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Recent Releases of HeuDiConv — flexible DICOM conversion into structured directory layouts

HeuDiConv — flexible DICOM conversion into structured directory layouts - v1.3.3

🐛 Bug Fix

  • Require nibabel >= 5.3.1 (fixes issues with enhanced DICOMs), and drop Python 3.8 support #800 (@bpinsard)
  • Do not create README if there is other allowed README.md or alike #818 (@yarikoptic)

🏠 Internal

📝 Documentation

  • Improve formatting in custom_seqinfo doc + provide url to an example #815 (@yarikoptic)
  • DOC: Replace gone pointer to "Usage" with "CLI Reference" #811 (@yarikoptic)

Authors: 3

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] 9 months ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v1.3.2

🐛 Bug Fix

🏠 Internal

  • Docker image: Use newer debian stable for the base and newer dcm2niix #790 (@yarikoptic)

🧪 Tests

Authors: 1

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 1 year ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v1.3.1

🐛 Bug Fix

  • Fix assignment of sensitive git-annex metadata data via glob patterns (regression introduced by #739) #793 (@bpinsard)

Authors: 1

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 1 year ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v1.3.0

🚀 Enhancement

🐛 Bug Fix

  • BF(workaround): if heuristic provided just a string and not list of types -- make it into a tuple #787 (@yarikoptic)
  • Refactor create_seqinfo tiny bit to avoid duplication and add logging; and in tests to reuse list of dicom paths #785 (@yarikoptic)
  • extract sequence_name from PulseSequenceName on Siemens XA** data #753 (@bpinsard)
  • Just INFO not WARNING if heuristic is missing intotoids #784 (@yarikoptic)

Authors: 3

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 1 year ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v1.2.0

🚀 Enhancement

  • [ENH] add PlainAcquisitionLabel IntendedFor method #768 (@octomike)

🐛 Bug Fix

  • Fixup testing: kludge for pydicom 3.0.0 in dcmstack, ignore some warnings from nipype for python 3.12 #782 (@yarikoptic)
  • Add JOSS paper badge to README.md (leading) (@yarikoptic)
  • Provide title matching JOSS publication as the title in .zenodo.json (@yarikoptic)

🏠 Internal

  • Rename s variable to curr_seqinfo in reproin heuristic #779 (@tsalo)

📝 Documentation

  • run pre-commit on all files to avoid unrelated errors in other PRs. #778 (@bpinsard)

🧪 Tests

Authors: 4

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 1 year ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v1.1.6

🏠 Internal

Authors: 1

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 1 year ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v1.1.5

🏠 Internal

Authors: 1

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 1 year ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v1.1.4

🏠 Internal

  • Replace CITATION.cff with .zenodo.json for correct (split) affiliations on Zenodo #764 (@yarikoptic)
  • Codespell tuneup: no dedicated workflow (part of tox -e lint), and fix few freshly detected typos #762 (@yarikoptic)

Authors: 1

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 1 year ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v1.1.3

📝 Documentation

Authors: 1

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 1 year ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v1.1.2

🏠 Internal

📝 Documentation

Authors: 3

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 1 year ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v1.1.1

🐛 Bug Fix

  • Handle cases where dates/times in DICOM are empty strings, not Nones (e.g. after some anonymization) #756 (@jennan @yarikoptic)

Authors: 2

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 1 year ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v1.1.0

🚀 Enhancement

  • Add support for a custom seqinfo to extract from DICOMs any additional metadata desired for a heuristic #581 (@yarikoptic @bpinsard)
  • codespell: ignore "build" folder which might be on the system #581 (@yarikoptic)

Authors: 2

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 2 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v1.0.2

🐛 Bug Fix

⚠️ Pushed to master

🏠 Internal

📝 Documentation

Authors: 6

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 2 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v1.0.1

🐛 Bug Fix

  • Drop Python 3.7 support #722 (@yarikoptic)
  • ReproIn: give an informative assertion message when multiple values are found #718 (@yarikoptic)
  • Convert assertion into a warning that we would not use dicom dir tempate option #709 (@yarikoptic)
  • Do not demand --files for all commands, even those which do not care about it (like populate-intended-for) #708 (@yarikoptic)

⚠️ Pushed to master

  • Add script to sensor dicoms -- for the error where dcm2niix might or might not fail but issues an Error (@yarikoptic)

