Changelog¶
All notable changes to this project will be documented in this file. The format is based on Keep a Changelog
3.7.0-dev¶
Added¶
- A BIDScoin installation test (
bidscoin -t
) - A bidseditor button to save the Options to a (default) template bidsmap
- Sub-/ses-prefix settings to bidsmap[’Options’][’bidscoin’]
Changed¶
- Plugins should now have a
is_sourcefile
and aget_attribute
function and have a simpler API (-> DataSource class) - The intricate filtering of the
nrfiles
property by the other filesystem properties has been removed and is now a pure/unfiltered file-system property
3.6.3 - 2021-06-07¶
Fixed¶
Remove regular expression metacharacters from the source attribute if needed (could cause a regexp compile error)
3.6.2 - 2021-05-31¶
Fixed¶
Removed the redundant importlib dependency from the requirements (could cause an installation error)
3.6.1 - 2021-05-20¶
Fixed¶
The bidscoiner no longer sometimes crashes when dcm2niix produces custom suffixes (e.g. for multi-echo data)
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 toexclude
- 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
3.5.1 - 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
3.0.5 - 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
3.0.1 - 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