Bidscoin Versions Save

This is a quick fix for the installation error in BIDScoin 3.7.1

A point release that has however some really nice goodies, most notably:

• Support for BIDS 1.7 (e.g. for the new B0FieldSource and B0FieldIdentifier fieldmap meta fields)
• A new nibabel2bids plugin to convert a wide variety of source datasets to BIDS
• 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

It should be a safe upgrade from 3.7.0

Just in time for X-mas, a new and significantly improved BIDScoin release! It's more user-friendly and the codebase has been refactored for a more flexible and powerful usage with plugins and, for advanced use cases, regular expressions. This release is described in more detail in this Frontiers in Neuroinformatics paper :-)

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-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

Changed

• Plugins should now have a is_sourcefile and a get_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 keyword has been replaced by the more flexible 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

Fixed

• Avoid storing Python literal structures as strings
• Various small bugs

Fixed

Remove regular expression metacharacters from the source attribute if needed (could cause a regexp compile error) Fixed for list of dynamic <<Intendended><For>> fields

Fixed

Removed the redundant importlib dependency from the requirements (could cause an installation error)

Thanks @marcpabst for reporting!

Fixed

Just a small bugfix release that prevents a possible bidscoiner crash for certain data acquisitions (e.g. for multi-echo data). It should be a safe upgrade for everyone using 3.6.0 (you can edit the 3.6.0 version string in the Options to 3.6.1 to get rid of the version conflict warning)

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)

Fixed

• Save non-standard fieldmaps in the derivative folder

Fixed:

• pypi upload

Added

• BIDScoin version update checks

Fixed

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