3.4.2

What's Changed

• MOST IMPORTANT FIX: extend read/execute permissions to all files used by BIBSnet by @scott-huberty in #134

• Updated documentation by @LuciMoore in #125 #126 #128 #129

New Contributors

• @scott-huberty made their first contribution in #134

Full Changelog: 3.4.1...3.4.2

3.4.1

What's Changed

• Image overcropping issue in preBIBSNet resolved through implementation of SynthStrip by @LuciMoore to use a brain mask to determine the optimal axial cutting plane and Dockerfile updated by @madisoth to install SynthStrip in #124
• Removal of all logic, flags, dependencies etc required for the former cropping method using robustfov. Additionally, because cropping is no longer age-dependent, a participants.tsv file is no longer required #124
• Created attribute which writes out volumes.json by @tjhendrickson and fix for brain mask file name issue by @lundq163 in #121

Full Changelog: 3.4.0...3.4.1

Summary of major updates from prior pre-releases (see full details in history below) include:

• Replaced previous models with new production models that now don't have chirality issues (uses the no Mirroring class and sets flipping=False when generating segmentations): 540 (T1+T2), 541 (T1-only), 542 (T2-only) by @lundq163
• Remove chirality correction steps from postbibsnet by @LuciMoore in #114
• Inclusion of volumes.tsv in final outputs containing total size of each region by @tjhendrickson

3.4.0

What's Changed

• Update stages.md by @LuciMoore in #118
• Remove chirality correction from postbibsnet by @LuciMoore in #114
• Replaced previous models with new production models that now don't have chirality issues: 540 (T1+T2), 541 (T1-only), 542 (T2-only)
• Updated Dockerfile commands for building container by @lundq163
• Inclusion of volumes.tsv in final outputs containing total size of each region by @tjhendrickson

Full Changelog: 3.3.2...3.4.0

Updated model to reduce chirality issues

NOTE: this release had an issue causing errors if model 540 is used -- to be fixed in 3.3.1

Now includes model 540 which uses the no Mirroring class and sets flipping=False when generating synthetic images. 540 is now the production model

BIBSnet v3.2.0

New Model

Model 526 is now included in BIBSnet.
This model is now the default for subjects with both T1 and T2 scans.
Model 552 is still available with the -model flag

Manual Cropping Reduction

New flag --reduce-cropping
This is useful for cases where the default age-specific brain z size specified by BIBSNet results in overcropping.
See usage for more information.

Data Archive Changes

Data archive is now stored at https://s3.msi.umn.edu/bibsnet-data/
Data is versioned to improve backwards compatibility.
Changes to permissions and exclusions of some files to help with building containers on docker hub

BIBSnet v3.1.2

• Modified chirality correction so that it runs in an iterative fashion
  • First crude correction splitting left and right hemispheres based on coronal plane
  • Second re-performs chirality correction with more refined LR mask
• Results reveal that it corrects superficial brain regions outside of the midline

v3.1.1

BIBSnet v3.1.1

• Updated templates for all ages
  • Updated in https://s3.msi.umn.edu/cabinet-data-targz/data.tar.gz and the dockerhub container
• postBIBSnet removes unconnected clusters from brain mask
  • added function remove_extra_culsters_from_mask
• Improved logging
  • added debug level available with the -d flag
• Bugfix for subjects with multiple sessions
  • BIBSnet no longer fails on subjects with multiple sessions when no work_dir is specified

v3.0.2

This release is primarily to address an issue with chirality correction using templates in the data directory. As this data directory is stored in an S3 bucket on msi.umn.edu the major update does not appear on GitHub. The following changes have been made to the data directory:

• replaced 1mo template with different subject and updated readme with new subject number
• deleted brainmasks folder and skull-stripped template files as these are not used in BIBSNet

In addition there are several minor documentation and logging improvements.

BIBSnet v3.0.1

Bugfix: -participant argument is now optional.

In 3.0.0 this was mistakenly made to be required and is now back to being optional as it was previously.

BIBSnet v3.0.0

CABINET is now BIBSnet

The codebase formerly known as CABINET has been primarily been used as a way to run BIBSnet with preBIBSnet and postBIBSnet.
This release makes BIBSnet the primary focus, moving BIBSnet into this repository and removing the code that was meant to be used by NiBabies and XCPD.
We're excited about our new version of CABINET that goes about running multiple containers in a different way.

What's new

Previously BIBSnet was only the stage that ran nnUNet. We moved that code into this codebase, instead of pulling it from a different repository.
We removed all of the code that was used for running NiBabies and XCPD. This includes the parameter JSON file.
You can run BIBSnet the same way you ran CABINET, but without a parameter JSON argument. The parameters formerly in the parameter JSON have their default set to the parameters in the container's version of the parameter JSON. See https://bibsnet.readthedocs.io/ for updated usage.

Where we're keeping BIBSnet related things

The renaming of this code means we've had to update some URLs.
We're now hosting containers on dockerhub at dcanumn/bibsnet. dcanumn/cabinet has some old images still, but will be sunset in the future.
Our readthedocs is now at https://bibsnet.readthedocs.io/. The old readthedocs will link you there.
github.com/DCAN-Labs/CABINET is now the home of a new codebase that was originally forked from this repository. It has diverged significantly, which is why we've made this change. We hope you give it a try when running multiple containers back to back.