🏠 Internal

  • Ran pre-commit on everything, black decided to adjust some formatting #721 (@yarikoptic)
  • Make sensor-dicoms use gnu-getopt if present (on OSX) #721 (@yarikoptic)

Authors: 1

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 2 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v1.0.0

💥 Breaking Change

🚀 Enhancement

  • Fix inconsistent behavior of existing session when using -d compared to --files option: raise an AssertionError instead of just a warning #682 (@neurorepro)

🐛 Bug Fix

🏠 Internal

  • Add codespell to lint tox env #706 (@yarikoptic)
  • test-compare-two-versions.sh: also ignore differences in HeudiconvVersion field in jsons since we have it there now #685 (@yarikoptic)

📝 Documentation

  • Add description of placeholders which could be used in the produced templates #681 (@yarikoptic)

Authors: 3

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 2 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v0.13.1

🐛 Bug Fix

  • Make .subsecond optional in BIDS/DICOM datetime entries #675 (@yarikoptic)

🏠 Internal

Authors: 2

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 2 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v0.13.0

🚀 Enhancement

  • Add type annotations #656 (@jwodder @yarikoptic)
  • ENH: Support extracting DICOMs from ZIP files (and possibly other archives) by switching to use shutil.unpack_archive instead of tarfile module functionality #471 (@HippocampusGirl @psadil)
  • Allow filling of acq_time when AcquisitionDate AcquisitionTime missing #614 (@psadil)

🐛 Bug Fix

  • BF(?): make _setter images be taken as scouts - only DICOMs are saved #570 (@yarikoptic)
  • Adjust .mailmap to account for mapping various folks with multiple emails so that git shortlog -sn -e provides entries without duplicates #570 (@yarikoptic)
  • Make an embed_dicom_and_nifti_metadata() annotation work on Python 3.7 #673 (@jwodder)
  • Merge branch 'featuredicomcompresslevel' #673 (@yarikoptic)
  • Update heudiconv/dicoms.py #669 (@octomike)
  • Don't call logging.basicConfig() in __init__.py #659 (@jwodder)

⚠️ Pushed to master

  • Mailmapping more contributors (@yarikoptic)
  • Adjust comment and remove trailing space flipping linting (@yarikoptic)

🏠 Internal

  • Declare custom_grouping return type instead of casting #671 (@jwodder)
  • Use pydicom.dcmread() instead of pydicom.read_file() #668 (@jwodder)
  • Add sample_nifti.json to .gitignore #663 (@jwodder)
  • Write command arguments as lists of strings instead of splitting strings on whitespace #664 (@jwodder)
  • Add & apply pre-commit and lint job #658 (@jwodder)
  • Fix some strings with \ (make them raw or double-), improve pytest config: move to tox.ini, make unknown warnings into errors #660 (@jwodder)
  • Replace py.path with pathlib #654 (@jwodder)

🧪 Tests

  • Make test_private_csa_header test write to temp dir #666 (@jwodder)

🔩 Dependency Updates

  • Replace third-party mock library with stdlib's unittest.mock #661 (@jwodder)
  • Remove kludgy support for older versions of pydicom and dcmstack #662 (@jwodder)
  • Remove use of six #655 (@jwodder)

Authors: 5

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 2 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v0.12.2

🏠 Internal

Authors: 1

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 3 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v0.12.1

🐛 Bug Fix

  • Re-add explicit instructions to install dcm2niix "manually" and remove it from install_requires #651 (@yarikoptic)

📝 Documentation

Authors: 3

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 3 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v0.12.0

🚀 Enhancement

🐛 Bug Fix

⚠️ Pushed to master

  • DOC: add clarification on where docs/requirements.txt should be "installed" from (@yarikoptic)
  • fix minor typo (@yarikoptic)
  • DOC: fixed the comment. Original was copy/pasted from DataLad (@yarikoptic)

🏠 Internal

  • dcm2niix explicitly noted as a (PyPI) dependency and removed from being installed via apt-get etc #628 (@TheChymera @yarikoptic)

📝 Documentation

🧪 Tests

Authors: 5

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 3 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v0.11.6

🏠 Internal

📝 Documentation

Authors: 2

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 3 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v0.11.5

