The answer to life, the universe, and everything...

Greetings, sentient beings of the digital cosmos! It is with great pleasure that we announce the release of BIDScoin version 4.2.0. This release, like the Ultimate Answer itself, brings a sense of fulfillment and excitement to the table. So grab your towel, don your favorite bathrobe, and let's dive headfirst into the infinite improbability of BIDScoin!

Added

• Users can now more easily view and edit their default BIDScoin settings
• In our quest for infinite knowledge and improved user experiences, BIDScoin has implemented a service that, in the style of a friendly, paranoid android, may track user behavior into the Total Perspective Vortex (github issue #200). Rest assured, I've consulted with Zaphod Beeblebrox to ensure that your personal data is never put to misuse. In the event you feel uneasy about our user tracking, you can adjust your privacy settings in the "Don't Panic" section in the new BIDScoin settings (see bidscoin --show).
• The option to pip-install dcm2niix as extras

Changed

• The template bidsmaps are now stored in [home]/.bidscoin/[version]/templates, i.e. in the user settings folder

Fixed

• Numerous infinitely small bugfixes and improbable tweaks

Go and explore BIDScoin 4.2.0 with the same sense of wonder and absurdity that you approach the rest of the universe 🙂

If it's broken, fix it!

Here's some good and some bad news. The bad news is there were a few glitches in BIDScoin 4.1.0, but the good news is that they are fixed in the new BIDScoin 4.1.1 release 🙂

The fixes in this new release are:

• Bugfixes to support (XA30) enhanced DICOM
• Bugfix to catch multi-echo series with dynamic runindex <<>>
• Prioritize fmap data discovery
• Remove invalid bval/bvec files
• Reduce filesize warnings

"I think rain that is wet", thought Zaphod Beeblebrox, " so who am I to judge?"

Most notable changes for this release:

• GUI upgraded from Qt5 to Qt6 -- now supporting the new Apple silicon
• A new <<>> dynamic run-index (default), that behaves the same as <<1>> when multiple runs are acquired, otherwise it is omitted/void (PR #195)
• Manpages (not on Windows)

"I do think," added Deep Thought, "that you're going to like it"

The new BIDScoin v4 series is here!

With a lot of important improvements that should make your (and my) life significantly easier :-). The most notable changes are:

Added

• Support for BIDS 1.8.0
• Support for handling of non-alphanumeric characters in sub/ses prefixes
• A new (optional) pet2bids plugin
• A skullstrip tool (a bids-wrapper around FreeSurfer/synthstrip)
• A slicereport QC tool (a bids-wrapper around FSL/slicesdir)
• A unit/integration test & CI framework
• New Dockerfile and Apptainer/Singularity definition files to run BIDScoin in a container
• A BIDSCOIN_DEBUG environment variable to run bidscoin in a more verbose debug mode
• VERBOSE and SUCCESS logging levels
• Checks using the bids-validator python module
• Options to perform study/template bidsmap tests with bidscoin -b / -t
• Option to list and install template bidsmaps
• Many bugfixes, user interface improvements and tweaks

Changed

• The default behaviour is now to not unzip data in the sourcefolders anymore. Instead, users can use the --unzip option in the bidsmapper
• The spec2nii plugin is no longer added by default but is optional
• The dcm2niix2bids plugin no longer handles PET data (this is now handled by the pet2bids plugin)
• Removed BIDScoin's redundant/confusing datatypes option from the bidsmap
• Removed the obscure participants option from bidscoiner
• Major code refactoring

Enjoy!

Those that have the capacity to become president should on no account be allowed to do the job

Added

• 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

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

Never been better :-)

Added

• The usage of json sidecar files as a datasource for attribute values
• A template bidsmap for the ScanSessionTool
• Usage of json sidecar files as an attribute source

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 bidsmapper
• Account for dynamic values with non-matching regular expressions (special thanks to Mateusz Pawlik)
• Various minor bugs

Fixing 3.7.1

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

Make code, not war

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

BIDScoin has been boostered!

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

Business as usual

Fixed

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