Sidecar JSONs

• Derivatives now include sidecar JSONs
• Bugfix for subjects with age = 0 in their accompanying .tsv file

Segmentations and Masks Output in T1-native and T2-native Space

Merge pull request #52 from DCAN-Labs/doc-dev

updated outputs

Zenodo Bug Fix

Adjusting .zenodo.json license in order to publish

Improved Segmentations with Model 551

• Addition of model 551 for T1 and T2 combined segmentation generation
• grabs age and brain_z_size from participants.tsv when there isn't a sessions.tsv or the information isn't provided in the sessions.tsv (note: this should only be the case when there are one or no sessions per subject)

sub-{}_session.tsv Implementation

• brain_z_size and age will now be grabbed from the sub-{}_sessions.tsv inside each subject's BIDS input directory at the level of the sessions directories instead of the participants.tsv for BIDS valid input directories
• readthedocs documentation now reflects this

Working Directory Implementation

• prebibsnet through postbibsnet changed to working directories
• the "precomputed" derivatives directory changed to "bibsnet" derivatives directory
• working directories removed at the end of postbibsnet if the user does not specify a --work-dir

Updated Zenodo Files and Dockerfile

• Removed python FSL install to allow the docker image to build on dockerhub
• Removed CITATIONS.cff
• Edited .zenodo.json

Improved Segmentations with Model 550

• bug fix in averaging multiple anatomical images of the same modality (T1w or T2w) in prebibsnet
• addition of model 550 (new T1w and T2w bibsnet model) to model.csv, allowing the application to run model 550 in the bibsnet stage
• removal of model 512 to save space in the container, replaced with model 550
• changed model 512 to model 550 in the readme

CABINET includes T1-only and T2-only models

• T1-only and T2-only models are now included
• Codebase automatically chooses model based on inputs
• User can specify model if desired
• ReadMe documentation for additional workflows and model description
• Bug fixes within non-ACPC alignment workflow

BIDS-ified CABINET Application

• CABINET can now run multiple subjects/sessions or subjects with no sessions
• Added issue templates
• BIDSified the application by moving args from param file to argparse
• Updated README.md to reflect these changes
• Implemented age-to-average-head-radius inference from table