sct-pipeline

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

pmj-based-csa

CSA measure based on distance from pontomedullary junction (PMJ)

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/gm-challenge

Spinal cord gray matter imaging challenge

sct-pipeline/bavaria-quebec

Bavaria (TUM) and Quebec (Polytechnique) collaboration on a project on spinal cord MS lesion segmentation.

sct-pipeline/contrast-agnostic-softseg-spinalcord

Contrast-agnostic spinal cord segmentation project with softseg

sct-pipeline/fmri-segmentation

Repository for the project on automatic spinal cord segmentation based on fMRI EPI data

sct-pipeline/gm-challenge-data

Dataset for the gray matter acquisition challenge

sct-pipeline/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/balgrist-sci

Pipeline for processing SCI patients using SCT

sct-pipeline/cord-erosion

Pipeline to erode the spinal cord mask in order to quantify MS lesions from the subpial surface.

sct-pipeline/inspired

Spinal cord analysis scripts based on SCT

sct-pipeline/pmj-based-csa

CSA measure based on distance from pontomedullary junction (PMJ)

sct-pipeline/csa-atrophy

Evaluate the sensitivity of atrophy detection with SCT

sct-pipeline/dcm-oklahoma

Analysis of DCM structural MRI and qMRI of the spinal cord

sct-pipeline/ke-berkeley

Pipeline to process DWI data

sct-pipeline/normative-metrics

Processing scripts for computation of qMRI metrics

sct-pipeline/pediatric-genova

Image analysis pipeline for neonatal Spinal Cord MRI data from University of Genoa in collaboration with Gaslini Children's Hospital.

sct-pipeline/rootlets-informed-reg2template

Spinal rootlets-informed registration to the template

sct-pipeline/tumor-segmentation

Pipeline for the segmentation of spinal tumors

sct-pipeline/vertebral-labeling-validation

Pipeline to validate the performance of new vertebral labeling methods.

sct-pipeline/dcm-metric-normalization

sct-pipeline/epi-ap-pa-registration

FMRI AP-PA registration to quantify EPI distortion

sct-pipeline/cervical_sc_study

sct-pipeline/critical-ms-lesion

Detection of critical MS lesion in the spinal cord

sct-pipeline/exvivo-template

Repository for generating high resolution ex-vivo MRI template.

sct-pipeline/levin-stroke

Repository for levin-stroke project.

sct-pipeline/manual-labeling

Scripts to loop over multiple subjects and perform manual labeling for use in machine learning projects.

sct-pipeline/mri-linac-longitudinal-registration

This project investigates the stability of spinal cord positioning across MRI-LINAC sessions

sct-pipeline/spine-park

Pipeline for multicontrast analysis in PD patients

sct-pipeline/STOP-MS-data

Compute CSA on upper spinal cord on MPRAGE from large MS cohort from Karolinska Institute.

sct-pipeline/template-pa78

Repository with code to generate the PA78 template.

sct-pipeline/venus-integration

Code to process data for integrating acquisition planning with VENUS