilkay Isik for contributions.

  • ENH: Set threshold on up-sampling ratio in conformation, report results (#601)
  • ENH: Censor non-steady-state volumes prior to CompCor (#603)
  • FIX: Conformation failure in thick-slice, oblique T1w datasets (#601)
  • FIX: Crash/report failure of phase-difference SDC pipeline (#602, #604)
  • FIX: Prevent AFNI NIfTI extensions from crashing reference EPI estimation (#619)
  • DOC: Save logs to output directory (#605)
  • ENH: Upgrade to ICA-AROMA 0.4.1-beta (#611)

0.5.4 (20th of July 2017)

  • DOC: Improved report summaries describing steps taken (#584)
  • ENH: Uniformize command-line argument style (#592)

0.5.3 (18th of July 2017)

With thanks to Yaroslav Halchenko for contributions.

  • ENH: High-pass filter time series prior to CompCor (#577)
  • ENH: Validate and minimally conform BOLD images (#581)
  • FIX: Bug that prevented PE direction estimation (#586)
  • DOC: Log version/time in report (#587)

0.5.2 (30th of June 2017)

With thanks to James Kent for contributions.

  • ENH: Calculate noise components in functional data with ICA-AROMA (#539)
  • FIX: Remove unused parameters from function node, resolving crash (#576)

0.5.1 (24th of June 2017)

  • FIX: Invalid parameter in bbreg_wf (#572)

0.5.0 (21st of June 2017)

With thanks to James Kent for contributions.

  • ENH: EXPERIMENTAL: Fieldmap-less susceptibility correction with --use-syn-sdc option (#544)
  • FIX: Reduce interpolation artifacts in ConformSeries (#564)
  • FIX: Improve consistency of handling of fieldmaps (#565)
  • FIX: Apply T2w pial surface refinement at correct stage of FreeSurfer pipeline (#568)
  • ENH: Add --anat-only workflow option (#560)
  • FIX: Output all tissue class/probability maps (#569)
  • ENH: Upgrade to ANTs 2.2.0 (#561)

0.4.6 (14th of June 2017)

  • ENH: Conform and minimally resample multiple T1w images (#545)
  • FIX: Return non-zero exit code on all errors (#554)
  • ENH: Improve error reporting for missing subjects (#558)

0.4.5 (12th of June 2017)

With thanks to Marcel Falkiewicz for contributions.

  • FIX: Correctly display help in fmriprep-docker (#533)
  • FIX: Avoid invalid symlinks when running FreeSurfer (#536)
  • ENH: Improve dependency management for users unable to use Docker/Singularity containers (#549)
  • FIX: Return correct exit code when a Function node fails (#554)

0.4.4 (20th of May 2017)

With thanks to Feilong Ma for contributions.

  • ENH: Option to provide a custom reference grid image (--output-grid-reference) for determining the field of view and resolution of output images (#480)
  • ENH: Improved EPI skull stripping and tissue contrast enhancements (#519)
  • ENH: Improve resource use estimates in FreeSurfer workflow (#506)
  • ENH: Moved missing values in the DVARS* and FramewiseDisplacement columns of the _confounds.tsv from last row to the first row (#523)
  • ENH: More robust initialization of the normalization procedure (#529)

0.4.3 (10th of May 2017)

  • ENH: --output-space template targets template specified by --template flag (MNI152NLin2009cAsym supported) (#498)
  • FIX: Fix a bug causing small numerical discrepancies in input data voxel size to lead to different FOV of the output files (#513)

0.4.2 (3rd of May 2017)

  • ENH: Use robust template generation for multiple T1w images (#481)
  • ENH: Anatomical MNI outputs respect --output-space selection (#490)
  • ENH: Added support for distortion correction using opposite phase encoding direction EPI images (#493)
  • ENH: Switched to FSL BET for skullstripping of EPI images (#493)
  • ENH: --omp-nthreads controls maximum per-process thread count; replaces --ants-nthreads (#500)

0.4.1 (20th of April 2017)

  • Hotfix release (dependencies and deployment system)

0.4.0 (20th of April 2017)

  • ENH: Added an option to choose the degrees of freedom used when doing BOLD to T1w coregistration (--bold2t1w_dof). Set default to 9 to account for field inhomogeneities and coils heating up (#448)
  • ENH: Added support for phase difference and GE style fieldmaps (#448)
  • ENH: Generate GrayWhite, Pial, MidThickness and inflated surfaces (#398)
  • ENH: Memory and performance improvements for calculating the EPI reference (#436)
  • ENH: Sample functional series to subject and fsaverage surfaces (#391)
  • ENH: Output spaces for functional data may be selected with --output-space option (#447)
  • ENH: --skip-native functionality replaced by --output-space (#447)
  • ENH: fmriprep-docker wrapper script simplifies running in a Docker environment (#317)

0.3.2 (7th of April 2017)

With thanks to Asier Erramuzpe for contributions.

  • ENH: Added optional slice time correction (#415)
  • ENH: Removed redundant motion parameter conversion step using avscale (#415)
  • ENH: FreeSurfer submillimeter reconstruction may be disabled with --no-submm-recon (#422)
  • ENH: Switch bbregister init from fsl to coreg (FreeSurfer native #423)
  • ENH: Motion estimation now uses a smart reference image that takes advantage of T1 saturation (#421)
  • FIX: Fix report generation with --reports-only (#427)

0.3.1 (24th of March 2017)

  • ENH: Perform bias field correction of EPI images prior to coregistration (#409)
  • FIX: Fix an orientation issue affecting some datasets when bbregister was used (#408)
  • ENH: Minor improvements to the reports aesthetics (#428)

0.3.0 (20th of March 2017)

  • FIX: Affine and warp MNI transforms are now applied in the correct order
  • ENH: Added preliminary support for reconstruction of cortical surfaces using FreeSurfer
  • ENH: Switched to bbregister for BOLD to T1 coregistration
  • ENH: Switched to sinc interpolation of preprocessed BOLD and T1w outputs
  • ENH: Preprocessed BOLD volumes are now saved in the T1w space instead of mean BOLD
  • FIX: Fixed a bug with MCFLIRT interpolation inducing slow drift
  • ENH: All files are now saved in Float32 instead of Float64 to save space

0.2.0 (13th of January 2017)

  • Initial public release

0.1.2 (3rd of October 2016)

  • FIX: Downloads from OSF, remove data downloader (now in niworkflows)
  • FIX: pybids was missing in the install_requires
  • FIX: Deprecated -S/--subject-id tag
  • ENH: Accept subjects with several T1w images (#114)
  • ENH: Documentation updates (#130, #131)
  • TST: Re-enabled CircleCI tests on one subject from ds054 of OpenfMRI
  • ENH: Add C3D to docker image, updated poldracklab hub (#128, #119)
  • ENH: CLI is now BIDS-Apps compliant (#123)

0.1.1 (30th of July 2016)

  • ENH: Grabbit integration (#113)
  • ENH: More outputs in MNI space (#99)
  • ENH: Implementation of phase-difference fieldmap estimation (#91)
  • ENH: Fixed bug using non-RAS EPI
  • ENH: Works on ds005 (datasets without fieldmap nor sbref)
  • ENH: Outputs start to follow BIDS-derivatives (WIP)

0.0.1

  • ENH: Added Docker images
  • DOC: Added base code for automatic publication to RTD.
  • Set up CircleCI with a first smoke test on one subject.
  • BIDS tree scrubbing and subject-session-run selection.
  • Refactored big workflow into consistent pieces.
  • Migrated Craig's original code