ivadomed/Bidsification

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ivadomed/Bidsification

ivadomed

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ivadomed

Repository on the collaborative IVADO medical imaging project between the Mila and NeuroPoly labs.

ms-challenge-2021

MS segmentation challenge

model_seg_sci

Deep-learning based segmentation of the spinal cord and intramedually lesions in traumatic and non-traumatic SCI

multimodal-registration

Repository for training and using a contrast agnostic registration model based on the work done in SynthMorph. The contrast agnostic registration model may later be used in IvadoMed’s pipeline.

utilities

Repository containing utility scripts for handling various aspects in a DL model training pipeline

model-spinal-rootlets

Deep-learning based segmentation of the spinal nerve rootlets

Jupyter Notebook

canproco

Code for preprocessing the CanProCo brain and spinal cord dataset

Jupyter Notebook

ms-lesion-agnostic

Deep Learning contrasts "agnostic" tool for MS lesion segmentation in the spinal cord

model_seg_gm-wm_t2star_7t_unet2d-multiclass

A deep learning model that allows robust SC/GM multi-class segmentation based on ultra-high resolution 7T T2*-w MR images

model-seg-dcm

Segmentation of lesions on MRI scans in patients with Degenerative Cervical Myelopathy (DCM)

model_seg_mouse-sc_wm-gm_t1

White and grey matter segmentation on T1-weighted exvivo mouse spinal cord

model_seg_ms_mp2rage

Model repository for MS lesion segmentation on MP2RAGE data from University of Basel

model_seg_csf_epi

Model repository for spinal cord csf segmentation on EPI data

model_sc_centerline

Repository for automated spinal cord centerline detection using deep learning

MEEG-Brainstorm

Repository for training MEEG datasets with the ivadomed framework in Brainstorm

model_find_disc_t2

training-nnunet

nnU-Net quick-start guide

pipeline-ms-lesion

Pre-processing pipeline for multi-contrast spinal MS lesion segmentation

article-softseg

data-testing

Light-weighted data for testing/tutorial

model_seg_sctumor-edema-cavity_t2-t1_unet3d-multichannel

Model to segment spinal cord tumor, edema, and cavity using as input T2w and gadolinium-enhanced T1w MRI scans.

findcord_tumor

Counterfactual_synthesis_for_lesion_segmentation

Jupyter Notebook