aggregated dataset: add monai-based scripts for conversion, training, and inference

sct-pipeline / contrast-agnostic-softseg-spinalcord

Contrast-agnostic spinal cord segmentation project with softseg

MIT License

4 stars 3 forks source link

aggregated dataset: add monai-based scripts for conversion, training, and inference #61

Closed louisfb01 closed 10 months ago

louisfb01 commented 1 year ago

This PR adds will add the required scripts for bids-msd dataset conversion for any number of dataset, training and running inference with MONAI models working on large sets of data aiming at fixing memory issues.

louisfb01 commented 1 year ago

The script for building the MSD dataset.json file now works with:

Basel-MP2RAGE, inspired, sci-colorado, canproco, fmri_sc_seg, dcm-zurich, sci-zurich, gmseg-challenge-2016, sci-paris, bavaria-quebec-spine-ms, beijing-tumor, uk-biobank-processed, sct-testing-large