27 Repositories
Python mri Libraries
Image-to-image regression with uncertainty quantification in PyTorch
Image-to-image regression with uncertainty quantification in PyTorch. Take any dataset and train a model to regress images to images with rigorous, distribution-free uncertainty quantification.
This repository contains the code for TABS, a 3D CNN-Transformer hybrid automated brain tissue segmentation algorithm using T1w structural MRI scans
This repository contains the code for TABS, a 3D CNN-Transformer hybrid automated brain tissue segmentation algorithm using T1w structural MRI scans. TABS relies on a Res-Unet backbone, with a Vision Transformer embedded between the encoder and decoder layers.
Pytorch implementation of PTNet for high-resolution and longitudinal infant MRI synthesis
Pyramid Transformer Net (PTNet) Project | Paper Pytorch implementation of PTNet for high-resolution and longitudinal infant MRI synthesis. PTNet: A Hi
Unsupervised MRI Reconstruction via Zero-Shot Learned Adversarial Transformers
Official TensorFlow implementation of the unsupervised reconstruction model using zero-Shot Learned Adversarial TransformERs (SLATER). (https://arxiv.
Task Transformer Network for Joint MRI Reconstruction and Super-Resolution (MICCAI 2021)
T2Net Task Transformer Network for Joint MRI Reconstruction and Super-Resolution (MICCAI 2021) [Paper][Code] Dependencies numpy==1.18.5 scikit_image==
VGG16 model-based classification project about brain tumor detection.
Brain-Tumor-Classification-with-MRI VGG16 model-based classification project about brain tumor detection. First, you can check what people are doing o
This is the official implementation of our proposed SwinMR
SwinMR This is the official implementation of our proposed SwinMR: Swin Transformer for Fast MRI Please cite: @article{huang2022swin, title={Swi
The final project of "Applying AI to 3D Medical Imaging Data" from "AI for Healthcare" nanodegree - Udacity.
Quantifying Hippocampus Volume for Alzheimer's Progression Background Alzheimer's disease (AD) is a progressive neurodegenerative disorder that result
This repository introduces a short project about Transfer Learning for Classification of MRI Images.
Transfer Learning for MRI Images Classification This repository introduces a short project made during my stay at Neuromatch Summer School 2021. This
A toolkit to generate MR sequence diagrams
mrsd: a toolkit to generate MR sequence diagrams mrsd is a Python toolkit to generate MR sequence diagrams, as shown below for the basic FLASH sequenc
Massively parallel Monte Carlo diffusion MR simulator written in Python.
Disimpy Disimpy is a Python package for generating simulated diffusion-weighted MR signals that can be useful in the development and validation of dat
The implementation code for "DAGAN: Deep De-Aliasing Generative Adversarial Networks for Fast Compressed Sensing MRI Reconstruction"
DAGAN This is the official implementation code for DAGAN: Deep De-Aliasing Generative Adversarial Networks for Fast Compressed Sensing MRI Reconstruct
Code for A Volumetric Transformer for Accurate 3D Tumor Segmentation
VT-UNet This repo contains the supported pytorch code and configuration files to reproduce 3D medical image segmentaion results of VT-UNet. Environmen
Multi-Template Mouse Brain MRI Atlas (MBMA): both in-vivo and ex-vivo
Multi-template MRI mouse brain atlas (both in vivo and ex vivo) Mouse Brain MRI atlas (both in-vivo and ex-vivo) (repository relocated from the origin
MRQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) data.
Front-end View Backend View Table of Contents Description Prerequisites Running Basic Information Measurements User Interface Feedback and usage Descr
MRI reconstruction (e.g., QSM) using deep learning methods
deepMRI: Deep learning methods for MRI Authors: Yang Gao, Hongfu Sun This repo is devloped based on Pytorch (1.8 or later) and matlab (R2019a or later
A flexible ML framework built to simplify medical image reconstruction and analysis experimentation.
meddlr Getting Started Meddlr is a config-driven ML framework built to simplify medical image reconstruction and analysis problems. Installation To av
Hierarchical probabilistic 3D U-Net, with attention mechanisms (βππ΅π΅π¦π―π΅πͺπ°π― π-ππ¦π΅, ππππ¦π΄ππ¦π΅) and a nested decoder structure with deep supervision (βπππ¦π΅++).
Hierarchical probabilistic 3D U-Net, with attention mechanisms (βππ΅π΅π¦π―π΅πͺπ°π― π-ππ¦π΅, ππππ¦π΄ππ¦π΅) and a nested decoder structure with deep supervision (βπππ¦π΅++). Built in TensorFlow 2.5. Configured for voxel-level clinically significant prostate cancer detection in multi-channel 3D bpMRI scans.
This is a deep learning-based method to segment deep brain structures and a brain mask from T1 weighted MRI.
DBSegment This tool generates 30 deep brain structures segmentation, as well as a brain mask from T1-Weighted MRI. The whole procedure should take ~1
QSIprep: Preprocessing and analysis of q-space images
QSIprep: Preprocessing and analysis of q-space images Full documentation at https://qsiprep.readthedocs.io About qsiprep configures pipelines for proc
Multiparametric Image Analysis
Documentation The documentation is available on populse_mia's website here Installation From PyPI, for users By cloning the package, for developers Fr
PyTorch Implementation of Small Lesion Segmentation in Brain MRIs with Subpixel Embedding (ORAL, MICCAIW 2021)
Small Lesion Segmentation in Brain MRIs with Subpixel Embedding PyTorch implementation of Small Lesion Segmentation in Brain MRIs with Subpixel Embedd
Python wrappers for external BART computational imaging tools and internal libraries
bartpy Python bindings for BART. Overview This repo contains code to generate an updated Python wrapper for the Berkeley Advance Reconstruction Toolbo
U-Net implementation in PyTorch for FLAIR abnormality segmentation in brain MRI
U-Net for brain segmentation U-Net implementation in PyTorch for FLAIR abnormality segmentation in brain MRI based on a deep learning segmentation alg
A large-scale dataset of both raw MRI measurements and clinical MRI images
fastMRI is a collaborative research project from Facebook AI Research (FAIR) and NYU Langone Health to investigate the use of AI to make MRI scans faster. NYU Langone Health has released fully anonymized knee and brain MRI datasets that can be downloaded from the fastMRI dataset page. Publications associated with the fastMRI project can be found at the end of this README.
Easy and comprehensive assessment of predictive power, with support for neuroimaging features
Documentation: https://raamana.github.io/neuropredict/ News As of v0.6, neuropredict now supports regression applications i.e. predicting continuous t
Machine learning for NeuroImaging in Python
nilearn Nilearn enables approachable and versatile analyses of brain volumes. It provides statistical and machine-learning tools, with instructive doc