Changelog¶
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¶
Added support for the ABCD GE pepolar pulse sequence
Use an orange bidsname font in the bidseditor for
.bidsignore
datatypesA (right-click) context menu in the bidseditor to import meta-data from disk into the meta-table
Changed¶
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
Fixed¶
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¶
Added¶
The usage of json sidecar files as a datasource for attribute values
A template bidsmap for the ScanSessionTool
Changed¶
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
Fixed¶
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 bidsmapperAccount for dynamic values with non-matching regular expressions (special thanks to Mateusz Pawlik)
Various minor bugs
3.7.1 - 2022-03-11¶
Added¶
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
Changed¶
Removed / changed redundant subject/session prefix input arguments (now stored in the bidsmap)
The
IntendedFor
search feature now works independent of plugins
Fixed¶
The bidscoin installation test in the bidseditor
The IntendedFor list when combining echos
3.7.0 - 2021-12-20¶
Added¶
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-imagesThe 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
Changed¶
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 propertyThe default
<<SourceFilePath>>
keyword has been replaced by the more flexible <filepath:/sub-(.*?)/> property to extract the subject / session labelThe dcm2bidsmap and the dcm2niix2bids plugins have been merged
The dicomsort utility has new naming-scheme functionality
Removed the obsolete bidsmap_template.yaml file
Fixed¶
Avoid storing Python literal structures as strings
3.6.3 - 2021-06-14¶
Fixed¶
Remove regular expression metacharacters from the source attribute if needed (could cause a regexp compile error)
Fixed for list of dynamic <
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) bidsmapsSupport 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 aroundSupport 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 filesCode 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