Python Anatomical-mri Resources

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. TABS relies on a Res-Unet backbone, with a Vision Transformer embedded between the encoder and decoder layers.

Pyramid Transformer Net (PTNet) Project | Paper Pytorch implementation of PTNet for high-resolution and longitudinal infant MRI synthesis. PTNet: A Hi

Official TensorFlow implementation of the unsupervised reconstruction model using zero-Shot Learned Adversarial TransformERs (SLATER). (https://arxiv.

T2Net Task Transformer Network for Joint MRI Reconstruction and Super-Resolution (MICCAI 2021) [Paper][Code] Dependencies numpy==1.18.5 scikit_image==

Brain-Tumor-Classification-with-MRI VGG16 model-based classification project about brain tumor detection. First, you can check what people are doing o

SwinMR This is the official implementation of our proposed SwinMR: Swin Transformer for Fast MRI Please cite: @article{huang2022swin, title={Swi

Quantifying Hippocampus Volume for Alzheimer's Progression Background Alzheimer's disease (AD) is a progressive neurodegenerative disorder that result

Transfer Learning for MRI Images Classification This repository introduces a short project made during my stay at Neuromatch Summer School 2021. This

line scanning repository This repository contains all of the tools used during the acquisition and postprocessing of line scanning data at the Spinoza

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

Disimpy Disimpy is a Python package for generating simulated diffusion-weighted MR signals that can be useful in the development and validation of dat

DAGAN This is the official implementation code for DAGAN: Deep De-Aliasing Generative Adversarial Networks for Fast Compressed Sensing MRI Reconstruct

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 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

Front-end View Backend View Table of Contents Description Prerequisites Running Basic Information Measurements User Interface Feedback and usage Descr

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

meddlr Getting Started Meddlr is a config-driven ML framework built to simplify medical image reconstruction and analysis problems. Installation To av

Feature Aggregation and Refinement Network for 2D Anatomical Landmark Detection Overview Localization of anatomical landmarks is essential for clinica

Hierarchical probabilistic 3D U-Net, with attention mechanisms (—𝘈𝘵𝘵𝘦𝘯𝘵𝘪𝘰𝘯 𝘜-𝘕𝘦𝘵, 𝘚𝘌𝘙𝘦𝘴𝘕𝘦𝘵) and a nested decoder structure with deep supervision (—𝘜𝘕𝘦𝘵++). Built in TensorFlow 2.5. Configured for voxel-level clinically significant prostate cancer detection in multi-channel 3D bpMRI scans.

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 Full documentation at https://qsiprep.readthedocs.io About qsiprep configures pipelines for proc

Documentation The documentation is available on populse_mia's website here Installation From PyPI, for users By cloning the package, for developers Fr

Small Lesion Segmentation in Brain MRIs with Subpixel Embedding PyTorch implementation of Small Lesion Segmentation in Brain MRIs with Subpixel Embedd

bartpy Python bindings for BART. Overview This repo contains code to generate an updated Python wrapper for the Berkeley Advance Reconstruction Toolbo

U-Net for brain segmentation U-Net implementation in PyTorch for FLAIR abnormality segmentation in brain MRI based on a deep learning segmentation alg

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.

Documentation: https://raamana.github.io/neuropredict/ News As of v0.6, neuropredict now supports regression applications i.e. predicting continuous t

nilearn Nilearn enables approachable and versatile analyses of brain volumes. It provides statistical and machine-learning tools, with instructive doc