Vision Transformer for 3D medical image registration (Pytorch).

Overview

ViT-V-Net: Vision Transformer for Volumetric Medical Image Registration

keywords: vision transformer, convolutional neural networks, image registration

This is a PyTorch implementation of my short paper:

Chen, Junyu, et al. "ViT-V-Net: Vision Transformer for Unsupervised Volumetric Medical Image Registration. " arXiv, 2021.

train.py is the training script. models.py contains ViT-V-Net model.

Pretrained ViT-V-Net: pretrained model

Dataset: Due to restrictions, we cannot distribute our brain MRI data. However, several brain MRI datasets are publicly available online: IXI, ADNI, OASIS, ABIDE, etc. Note that those datasets may not contain labels (segmentation). To generate labels, you can use FreeSurfer, which is an open-source software for normalizing brain MRI images. Here are some useful commands in FreeSurfer: Brain MRI preprocessing and subcortical segmentation using FreeSurfer.

Model Architecture:

Vision Transformer Achitecture:

Example Results:

Quantitative Results:

Reference:

TransUnet

ViT-pytorch

VoxelMorph

If you find this code is useful in your research, please consider to cite:

@misc{chen2021vitvnet,
title={ViT-V-Net: Vision Transformer for Unsupervised Volumetric Medical Image Registration}, 
author={Junyu Chen and Yufan He and Eric C. Frey and Ye Li and Yong Du},
year={2021},
eprint={2104.06468},
archivePrefix={arXiv},
primaryClass={eess.IV}
}

About Me

Owner
Junyu Chen
Ph.D. student in the Department of Electrical and Computer Engineering & the Department of Radiology and Radiological Science @ Johns Hopkins University
Junyu Chen
[ICCV'21] Learning Conditional Knowledge Distillation for Degraded-Reference Image Quality Assessment

CKDN The official implementation of the ICCV2021 paper "Learning Conditional Knowledge Distillation for Degraded-Reference Image Quality Assessment" O

Multimedia Research 50 Dec 13, 2022
A-SDF: Learning Disentangled Signed Distance Functions for Articulated Shape Representation (ICCV 2021)

A-SDF: Learning Disentangled Signed Distance Functions for Articulated Shape Representation (ICCV 2021) This repository contains the official implemen

81 Dec 14, 2022
Demo code for paper "Learning optical flow from still images", CVPR 2021.

Depthstillation Demo code for "Learning optical flow from still images", CVPR 2021. [Project page] - [Paper] - [Supplementary] This code is provided t

130 Dec 25, 2022
cisip-FIRe - Fast Image Retrieval

Fast Image Retrieval (FIRe) is an open source image retrieval project release by Center of Image and Signal Processing Lab (CISiP Lab), Universiti Malaya. This project implements most of the major bi

CISiP Lab 39 Nov 25, 2022
Polynomial-time Meta-Interpretive Learning

Louise - polynomial-time Program Learning Getting help with Louise Louise's author can be reached by email at Stassa Patsantzis 64 Dec 26, 2022

Alias-Free Generative Adversarial Networks (StyleGAN3) Official PyTorch implementation

Alias-Free Generative Adversarial Networks (StyleGAN3) Official PyTorch implementation

NVIDIA Research Projects 4.8k Jan 09, 2023
On Uncertainty, Tempering, and Data Augmentation in Bayesian Classification

Understanding Bayesian Classification This repository hosts the code to reproduce the results presented in the paper On Uncertainty, Tempering, and Da

Sanyam Kapoor 18 Nov 17, 2022
[NeurIPS 2021] Better Safe Than Sorry: Preventing Delusive Adversaries with Adversarial Training

Better Safe Than Sorry: Preventing Delusive Adversaries with Adversarial Training Code for NeurIPS 2021 paper "Better Safe Than Sorry: Preventing Delu

Lue Tao 29 Sep 20, 2022
Dark Finix: All in one hacking framework with almost 100 tools

Dark Finix - Hacking Framework. Dark Finix is a all in one hacking framework wit

Md. Nur habib 2 Feb 18, 2022
Code release for "Conditional Adversarial Domain Adaptation" (NIPS 2018)

CDAN Code release for "Conditional Adversarial Domain Adaptation" (NIPS 2018) New version: https://github.com/thuml/Transfer-Learning-Library Dataset

THUML @ Tsinghua University 363 Dec 20, 2022
Code for T-Few from "Few-Shot Parameter-Efficient Fine-Tuning is Better and Cheaper than In-Context Learning"

T-Few This repository contains the official code for the paper: "Few-Shot Parameter-Efficient Fine-Tuning is Better and Cheaper than In-Context Learni

220 Dec 31, 2022
DeepLab resnet v2 model in pytorch

pytorch-deeplab-resnet DeepLab resnet v2 model implementation in pytorch. The architecture of deepLab-ResNet has been replicated exactly as it is from

Isht Dwivedi 601 Dec 22, 2022
Official repository for the paper "GN-Transformer: Fusing AST and Source Code information in Graph Networks".

GN-Transformer AST This is the official repository for the paper "GN-Transformer: Fusing AST and Source Code information in Graph Networks". Data Prep

Cheng Jun-Yan 10 Nov 26, 2022
Clustering is a popular approach to detect patterns in unlabeled data

Visual Clustering Clustering is a popular approach to detect patterns in unlabeled data. Existing clustering methods typically treat samples in a data

Tarek Naous 24 Nov 11, 2022
Deep learning for Engineers - Physics Informed Deep Learning

SciANN: Neural Networks for Scientific Computations SciANN is a Keras wrapper for scientific computations and physics-informed deep learning. New to S

SciANN 195 Jan 03, 2023
Gym environments used in the paper: "Developmental Reinforcement Learning of Control Policy of a Quadcopter UAV with Thrust Vectoring Rotors"

gym_multirotor Gym to train reinforcement learning agents on UAV platforms Quadrotor Tiltrotor Requirements This package has been tested on Ubuntu 18.

Aditya M. Deshpande 19 Dec 29, 2022
Codebase for arXiv preprint "NeRF++: Analyzing and Improving Neural Radiance Fields"

NeRF++ Codebase for arXiv preprint "NeRF++: Analyzing and Improving Neural Radiance Fields" Work with 360 capture of large-scale unbounded scenes. Sup

Kai Zhang 722 Dec 28, 2022
Instantaneous Motion Generation for Robots and Machines.

Ruckig Instantaneous Motion Generation for Robots and Machines. Ruckig generates trajectories on-the-fly, allowing robots and machines to react instan

Berscheid 374 Dec 23, 2022
Paddle-Adversarial-Toolbox (PAT) is a Python library for Deep Learning Security based on PaddlePaddle.

Paddle-Adversarial-Toolbox Paddle-Adversarial-Toolbox (PAT) is a Python library for Deep Learning Security based on PaddlePaddle. Model Zoo Common FGS

AgentMaker 17 Nov 08, 2022
Graph Convolutional Neural Networks with Data-driven Graph Filter (GCNN-DDGF)

Graph Convolutional Gated Recurrent Neural Network (GCGRNN) Improved from Graph Convolutional Neural Networks with Data-driven Graph Filter (GCNN-DDGF

Lei Lin 21 Dec 18, 2022