1.2.0

Changes

🚀 Features

• added --version to CLI (via snakebids.yml) @akhanf (#210)
• allows output of subfields using multiple unfolded atlases @jordandekraker (#200)

🐛 Bug Fixes

• subfields label.gii wasn't being generated properly (fixes #208) @akhanf (#211)
• subfield+tissue for new atlases, and tsv files @akhanf (#208)
• hippdwi bounding box for L and R flipped @akhanf (#204)

🧰 Maintenance

• updated deploy workflow with bumpversion changes @akhanf (#213)
• Extras moved to toolbox @jordandekraker (#207)
• Unfolddentatetemplate patch @jordandekraker (#203)

📝 Documentation

• Major online documentation overhaul @akhanf (#209)
• Multiple atlases updating docs & coding style @akhanf (#205)

1.1.0

Changes

🚀 Features

• freeview formatted subfield label file @jordandekraker (#195)
• Freesurfer atlas @akhanf (#186)
• expose crop_native_box as a config and CLI variable @akhanf (#184)
• Custom atlas @akhanf (#176)
• myelin mapping (T1w/T2w) @akhanf (#172)

🐛 Bug Fixes

• Force creation of .snakebids file @akhanf (#192)
• fixes group-level analysis @akhanf (#189)
• change --nnunet-disable-tta to --nnunet-enable-tta @akhanf (#187)
• updates to add imagemagick and graphviz @akhanf (#161)
• bugfix for warps hemi-L @jordandekraker (#180)
• fixes to get group analysis_level working again @akhanf (#166)

🧰 Maintenance

• Update Dockerfile @akhanf (#199)
• Drop generic copy_to_results rule @akhanf (#194)
• update snakebids dependency @akhanf (#190)
• update release drafter @akhanf (#181)
• adds missing output space default @akhanf (#177)
• CI updates, remove circleci, use github actions to build/push to dockerhub @akhanf (#175)
• upgrade to autotop_deps v0.4.2 - python 3.9 @akhanf (#167)

📝 Documentation

• adds unsupported note for M1 @akhanf (#198)
• doc updates @akhanf (#183)
• added myelin map to docs @akhanf (#179)
• added details about downloading models @akhanf (#170)
• Updates to Docs with environment management tips @jordandekraker (#169)
• replace pypi badge with github version tag @akhanf (#163)

1.0.0

Changes

🚀 Features

• workflow updates to allow T2w without T1w @akhanf (#153)
• Unfold DG @jordandekraker (#146)
• single modality at a time @akhanf (#137)
• Neonate T1w workflow updates @akhanf (#124)
• added refvol to results for easier unfolded transforms @jordandekraker (#144)
• adds rules for composite warps from unfold and remove map to full grid @akhanf (#143)
• Cosine_rep to generate smooth, simple nativespace surfaces @jordandekraker (#117)
• updated hippb500 model @akhanf (#118)
• adds coords on surfaces, & pre-smoothing for curv @akhanf (#110)
• Cropseg patch @akhanf (#105)
• Switch IO laplace (isopotential) coordinates to isovolume @jordandekraker (#96)
• add flag --no_reg_template for inputs that are already in space-CITI168 @jordandekraker (#99)
• new gyrification as surface area ratio @akhanf (#93)

🐛 Bug Fixes

• allowing qc to use corobl @jordandekraker (#159)
• quick patch to prevent source config file from being modified @akhanf (#157)
• patch for skip_templateshape @jordandekraker (#152)
• minor fix to template shape injection @akhanf (#119)
• qc fixes @akhanf (#120)
• temporarily disable the vis regqc rule @akhanf (#114)
• added missing group directive @akhanf (#112)
• minor correction to subfield label names @jordandekraker (#108)
• fix typo in help usage @akhanf (#103)
• bugfix: pin version of batchgenerators @akhanf (#100)
• No more overlapping points in griddata interpolation in create_warps.py @jordandekraker (#95)

🧰 Maintenance

• added logging @akhanf (#160)
• output refactoring, removed datatype=seg folders, added coords, warps @akhanf (#155)
• add generate dags github workflow @akhanf (#149)
• Auto-formatting and quality-checks @akhanf (#148)
• root dir change for snakebids 0.4.0 @akhanf (#145)
• Update release-drafter.yml @akhanf (#147)
• Update deps @akhanf (#140)
• removes deprecated and unused files @akhanf (#138)
• Add download model console script to pyproject @akhanf (#136)
• add requirements.txt from poetry export @akhanf (#135)
• remove old deploy github actions @akhanf (#134)
• replaces setup.py with pyproject.toml and poetry @akhanf (#131)
• Create manual_release_drafter.yml @akhanf (#133)
• adds bump_version and release drafter @akhanf (#132)
• pin docutils<0.18 @akhanf (#115)
• update autotop v0.4.1, remove deprecated mcr cfg @akhanf (#109)

📝 Documentation

• simple version for non-contributors @jordandekraker (#151)
• Docs from RST to Markdown @akhanf (#150)
• clarification and details for documentation @jordandekraker (#106)
• Tutorials & examples @jordandekraker (#97)

surface density, cropseg, hemi flag, fast laplace init

• new unfold templates with variable density
• included DG in template shape injection
• updated documentation
• Dice qc (#76)
• added cropseg modality type
• update input for shape inject, target rules
• added space wildcard for giftis
• allow autotop to run with no initialization
• added --hemi option
• fix nan vertices in output surfaces (#90)
• fast laplace via initialization (#88)

patch itk warps, pin numpy version

• fixes bug in ITK warps
• pins numpy version in setup.py (was installing older version in some venvs)

No matlab release

• first release without matlab/mcr dependencies
• reduces container size and runtime considerably
• pypi deployment

fix spec file, --archive_work, refactor targets

• fixes cifti structure error in spec files
• adds --archive_work option to tar work folders upon completion
• updates to docs
• adds more QC images

bugfix for Dockerfile

• fixes problem with missing ComposeMultiTransform dependency in docker container

Snakebids v0.3, various features and fixes added

Now uses Snakebids v0.3.9, which provides the --path option to specify inputs with wildcards, so a BIDS dataset is not actually needed if all inputs specified.

Various other feature additions and fixes:

• visualization qc reports #32
• updates to docs, model hosting on zenodo, CI #29
• provides composite warps from T1w to unfold #36 #44
• added deps for report generation #37
• fixes to manual seg workflow #34 #51
• added longitudinal test case #47
• upgrade to use snakebids v0.3.9 #49
• added hippdwi b500 workflow #38
• added CIFTI outputs, fixed invalid structure for left #41

OHBM 2021 abstract submission release

• first major release since creating as a snakebids app and implementing surface-based outputs
• uses nnU-net with CPU/GPU inference