v1.5.1

Cumulative changes in testing of dependencies and dockerfile

What's Changed

• fix dependency versions for snakebids, pulp by @jordandekraker in #313
• Import patch by @jordandekraker in #314
• Update Dockerfile to latest version with dependencies by @jordandekraker in #315
• Jordandekraker patch 1 by @jordandekraker in #317

Full Changelog: v1.5.0...v1.5.1

1.5.0

💪 Changes

• use naturalneighbour interpolation instead of linear barycentric @jordandekraker (#306). This generally improves the quality of unfolded-folded warps and fixes some issues of misplaced vertices in subject-folded space (especially common in the DG and anterior/posterior tips)

🚀 Features

• Templateseg workflow instead of UNet. This method is meant for cases with not much training data or with low inter-subject variability, such as non-human or neonatal data.
  • bigbrain templateseg (#309, #304)
  • dHCP templateseg(#307)
  • ABAv3 mouse atlas+template (#299)
  • initial docs for templateseg (#292)
  • Template inject Lflip vs R bug fix (#310)
• macaque subfields atlas added atlas (#297)
• Wet-run test data Documentation (#303) see also #311

1.4.1

🐛 Bug Fixes

• Fix session bug, where BIDS parsing was faulty when subjects had different sessions @akhanf (#261)

1.4.0

Changes

🚀 Features

• rename histologyReference2023 to multihist7 @akhanf (#256)

📝 Documentation

• Latest tag @akhanf (#260)

1.3.3

Changes

🐛 Bug Fixes

• fixes subfields label.gii bug introduced in unfold_reg by reverting @akhanf (#255)

1.3.2

Changes

🐛 Bug Fixes

• replace use of HTTP.remote() with wget @akhanf (#251)

📝 Documentation

• Update README.md @akhanf (#250, #252)

1.3.1

Changes

🧰 Maintenance

• Download models inside workflow @akhanf (#247)
• added neonate_v2 model, minor workflow update for it @akhanf (#249)

📝 Documentation

• Download models inside workflow @akhanf (#247)
• Update README.md @akhanf (#246)

v1.3.0: unfolded registration

Major changes (full Methods here):

• 🎉 Inter-subject alignment is now further refined using registration in unfolded space!
• 🚀 The default subfield parcellation scheme is now based on the maxprob of seven histology samples.
• Together these changes align subfield boundaries to within approximately 0.5mm!
• 💻 Can (optionally) specify alternative U-Net tissue segmentation models, including contrast-agnositic synthseg (#244)

Minor chages:

• 🐛 Bug fix for inner/outer surfaces sometimes being pushed outside of hippocampus (#236)
• 🐛 Curvature is no longer calculated on a smoothed surface, and is instead normalized via a tanh function (#242)
• 📝 Improvements to Documentation clarity

Notes:

• The effects of inter-subject alignment are most evident at high resolution, such as 7T, ex-vivo scanning, or histology. However this will still improve alignment of in-vivo scans, leading to sharper group-averaged images. Check out our full evaluation here
• The new default subfield parcellation scheme includes the previous labelling from 3D BigBrain with some added corrections. Previous labelling schemes can optionally also be applied.
• The new synthseg models should be considered experimental. These should be applicable to any scanning modality and sometimes to 3D histology. They also provide better segmentation detail, leading to clearer definition of digitations/gyrifications. However, these models have not yet been formally evaluated, and may stil undergo additional training iterations.
• Check out our associated toolbox for helpful Python/Matlab analysis tools, tutorials, and examples!

Contributors

• @jordandekraker
• @akhanf
• @kaitj
• @Bradley-Karat

1.2.1

Changes

🚀 Features

• add cli arg for specifying crop-native-res in mm, default as 0.2mm iso @jordandekraker (#224)

🐛 Bug Fixes

• fix for input type in dseg qc @jordandekraker (#226)
• T1T2w model file/url was missing from the config @akhanf (#232)
• fix bug in crop native box @akhanf (#230)
• bugfix for cropref @jordandekraker (#225)
• aligns laplace_coords.py behaviour to laplace_coords_withinit.py @jordandekraker (#220)
• Added missing container for hippdwi_to_template @kaitj (#216)

📝 Documentation

• Add accepted in eLife mention and link to readme @akhanf (#227)
• Note on autotop_deps @jordandekraker (#223)
• Updates for Windows @jordandekraker (#222)
• update docs for running singularity in linux @akhanf (#219)
• Update_documentation @mcespedes99 (#214)

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)