Changelog

All notable changes to this project will be documented in this file. The format is based on Keep a Changelog

[3.6.1] - 2021-05-20

Fixed

  • The bidscoiner no longer sometimes crashes when dcm2niix produced custom suffixes

[3.6.0] - 2021-05-13

Added

  • Support for BIDS v1.6.0 (-> PET)
  • Separate tabs for DICOM and PAR to edit all the mappings of mixed datasets in a single bidseditor session
  • Run-item matching on filesystem properties, i.e. on the pathname, filename and filesize and nr of files in the folder. This can be used in conjunction with the (DICOM/PAR) attributes
  • A meta-data dictionary that can be edited with the bidseditor and that will be added to the json sidecar files by the bidscoiner
  • More user feedback in the GUI for new BIDS-compliancy checks on missing or invalid bids data
  • A right-click menu option to remove a run-item from the bidsmap (advanced usage)
  • The option to load a new bidsmap in the bidseditor
  • Enable the user to edit json, yaml, tsv and other non-DICOM / non-PAR files with double-clicks in the data browser
  • A central ‘bidscoin’ package function with various utilities, such as listing and installing BIDScoin plugins or executables
  • Plugins can have their own ‘test’ routine that can be called from the bidseditor

Changed

  • Using regular expressions instead of fnmatch to match (template bidsmap) attribute values. This makes the templates more powerful and flexible
  • Moved the bidsmapping and bidscoining functionality to stand-alone plugins (changed API), making plugins a first-class BIDScoin citizen
  • The plugins have moved to the bidsmap[’Options’], where they have their own key-value options dictionary (changed API)
  • Move IntendedFor field over to the new meta-data dictionary
  • Renamed the leave_out datatype to exclude
  • Re-introduced skipping hidden folders (hidden files are also skipped)
  • Moved the ‘pulltutorial’ function over to the new ‘bidscoin’ function

Removed

  • P7 and nifti support (it was never implemented anyhow)
  • The option to edit new mappings on-the-fly in the bidsmapper (-i 2)

3.5.3 - 2021-04-13

Fixed

  • Save non-standard fieldmaps in the derivative folder
  • Add ‘AcquisitionTime’ to physio json-files and add the physio-files to the *_scans.tsv file

3.5.2 - 2021-03-21

Fixed:

  • pypi upload

3.5.1 - 2021-03-21

Added

  • BIDScoin version update checks

Fixed

  • Speed optimizations
  • Code clean-up
  • More robust dcm2niix output handling

3.5 - 2021-03-08

A significant rewrite and evolution of BIDScoin!

Added

  • Support for BIDS v1.5
  • Support for Siemens advanced physiological logging data
  • Improved GUI help tooltips and user feedback
  • Improved feedback and control for invalid bidsnames
  • Validation of run-items and bidsmaps against the BIDS schema

Changed

  • Use the dccn template bidsmap as the default

Fixed

  • Simplified and improved (hopefully) handling of fieldmaps

3.0.8 - 2020-09-28

Fixed

  • Various minor bugs

3.0.6 - 2020-08-05

Fixed

  • Minor but important bugfix in the setup :-)

3.0.5 - 2020-08-05

Added

  • A download tool for tutorial data
  • A tool for regenerating the participants.tsv file

Fixed

  • Various bugs

3.0.4 - 2020-05-14

Added

  • Export function in the bidseditor to allow for adding run items to existing (template) bidsmaps
  • Support for Unix-shell style wildcards for matching run items in the bidsmap

Changed

  • Improved DCCN example template bidsmap

Fixed

  • Various minor bugs

3.0.3 - 2020-04-14

Fixed

  • A small bugfix to properly handle appending dcm2niix suffices to the BIDS acq-label

3.0.2 - 2020-04-06

Fixed

  • Special thanks to Thom Shaw, who was patient enough to keep testing untested bugfixes (#56) and helped making BIDScoin better :-)

3.0.1 - 2020-04-04

Added

  • A ‘provenance store’ in the bidsmapper to fix a bug (#56 ) and allow for moving the bids-folder around
  • Support for zipped/tarred DICOM directories

3.0 - 2020-04-01

A Significant rewrite to make BIDScoin more robust, user friendly and feature-rich :-)

Added

  • First support for Philips PAR / REC data format
  • A BIDS compliant defacing tool
  • A BIDS compliant multi-echo combination tool
  • Much improved documentation (https://bidscoin.readthedocs.io)

2.3.1 - 2019-09-12

Fixed

  • a small but important bug that caused datasets without fieldmaps to crash (my test datasets all had fieldmaps :-))

2.3 - 2019-08-29

A lot of improvements have landed in 2.3, making it the best release of the 2-series by far!

Added

  • The possibility to edit Participant labels
  • Various tests and checks in Options to ensure creating good working bidsmaps / BIDS output data
  • Upgraded compliance with bids v1.2.1
  • The possibility to leave-out certain data types / runs

Changed

  • A new workflow that is easier and more consistent
  • Greatly improved graphical user interface and error/warning reporting
  • Improved bidsmap_dccn template

Fixed

  • Significant code refactoring to squash a number of important bugs and make the code more robust and maintainable

2.2 - 2019-07-11

Added

  • Options tab to edit and test the bidscoin Options
  • A leave-out option (to ignore runs / prevent them from showing up in the BIDS directory)
  • A graphical interface to the bidsmapper
  • Improved logging
  • Improved the DICOM attribute wildcard feature

Changed

  • New layout of the main and edit windows

Fixed

  • Various bugfixes

2.1 - 2019-06-23

Added

  • Editing of bidsmap Options

Fixed

  • IntendedFor in fieldmap json sidecar files
  • Code redundancy

2.0 - 2019-06-18

A major release and rewrite with important user-facing improvements

Added

  • A shiny GUI :-)
  • A new and much easier workflow

Fixed

  • Various bugfixes

1.5 - 2019-03-06

Added

  • Support for PET scans
  • Support for DICOMDIR data
  • Saving of template sidecar files in the bids output directory

Changed

  • increased flexibility for renaming / reorganising the raw (input) data structure
  • Added provenance data to the bidsmap/yaml files

Fixed

  • various bugfixes

1.4 - 2018-10-22

Added

  • Cross platform support
  • Installation as a python module
  • Improved version control
  • Improved BIDS compliance

1.3 - 2018-09-28

Changed

  • Refactored bidsmap naming

Fixed

  • Various bugs

1.2 - 2018-09-14

Added

  • Improved fieldmap support

Changed

  • Yaml-syntax

1.0 - 2018-07-04

A first stable release of BIDScoin :-)

Added

  • Support the conversion of organised sub/ses DICOM folders to BIDS

To do

  • Add support for non-imaging data