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Spinal cord MRI segmentation in the browser
SpinalCordToolbox is a browser-based tool for SCT stable spinal cord MRI segmentation workflows.
All image computation runs locally in your browser using ONNX Runtime Web. Patient image data is not uploaded to any server.
SpinalCordToolbox runs entirely in your web browser using WebAssembly and ONNX Runtime. All processing occurs locally on your machine.
SpinalCordToolbox uses ONNX Runtime Web to run browser-compatible deep learning models directly in the browser via WebAssembly. Your NIfTI or DICOM files are read into browser memory, processed locally, and results are displayed without patient-data network transfer.
SpinalCordToolbox may collect telemetry for non-patient usage statistics. Telemetry must not include patient image data, DICOM metadata, filenames, voxel values, masks, segmentations, screenshots, free-text patient-derived logs, or downloaded outputs.
Spinal Cord Toolbox provides spinal cord MRI analysis workflows and model provenance used by this browser interface.
https://spinalcordtoolbox.com/stable/SpinalCordToolbox uses the following methods and tools:
Paszke A, et al. PyTorch: An Imperative Style, High-Performance Deep Learning Library. NeurIPS 2019.
https://pytorch.orgMicrosoft. ONNX Runtime: cross-platform, high performance ML inferencing and training accelerator.
https://onnxruntime.aiLi X, Morgan PS, Ashburner J, Smith J, Rorden C. The first step for neuroimaging data analysis: DICOM to NIfTI conversion. J Neurosci Methods. 2016;264:47-56.
https://github.com/rordenlab/dcm2niixStewart A. QSM.rs: Quantitative Susceptibility Mapping in Rust. FSL-BET2 brain extraction algorithm.
https://github.com/astewartau/QSM.rsSmith SM. Fast robust automated brain extraction. Human Brain Mapping. 2002;17(3):143-155.
https://doi.org/10.1002/hbm.10062Hoopes A, Mora JS, Dalca AV, Fischl B, Hoffmann M. SynthStrip: Skull-Stripping for Any Brain Image. NeuroImage. 2022;260:119474.
https://doi.org/10.1016/j.neuroimage.2022.119474NiiVue Contributors. NiiVue: a WebGL2 medical image viewer.
https://github.com/niivue/niivue