neuropoly/docker

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neuropoly/docker

neuropoly

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Collection of dockerfiles

gmseg

Spinal cord gray matter segmentation using deep dilated convolutions.

Jupyter Notebook

domainadaptation

Repository for the article "Unsupervised domain adaptation for medical imaging segmentation with self-ensembling".

deep-active-learning

Implementation of active learning features for AxonDeepSeg software (axon-myelin segmentation)

Jupyter Notebook

axonseg

Segment axon and myelin from microscopy data. Written in Matlab.

multiclass-segmentation

Repository for the code related to the NIH marmoset longitudinal segmentation project.

gifmaker

Convert images to GIF animation.

vertebral-labeling-deep-learning

Deep Learning method for intervertebral disc detection and labeling (WIP)

totalspineseg

Robust Instance Segmentation of Vertebrae, Intervertebral Discs, Spinal Cord, and Spinal Canal in MRI Images Using nnU-Net and Iterative Algorithm.

axonpacking

template

A framework for creating unbiased MRI templates of the spinal cord

mp2rage

Function which computes T1 from mp2rage

t2star-mapping

Collection of scripts to fit T2* MRI data

Susceptibility-Separation-Phantom

This project aims to create and simulate a realistic phantom for susceptibility separation algorithm validation.

lesion-mapping

Set of tools for mapping lesions in the brain and/or spinal cord

qDLab

Quantitative Diffusion MRI Made Easy with qDLab: a Software for Data Simulation, Analysis and Visualization

qMTLab

surface_based_tools

Tools related to Freesurfer pipeline

intranet.neuro.polymtl.ca

NeuroPoly's lab manual

data-management

Repo that deals with datalad aspects for internal use

agilent_7t

Various matlab code to manage data from Agilent 7T scanner at MHI

neuro.polymtl.ca

NeuroPoly's Website

slicer-manual-annotation

phantom-spinoza

CAD model and recipe for MRI head-torso phantom fabrication

bibeasy

Set of tools to manage academic bibliography

simulation-fourier-reconstruction

Code to investigate what might cause the different Fourier-related artifacts that we encounter during our experiments.

Jupyter Notebook

coil_simulation_web

web version of program for simulating RF coil array for MRI

paradim-segmentation-brain

Repository for implementing pre-existing brain segmentation models trained with deep learning in PARADIM

idea-projects

Ideas for cool projects

bids_neuropoly

Python package that deals with BIDS structure for filtering data (specific to NeuroPoly developments)

partial_volume_correction

This repository moved to the following address:

distriploy

Release & deployment helper

atlas-rat

Scripts to generate a microstructure atlas of the rat spinal cord

changelog

Create a changelog file from all the merged pull requests

pediatric-DL-registration