🐛 Bug Fix

  • Fix certificate issue as indicated in #595 #597 (@neurorepro)
  • BF docker build: use python3.9 (not 3.7 which gets upgraded to 3.9) and newer dcm2niix #596 (@yarikoptic)
  • Fixup miniconda spec for neurodocker so it produces dockerfile now #596 (@yarikoptic)

🏠 Internal

📝 Documentation

Authors: 3

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 3 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v0.11.4

🐛 Bug Fix

  • install dcmstack straight from github until it is released #593 (@yarikoptic)
  • DOC: provide rudimentary How to contribute section in README.rst (@yarikoptic)

⚠️ Pushed to master

  • Check out a full clone when testing (@jwodder)
  • Convert Travis workflow to GitHub Actions (@jwodder)
  • BF(docker): replace old -tipsy with -y -all for conda clean as neurodocker does now (@yarikoptic)
  • adjusted script for neurodocker although it does not work (@yarikoptic)

🏠 Internal

  • 0.9 of dcmstack was released, no need for github version #594 (@yarikoptic)
  • Minor face-lifts to ReproIn: align doc and code better to BIDS terms, address deprecation warnings etc #569 (@yarikoptic)

Authors: 2

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 3 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v0.11.3

🏠 Internal

Authors: 1

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 3 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v0.11.2

🏠 Internal

  • Make versioningit write version to file; make setup.py read version as fallback #566 (@jwodder)
  • BF: add fetch-depth: 0 to get all tags into docker builds of master #566 (@yarikoptic)

Authors: 2

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 3 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v0.11.1

🏠 Internal

  • Remove .git/ from .dockerignore so that versioning works while building docker image #564 (@yarikoptic)

Authors: 1

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 3 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v0.11.0

🚀 Enhancement

🐛 Bug Fix

  • bids_ME heuristic: add test for the dataset that raised #541, add support for MEGRE #547 (@pvelasco @yarikoptic)
  • reproin heuristic: specify POPULATEINTENDEDFOR_OPTS #546 (@yarikoptic)
  • FIX: Convert sets to lists for filename updaters #461 (@tsalo)
  • Added new infofilestyle compatible with BIDS #12 (@chrisgorgo)
  • try a simple fix for wrongly ordered files in tar file #535 (@bpinsard)
  • BF: Fix the order of the 'echo' entity in the filename #542 (@pvelasco)
  • ENH: add HeudiconvVersion to sidecar .json files #529 (@yarikoptic)
  • BF (TST): make anonymize_script actually output anything and map determinstically #511 (@yarikoptic)
  • Rename DICOMCONVERT_README.md to README.md #4 (@satra)

⚠️ Pushed to master

  • Dockerfile - use bullseye for the base and fresh dcm2niix (@yarikoptic)

🏠 Internal

🧪 Tests

  • BF(TST): use caplog to control logging level, use python3 in shebang #553 (@yarikoptic)
  • BF(TST): use caplog instead of capfd for testing if we log a warning #534 (@yarikoptic)
  • Travis - Use bionic for the base #533 (@yarikoptic)

Authors: 9

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 3 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts -

Scientific Software - Peer-reviewed - Python
Published by yarikoptic about 4 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts -

Scientific Software - Peer-reviewed - Python
Published by yarikoptic about 5 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts -

Scientific Software - Peer-reviewed - Python
Published by yarikoptic over 5 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts -

Scientific Software - Peer-reviewed - Python
Published by yarikoptic almost 6 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts -

Scientific Software - Peer-reviewed - Python
Published by yarikoptic about 6 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - v0.5.4: [0.5.4] - 2019-04-29

[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 push versioned releases to DockerHub. Finally, to more accurately reflect on-going development, the latest tag has been renamed to unstable. We encourage users to check https://hub.docker.com/r/nipy/heudiconv/tags to ensure you are using the most up-to-date version.

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

Scientific Software - Peer-reviewed - Python
Published by mgxd over 6 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts -

Scientific Software - Peer-reviewed - Python
Published by yarikoptic almost 7 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts -

Scientific Software - Peer-reviewed - Python
Published by yarikoptic almost 7 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts - Heudiconv v0.5.1

[0.5.1] - 2018-06-29

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

Scientific Software - Peer-reviewed - Python
Published by mgxd over 7 years ago

HeuDiConv — flexible DICOM conversion into structured directory layouts -

Scientific Software - Peer-reviewed - Python
Published by yarikoptic about 8 years ago