All notable changes to this project will be documented in this file. The format is based on Keep a Changelog
3.7.4 - 2022-21-10
- Added support for the ABCD GE pepolar pulse sequence
- Use an orange bidsname font in the bidseditor for
.bidsignore
datatypes - A (right-click) context menu in the bidseditor to import meta-data from disk into the meta-table
- Remove the DCCN specific dcm2niix module usage in the bidsmap template
- Add
-l n
to the dcm2niix arguments to revert old UIN16 -> INT16 behaviour (otherwise fmriprep outputs are twice as large) - No longer enforce BIDS compliance on
.bidsignore
datatypes
- Sorting flat DICOM data (in a temporary working directory)
- The dcm2niix module (if not removed) raised an error that prevented handling dcm2niix suffixes
3.7.3 - 2022-07-13
- The usage of json sidecar files as a datasource for attribute values
- A template bidsmap for the ScanSessionTool
- Dicomsort now searches recursively over the sessionfolder
- The dcm2niix2bids plugin now searches recursively for DICOM Series folders
- Images that have already been defaced are now skipped
- Prepend the rawfolder name & subprefix for more robust subject- / session-label filepath extraction
- Pydeface not parsing subject / session labels from the filepath
- The non-HPC use of pydeface no longer requires DRMAA installation
- Account for
*
and?
wildcards in the sub/ses prefixes in the bidsmapper - Account for dynamic values with non-matching regular expressions (special thanks to Mateusz Pawlik)
- Various minor bugs
3.7.2 - 2022-03-13
- The installation of the BIDS schema files
3.7.1 - 2022-03-11
- IntendedFor can now be appended with a "bounding" term to deal with duplicated fieldmaps from interrupted sessions
- The possibility to process subject folders without prefix
- Support for BIDS 1.7 (e.g. for the new
B0FieldSource
andB0FieldIdentifier
fieldmap meta fields) - A
nibabel2bids
plugin (e.g. to convert nifti datasets to BIDS) - Plugin
meta
option setting to enrich json sidecar files or add data that is not supported
- Removed / changed redundant subject/session prefix input arguments (now stored in the bidsmap)
- The
IntendedFor
search feature now works independent of plugins
- The bidscoin installation test in the bidseditor
- The IntendedFor list when combining echos
3.7.0 - 2021-12-20
- A BIDScoin installation test (
bidscoin -t
) - Option to install extra packages, such as phys2bids
- A bidseditor button to save the Options to a (default) template bidsmap
- Sub-/ses-prefix settings and BIDS / extra_data / excluded datatypes in bidsmap['Options']['bidscoin']
- Regular expressions for extracting property and attribute substrings from dynamic values via a <key:regular_expression> syntax
- A plugin for spec2nii to convert MR spectroscopy data
- An experimental plugin for phys2bids to convert physiological data
- An experimental plugin for pet2bids to convert MR spectroscopy data
- Added a multi-echo deface function
medeface
that uses the same defacemask for all echo-images - The possibility to extract DICOM values using pydicom-style tag numbers (in addition to the attribute name)
- The possibility for plugins to set default bidsmappings and Options when installed
- A Singularity container configuration file
- Improved (more fine-grained) plugin installation procedures
- The option to remove decimals from age and discard acquisition dates from the meta data
- Plugins should now have a
is_sourcefile
and aget_attribute
function and have a simpler/changed 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 - The default
<<SourceFilePath>>
keyword has been replaced by the more flexible <filepath:/sub-(.*?)/> property to extract the subject / session label - The dcm2bidsmap and the dcm2niix2bids plugins have been merged
- The dicomsort utility has new naming-scheme functionality
- Removed the obsolete bidsmap_template.yaml file
- Avoid storing Python literal structures as strings
3.6.3 - 2021-06-14
Remove regular expression metacharacters from the source attribute if needed (could cause a regexp compile error) Fixed for list of dynamic <> fields
3.6.2 - 2021-05-31
Removed the redundant importlib dependency from the requirements (could cause an installation error)
3.6.1 - 2021-05-20
The bidscoiner no longer sometimes crashes when dcm2niix produces custom suffixes (e.g. for multi-echo data)
3.6.0 - 2021-05-13
- 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
- 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
- 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
- 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
- pypi upload
3.5.1 - 2021-03-21
- BIDScoin version update checks
- Speed optimizations
- Code clean-up
- More robust dcm2niix output handling
3.5 - 2021-03-08
A significant rewrite and evolution of BIDScoin!
- 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
- Use the dccn template bidsmap as the default
- Simplified and improved (hopefully) handling of fieldmaps
3.0.8 - 2020-09-28
- Various minor bugs
3.0.6 - 2020-08-05
- Minor but important bugfix in the setup :-)
3.0.5 - 2020-08-05
- A download tool for tutorial data
- A tool for regenerating the participants.tsv file
- Various bugs
3.0.4 - 2020-05-14
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
- Improved DCCN example template bidsmap
- Various minor bugs
3.0.3 - 2020-04-14
- A small bugfix to properly handle appending dcm2niix suffices to the BIDS acq-label
3.0.2 - 2020-04-06
- 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
- 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 :-)
- 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
- 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!
- 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
- A new workflow that is easier and more consistent
- Greatly improved graphical user interface and error/warning reporting
- Improved bidsmap_dccn template
- Significant code refactoring to squash a number of important bugs and make the code more robust and maintainable
2.2 - 2019-07-11
- 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
- New layout of the main and edit windows
- Various bugfixes
2.1 - 2019-06-23
- Editing of bidsmap Options
IntendedFor
in fieldmap json sidecar files- Code redundancy
2.0 - 2019-06-18
A major release and rewrite with important user-facing improvements
- A shiny GUI :-)
- A new and much easier workflow
- Various bugfixes
1.5 - 2019-03-06
- Support for PET scans
- Support for DICOMDIR data
- Saving of template sidecar files in the bids output directory
- increased flexibility for renaming / reorganising the raw (input) data structure
- Added provenance data to the bidsmap/yaml files
- various bugfixes
1.4 - 2018-10-22
- Cross platform support
- Installation as a Python module
- Improved version control
- Improved BIDS compliance
1.3 - 2018-09-28
- Refactored bidsmap naming
- Various bugs
1.2 - 2018-09-14
- Improved fieldmap support
- Yaml-syntax
A first stable release of BIDScoin :-)
- Support the conversion of organised sub/ses DICOM folders to BIDS
- Add support for non-imaging data