Warning: This document is for an old version of dmriprep. The main version is master.

What’s new?

Latest release - 0.5.0 (March 11, 2021)

A new minor release going forward with some of the items of our roadmap. The most salient features are the integration of FSL Eddy and the adoption of the new SDCFlows 2.0 API.

Author list for papers based on dMRIPrep 0.5.x series

As described in the Contributor Guidelines, anyone listed as developer or contributor may write and submit manuscripts about dMRIPrep. To do so, please move the author(s) name(s) to the front of the following list:

Joseph, Michael 1; Mansour, Salim 1; Pisner, Derek 2; Richie-Halford, Adam 3; Lerma-Usabiaga, Garikoitz 4, 5; Keshavan, Anisha 3; Kent, James D. 6; Dickie, Erin W. 7; Cieslak, Matthew 8; Poldrack, Russell A. 5; Veraart, Jelle 9; Rokem, Ariel 10; Esteban, Oscar 11.

Affiliations:

  1. The Centre for Addiction and Mental Health

  2. Department of Psychology, University of Texas at Austin, TX, USA

  3. The University of Washington, eScience Institute

  4. Basque Center on Cognition, Brain and Language (BCBL)

  5. Department of Psychology, Stanford University

  6. Neuroscience Program, University of Iowa

  7. Krembil Centre for Neuroinformatics, The Centre for Addiction and Mental Health, Dept. of Psychiatry, University of Toronto

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

  9. School of Medicine, New York University

  10. The University of Washington eScience Institute

  11. Dept. of Radiology, Lausanne University Hospital and University of Lausanne

  • FIX: PEPOLAR & mapped fieldmaps not showing up in reports (#158)

  • FIX: Update to new NiWorkflows API (#156)

  • FIX: Change in _svgutils_ API (0.3.2) breaks our reportlet generation (#151)

  • FIX: Correctly check SDCFlows’ registry of IntendedFor files (#141)

  • FIX: Honor --nprocs flag (#142)

  • ENH: fieldmap-less integration from SDCFlows 2.0 (#153)

  • ENH: Temporary integration of FSL Eddy (#144)

  • ENH: Connect fieldmap estimation to preprocessing pipeline of individual DWI runs (#140)

  • ENH: Refactor workflow for simplicity - explicit iteration over DWIs (#138)

  • ENH: Run fieldmap estimation using SDCFlows 2.0 (#137)

  • FIX/MAINT: Drop Python 3.6 + Revise Python environment (versions pinned) in Dockerfile (#146)

  • MAINT: Refactor Dockerfile with better use of miniconda (#155)

  • MAINT: Update SDCFlows pinning to the latest 2.0.0 release (#152)

  • DOC: Revise dMRIPrep’s road-map (#147)

  • DOC: Add FSL topup reference in citation boilerplate (#148)

  • DOC: change “functional” to “diffusion” (#143)

Previous releases

0.4.0 (December 10, 2020)

A minor release including T1w-DWI registration with FreeSurfer’s bbregister. This minor release also includes some documentation improvements and a fair amount of maintenance tasks, the most salient of which is migrating our test data to a DataLad + GiHub + OSF infrastructure that will allow more flexibly update test datasets.

  • ENH: Use bbregister upstreamed to NiWorkflows, with sloppy mode (#131)

  • ENH: Port bbregister T1w-DWI registration from fMRIPrep (#125)

  • DOC: Link NeuroHackademy session’s video. (#120)

  • DOC: Update readme and delete contributing guidelines in favour of nipreps website (#127)

  • DOC: Add base SVG file for the “figure1” (aka the workflow) flowchart (#124)

  • MAINT: Move test data to a full-datalad settings (#134)

  • MAINT: Move packaging tests from TravisCI to GitHub Actions (#135)

  • STY/MAINT: Preparing the first large overhaul of dMRIPrep (#130)

  • MAINT: Adding J. Veraart and E. Dickie to the contributors list (#126, #133)

0.3.0 (October 13, 2020)

A long overdue minor release initiating the 0.3.x series and including the milestones set for the 0.3.0 version in our roadmap.

A full list of changes can be found below.

