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:

Department of Psychology, Stanford University

Montreal Neurological Institute, McGill University

Neuroscience Program, University of Iowa

Department of Psychology, Florida International University

University of Texas at Austin

Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń

Department of Neuroscience, University of Pennsylvania, PA, USA

Department of Psychology, New York University

Computational Neuroimaging Lab, BioCruces Health Research Institute

Department of Psychology, Columbia University

Department of Psychology, University of California, Berkeley

SIMEXP Lab, CRIUGM, University of Montréal, Montréal, Canada

Child Mind Institute

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

McLean Hospital Brain Imaging Center, MA, USA

Consolidated Department of Psychiatry, Harvard Medical School, MA, USA

Center for Lifespan Changes in Brain and Cognition, University of Oslo

URPP Dynamics of Healthy Aging, University of Zurich

Perelman School of Medicine, University of Pennsylvania, PA, USA

Center for Brain Imaging, New York University

Department of Psychology, New York University, NY, USA

Dartmouth College: Hanover, NH, United States

Department of Psychiatry, McGill University

McGovern Institute for Brain Research, MIT, MA, USA

Department of Otolaryngology, Harvard Medical School, MA, USA

Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen

Max Planck Institute for Empirical Aesthetics

Cyceron, UMS 3408 (CNRS - UCBN), France

Speech & Hearing Bioscience & Technology Program, Harvard University

Max Planck UCL Centre for Computational Psychiatry and Ageing Research, University College London

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.

FIX: Do not reorient magnitude images (nipreps/sdcflows#98)

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)

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:

Department of Psychology, Stanford University

Montreal Neurological Institute, McGill University

Neuroscience Program, University of Iowa

Department of Psychology, Florida International University

University of Texas at Austin

Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń

Computational Neuroimaging Lab, BioCruces Health Research Institute

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

Department of Psychology, Columbia University

Department of Psychology, University of California, Berkeley

Child Mind Institute

Dartmouth College: Hanover, NH, United States

Center for Lifespan Changes in Brain and Cognition, University of Oslo

Department of Psychiatry, McGill University

URPP Dynamics of Healthy Aging, University of Zurich

Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen

Perelman School of Medicine, University of Pennsylvania, PA, USA

Center for Brain Imaging, New York University

Department of Psychology, New York University, NY, USA

McGovern Institute for Brain Research, MIT, MA, USA

Department of Otolaryngology, Harvard Medical School, MA, USA

Max Planck Institute for Empirical Aesthetics

Cyceron, UMS 3408 (CNRS - UCBN), France

Speech & Hearing Bioscience & Technology Program, Harvard University

Max Planck UCL Centre for Computational Psychiatry and Ageing Research, University College London

Department of Neuroscience, University of Pennsylvania, PA, USA

State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University