contrast-agnostic-softseg-spinalcord v2.0

About

This release contains the official code for the submission to Medical Image Analysis Journal. The model weights are uploaded as release assets along with all the scripts for preprocessing, training, CSA and QC generation.

What's Changed

• Add subjects with missing contrasts to exclude by @sandrinebedard in #53
• Add script to compute CSA binarized and run QC on binarized prediction for ivadomed by @sandrinebedard in #58
• Modify post processing nnunet for CSA computation and QC report by @sandrinebedard in #57
• Naga/nnunet by @sandrinebedard in #65
• add monai-based scripts for dataset conversion, training, and inference by @naga-karthik in #60
• Clean up processing and repository by @sandrinebedard in #64
• add requirements for gpu inference by @naga-karthik in #76
• add qc generation script for epi data by @naga-karthik in #77
• Update main readme by @naga-karthik in #78
• Upgrade and pin monai to 1.3.0 by @naga-karthik in #79
• Finalise script for figures by @sandrinebedard in #80
• add anima metrics by @naga-karthik in #81
• Add anova test on soft all and hard all by @sandrinebedard in #82

New Contributors

• @naga-karthik made their first contribution in #60

Full Changelog: v1.2...v2.0