Python Structural-mri Resources

Molecular Nodes 🧬 🔬 💻 Buy Me a Coffee to Keep Development Going! Join a Community of Blender SciVis People! What is Molecular Nodes? Molecular Node

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==

package tests docs license stats support This repository contains FEDOT - an open-source framework for automated modeling and machine learning (AutoML

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

VolumeGAN - 3D-aware Image Synthesis via Learning Structural and Textural Representations 3D-aware Image Synthesis via Learning Structural and Textura

A collection of graph classification methods, covering embedding, deep learning, graph kernel and factorization papers

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

VolumeGAN - 3D-aware Image Synthesis via Learning Structural and Textural Representations 3D-aware Image Synthesis via Learning Structural and Textura

script-SV-genotyping These are the scripts used for the project of ‘Assembly of a pan-genome for global cattle reveals missing sequence and novel stru

An easy to use elastic 3D structural engineering finite element analysis library for Python.

CCasGNN A new framework, collaborative cascade prediction based on graph neural networks (CCasGNN) to jointly utilize the structural characteristics,

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

slientruss3d : Python for stable truss analysis tool Desciption slientruss3d is a python package which can solve the resistances, internal forces and

Structural Guidance for Transformer Language Models This repository accompanies the paper, Structural Guidance for Transformer Language Models, publis

VT-UNet This repo contains the supported pytorch code and configuration files to reproduce 3D medical image segmentaion results of VT-UNet. Environmen

structural-probes Codebase for testing whether hidden states of neural networks encode discrete structures. Based on the paper A Structural Probe for

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

LexPOS_ko Generating Korean Slogans with phonetic and structural repetition Generating Slogans with Linguistic Features LexPOS is a sequence-to-sequen

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

counterfactual-tpp This is a repository containing code and real data for the paper Counterfactual Temporal Point Processes. Pre-requisites This code

===================================== README: Inpainting based PatchMatch ===================================== @Author: Younesse ANDAM @Conta

counterfactual-tpp This is a repository containing code and real data for the paper Counterfactual Temporal Point Processes. Pre-requisites This code

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

Python Causal Impact Causal inference using Bayesian structural time-series models. This package aims at defining a python equivalent of the R CausalI

3DFEM Python 3D finite element code This python code allows for solving 3D structural problems using the finite element method. New features will be a

AlphaFold Analyser This program produces high quality visualisations of predicted structures produced by AlphaFold. These visualisations allow the use

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

Structural Constraints on Information Content in Human Brain States Code accompanying the paper "The information content of brain states is explained

xtbreak estimating and testing for many known and unknown structural breaks in time series and panel data. For an overview of xtbreak test see xtbreak

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.

Role-based network embedding via structural features reconstruction with degree-regularized constraint Train python main.py --dataset brazil-flights

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

Graph Neural Networks with Learnable Structural and Positional Representations Source code for the paper "Graph Neural Networks with Learnable Structu

PurNet Project for the TIP 2021 Paper "Salient Object Detection with Purificatory Mechanism and Structural Similarity Loss" Abstract Image-based salie

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

MangaLineExtraction_PyTorch The (Official) PyTorch Implementation of the paper "Deep Extraction of Manga Structural Lines" Usage model_torch.py [sourc

StructDepth PyTorch implementation of our ICCV2021 paper: StructDepth: Leveraging the structural regularities for self-supervised indoor depth estimat

DIML Created by Wenliang Zhao*, Yongming Rao*, Ziyi Wang, Jiwen Lu, Jie Zhou This repository contains PyTorch implementation for paper Towards Interpr

Attention Walk ⠀⠀ A PyTorch Implementation of Watch Your Step: Learning Node Embeddings via Graph Attention (NIPS 2018). Abstract Graph embedding meth

GAM ⠀⠀ A PyTorch implementation of Graph Classification Using Structural Attention (KDD 2018). Abstract Graph classification is a problem with practic

Visual-Reasoning-eXplanation [CVPR 2021 A Peek Into the Reasoning of Neural Networks: Interpreting with Structural Visual Concepts] Project Page | Vid

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

This repository contains FEDOT - an open-source framework for automated modeling and machine learning (AutoML). It can build custom modeling pipelines for different real-world processes in an automated way using an evolutionary approach. FEDOT supports classification (binary and multiclass), regression, clustering, and time series prediction tasks.

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.

Learning Structural Edits via Incremental Tree Transformations Code for "Learning Structural Edits via Incremental Tree Transformations" (ICLR'21) 1.

Structural basis for solubility in protein expression systems Large-scale protein production for biotechnology and biopharmaceutical applications rely

Commonsense Knowledge Base Completion with Structural and Semantic Context Code for the paper Commonsense Knowledge Base Completion with Structural an

SLM: Structural Language Models of Code This is an official implementation of the model described in: "Structural Language Models of Code" [PDF] To ap

Awesome Pattern Matching (apm) for Python pip install awesome-pattern-matching Simple Powerful Extensible Composable Functional Python 3.7+, PyPy3.7+

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