Summer is here!

It's finally here, and feels great, no reason to postpone BIDScoin 4.3.3!

It's a minor release but it comes with two nice (advanced) user-facing new features:

• A bidseditor context menu for comparing, editing or adding multiple run-items. The latter is particularly useful for mapping exceptions, e.g. when your data acquisition had some irregularities
• A fixmeta bidsapp for retrospective metadata editing

HOTFIX for 4.3.1

This is a hotfix release for v4.3.1, which was just released but was giving undesired results after changing the data type in the bidseditor. Apart from the fix in this release (see Github issue #229 for full explanation) nothing else has changed

For a moment, nothing happened. Then, after a second or so, nothing continued to happen -DA

IMPORTANT UPDATE:

This release contains a bug that can yield undesired output, please upgrade to 4.3.2

--------------- original notes ------------------
Here is a minor and safe BIDScoin upgrade, with fixes and two new features:

• Update B0FieldIdentifier/Source when having multiple fieldmap runs (Github issue #198). For more info see here
• Slicereport support for all nibabel file-formats

Enjoy!

BIDScoin is on a roll

With this major release, BIDScoin became more robust and solid than ever before, while gaining several new features that add to its flexibility and user-friendliness. Amongst others, the major new highlights are:

• Support for the recently released BIDS v1.9.0 specifications
• A --cluster option for running bidscoiner in parallel on a (DRMAA enabled) HPC
• A new bidsmap_bids2bids template bidsmap for nibabel2bids to edit existing BIDS datasets
• New special dynamic values, such as <<session>>, <<dir>> and <<PhaseEncodingDirection>>
• Parsing of DICOM tags from the Siemens CSA headers
• A bidscoiner.tsv log-file for easier tracking of file conversions / data provenance
• Integrated fslmaths preprocessing on slicereport input images
• BIDScoin duecredit reports

For more details see the changelog

Updates make life better

A bugfix release with some additions

Added

• A bidsmap schema file
• Enhanced DICOM (XA-30) support for physiological data (backported from the CMRR repository)
• Slurm support for the skullstrip and slicereport bidsapps

Changed

• Use a true list (instead of a semi-colon separated string) for the bidsmap's bidsignore field
• The telemetry url

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