  • FIX: Revise vector tests broken when addressing other issues (#103)

  • FIX: Minor refactor of DWI/brainmasks utilities and dtypes (#101)

  • FIX: Test pin to reports_bug branch (#59)

  • FIX: CircleCI on_fail command (#61)

  • ENH: An initial implementation of SD estimation. (#97)

  • ENH: Minor refactor reorganizing base workflows, in prep for #97 (#110)

  • ENH: Use new DerivativesDataSink from NiWorkflows 1.2.0 (#108)

  • ENH: Port the new anatomical fast-track from fMRIPrep (#109)

  • ENH: Data-driven b0 identification tool (#107)

  • ENH: Do not raise error in all instances of b-vecs/vals inconsistencies (#100)

  • ENH: Update DiffusionGradientTable interface to support vector reorientation (#89)

  • ENH: Update image utility output path behavior (#81)

  • ENH: Adopt config module (#88)

  • ENH: Added ds001771/sub-36 dataset and FS derivatives (#67)

  • DOC: Add nipreps developers and year to LICENSE file (#69)

  • DOC: Roadmap documentation (#58)

  • DOC: Document the fact that we are using popylar/GA for usage tracking (#63)

  • MAINT: Remove the leftovers of AFQ in .afq/ (#106)

  • MAINT: Refactor the workflow to use Nipype iterables (#105)

  • MAINT: Add ds001771 to the smoke-tests battery (#91)

  • MAINT: Revisions after previous maintenance commit (#83) (#85)

  • MAINT: Update dependencies (#83)

Author list for papers based on dMRIPrep 0.3.x series

As described in the Contributor Guidelines, anyone listed as developer or contributor may write and submit manuscripts about dMRIPrep. To do so, please move the author(s) name(s) to the front of the following list:

Joseph, Michael 1; Pisner, Derek 2; Richie-Halford, Adam 3; Lerma-Usabiaga, Garikoitz 4; Keshavan, Anisha 3; Kent, James D. 5; Cieslak, Matthew 6; Poldrack, Russell A. 7; Rokem, Ariel 8; Esteban, Oscar 9.

Affiliations:

  1. The Centre for Addiction and Mental Health

  2. Department of Psychology, University of Texas at Austin, TX, USA

  3. The University of Washington, eScience Institute

  4. Department of Psychology, Stanford University, CA, USA

  5. Neuroscience Program, University of Iowa

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

  7. Department of Psychology, Stanford University

  8. The University of Washington eScience Institute

  9. Dep. of Radiology, Lausanne University Hospital and University of Lausanne

0.2.x series

0.2.2 (January 15, 2020)

A release to show the deployment process on the Sprint.

  • ENH: b0 reference and skullstrip workflow (#50)

  • FIX: Version on docker target of Makefile (#54)

  • FIX/ENH: Remove sentry tracking and add popylar tracking. (#51)

  • MAINT: Some small changes to the Dockerfile. (#53)

  • ENH: Set up customized report specification (#34)

  • MAINT: Use a local docker registry instead of load/save (#46)

0.2.1 (December 12, 2019)

A bugfix release to test that versioned documentation is working.

  • FIX: Remove count of DWI scans according to task_id (#10)

  • ENH: Vector representation and checking utilities (#26)

  • ENH: Start running smoke tests on CircleCI (#31)

  • ENH: Add config for CircleCI (#13)

  • DOC: Build versioned docs and deploy them to gh-pages (#45)

  • MAINT: Revise execution options in CircleCi (#33)

  • MAINT: A minimal infrastructure for unit-tests, with some initial test files (#32)

  • MAINT: Add a branch step to the contribution guidelines. (#21)

  • MAINT: Add maintenance script to update the changelog, update CHANGES (#22)

  • MAINT: Add a base of CONTRIBUTING.md guidelines (#14)

  • MAINT: Fix typos and add Makefiles (#11)

  • MAINT: Add TravisCI for code linting with flake8 (#18)

0.2.0 (September 06, 2019)

A first attempt to roll out a release capable of running sMRIPrep for the anatomical processing. This release will also serve to exercise the continuous deployment set-up.

0.1.x series

0.1.1a0 (September 05, 2019)

Testing Zenodo integration.

0.1.1 (September 05, 2019)

Tag to mark the start of a big refactor to adhere to fMRIPrep’s principles. dMRIPrep will bring the contents of this branch back in as a plugin.

0.1.0 (November 21, 2018)

First release on GitHub.