sct-pipeline
This site gathers various pipelines compatible with the Spinal Cord Toolbox (SCT) for processing MRI data.
Pinned Repositories
balgrist-sci
Pipeline for processing SCI patients using SCT
bavaria-quebec
Bavaria (TUM) and Quebec (Polytechnique) collaboration on a project on spinal cord MS lesion segmentation.
contrast-agnostic-softseg-spinalcord
Contrast-agnostic spinal cord segmentation project with softseg
deepseg-training
Pipeline for training new models with sct_deepseg_lesion
fmri-segmentation
Repository for the project on automatic spinal cord segmentation based on fMRI EPI data
gm-challenge
Spinal cord gray matter imaging challenge
gm-challenge-data
Dataset for the gray matter acquisition challenge
inspired
Spinal cord analysis scripts based on SCT
sagittal_lumbar_seg
This tutorial explains how to segment spinal cords on images with sagittal orientation and thick slices.
ukbiobank-spinalcord-csa
Measure of the averaged cross-sectional area (cord CSA) between C2 and C3 of the spinal cord with UK Biobank Brain MRI dataset.
sct-pipeline's Repositories
sct-pipeline/hagiwara-ms
Pipeline for processing MS patients
sct-pipeline/binder-example
Example of end-to-end processing pipeline: from Dicom data to MR quantitative results.
sct-pipeline/multiparametric-fixed-fov
Processing pipeline (multi-subjects) for extracting multi-parametric data when FOV is systematically centered at a particular vertebral level.
sct-pipeline/wm-gm_csa
This pipeline extract cross-sectional area (CSA) in the WM and GM and compute aggregate metrics.
sct-pipeline/deepseg-training
Pipeline for training new models with sct_deepseg_lesion
sct-pipeline/claudia
Pipeline for computing cord morphometry measures across the cervical, thoracic and lumbar levels.
sct-pipeline/mouse_segmentation
This tutorial explains how to segment spinal cords from small animals (e.g. mouse)
sct-pipeline/sagittal_lumbar_seg
This tutorial explains how to segment spinal cords on images with sagittal orientation and thick slices.
sct-pipeline/jennifer
Pipeline to standardize intensity ranges between a set of images.
sct-pipeline/nadia
Pipeline for computing MT and DTI metrics using various vertebral levels