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Changelog

All notable changes to this project will be documented (for humans) in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[0.5.4] - 2019-04-29

This release includes fixes to BIDS multi-echo conversions, the re-implementation of queuing support (currently just SLURM), as well as some bugfixes.

Starting today, we will (finally) push versioned releases to DockerHub. Finally, to more accurately reflect on-going development, the latest tag has been renamed to unstable.

Added

  • Readthedocs documentation ([#327][])

Changed

  • Update Docker dcm2niix to v.1.0.20190410 ([#334][])
  • Allow usage of --files with basic heuristics. This requires use of --subject flag, and is limited to one subject. (#293)

Deprecated

Fixed

  • Improve support for multiple --queue-args ([#328][])
  • Fixed an issue where generated BIDS sidecar files were missing additional information - treating all conversions as if the --minmeta flag was used (#306)
  • Re-enable SLURM queuing support (#304)
  • BIDS multi-echo support for EPI + T1 images (#293)
  • Correctly handle the case when outtype of heuristic has "dicom" before '.nii.gz'. Previously would have lead to absent additional metadata extraction etc (#310)

Removed

  • --sbargs argument was renamed to --queue-args (#304)

Security

[0.5.3] - 2019-01-12

Minor hot bugfix release

Fixed

  • Do not shorten spaces in the dates while pretty printing .json

[0.5.2] - 2019-01-04

A variety of bugfixes

Changed

  • Reproin heuristic: __dup indices would now be assigned incrementally individually per each sequence, so there is a chance to properly treat associate for multi-file (e.g. fmap) sequences
  • Reproin heuristic: also split StudyDescription by space not only by ^
  • tests/ moved under heudiconv/tests to ease maintenance and facilitate testing of an installed heudiconv
  • Protocol name will also be accessed from private Siemens csa.tProtocolName header field if not present in public one
  • nipype>=0.12.0 is required now

Fixed

  • Multiple files produced by dcm2niix are first sorted to guarantee correct order e.g. of magnitude files in fieldmaps, which otherwise resulted in incorrect according to BIDS ordering of them
  • Aggregated top level .json files now would contain only the fields with the same values from all scanned files. In prior versions, those files were not regenerated after an initial conversion
  • Unicode handling in anonimization scripts

[0.5.1] - 2018-07-05

Bugfix release

Added

  • Video tutorial / updated slides
  • Helper to set metadata restrictions correctly
  • Usage is now shown when run without arguments
  • New fields to Seqinfo
    • series_uid
  • Reproin heuristic support for xnat

Changed

  • Dockerfile updated to use dcm2niix v1.0.20180622
  • Conversion table will be regenerated if heurisic has changed
  • Do not touch existing BIDS files
    • events.tsv
    • task JSON

Fixed

  • Python 2.7.8 and older installation
  • Support for updated packages
    • Datalad 0.10
    • pydicom 1.0.2
  • Later versions of pydicom are prioritized first
  • JSON pretty print should not remove spaces
  • Phasediff fieldmaps behavior
    • ensure phasediff exists
    • support for single magnitude acquisitions

[0.5] - 2018-03-01

The first release after major refactoring:

Changed

  • Refactored into a proper heudiconv Python module
    • heuristics is now a heudiconv.heuristics submodule
    • you can specify shipped heuristics by name (e.g. -f reproin) without providing full path to their files
    • you need to use --files (not just positional argument(s)) if not using --dicom_dir_templates or --subjects to point to data files or directories with input DICOMs
  • Dockerfile is generated by neurodocker
  • Logging verbosity reduced
  • Increased leniency with missing DICOM fields
  • dbic_bids heuristic renamed into reproin

Added

Removed

  • Support for converters other than dcm2niix, which is now the default. Explicitly specify -c none to only prepare conversion specification files without performing actual conversion

Fixed

  • Compatibility with Nipype 1.0, PyDicom 1.0, and upcoming DataLad 0.10
  • Consistency with converted files permissions
  • Ensured subject id for BIDS conversions will be BIDS compliant
  • Re-add seqinfo fields as column names in generated dicominfo
  • More robust sanity check of the regex reformatted .json file to avoid numeric precision issues
  • Many other various issues

[0.4] - 2017-10-15

A usable release to support DBIC use-case

Added

  • more testing

Changes

  • Dockerfile updates (added pigz, progressed forward dcm2niix)

Fixed

  • correct date/time in BIDS _scans files
  • sort entries in _scans by date and then filename

[0.3] - 2017-07-10

A somewhat working release on the way to support DBIC use-case

Added

  • more tests
  • groupping of dicoms by series if provided
  • many more features and fixes

[0.2] - 2016-10-20

An initial release on the way to support DBIC use-case

Added

  • basic Python project assets (setup.py, etc)
  • basic tests
  • datalad support
  • dbic_bids heuristic
  • --dbg command line flag to enter pdb environment upon failure

Fixed

  • Better Python3 support
  • Better PEP8 compliance

[0.1] - 2015-09-23

Initial version

Just a template for future records:

[Unreleased] - Date

TODO Summary

Added

Changed

Deprecated

Fixed

Removed

Security

References