r20231108

A release of the SCISeg model submitted to ISMRM 2024. Contains data conversion, nnUNet training/testing, lesion metrics evaluation scripts. Model was trained on Zurich sagittal and Colorado axial T2w images with heterogeneous resolutions.

What's Changed

• New preprocessing script with centerline extraction by @naga-karthik in #30
• Add masks{Tr, Ts} folders to nnUNet dataset format by @valosekj in #32
• add zurich & spine-generic data conversion script by @naga-karthik in #34
• Generate sagittal QC for all subjects by @valosekj in #42
• Generate new lesion by @valosekj in #31
• Add script to segment SC for sci-paris by @valosekj in #47
• Minor improvements of anima script by @valosekj in #48
• Add a scripts for conversion of all datasets by @valosekj in #50
• Update preprocess_data_sci-zurich.sh script by @valosekj in #35
• packaging nnunet for inference by @naga-karthik in #40
• Get orientation for each file by @valosekj in #53
• Add script to compare our nnUNet model with other methods by @valosekj in #55
• Fetch sequence parameters by @valosekj in #58
• Run inference on sci-zurich axial T2w images by @valosekj in #57
• Add script for cropping the images around the SC by @valosekj in #62

New Contributors

• @valosekj made their first contribution in #32

Full Changelog: v0.1...r20231108