lusi-bach

MRSignalsSeqs

Stanford University Rad229 Class Code: MRI Signals and Sequences

cardiac-segmentation

Right Ventricle Cardiac MRI Segmentation

Finger_vein_extract

手指静脉图像的提取与快速配准

MRI-Pre-processing

Almost in every image processing or analysis work, image pre-preprocessing is crucial step. In medical image analysis, pre-processing is a very important step because the further success or performance of the algorithm mostly dependent on pre-processed image. In this lab, we are working with 3D Brain MRI data. In case of working with brain MRI removing the noise and bias field (which is due to inhomogeneity of the magnetic field) is very important part of preprocessing of brain MRI. To do so, we widely used algorithm Anisotropic diffusion, isotropic diffusion which can diffuse in any direction, and Multiplicative intrinsic component optimization (MICO) have been used for noise removal and bias field correction respectfully. Both quantitative and qualitative performance of the algorithms also have been analyzed.

autodmri

Automated characterization of noise distributions in diffusion MRI data

MRI-Denoising-Using-SCSA

I worked on the Semi Classical Signal Analysis in the summers of 2019 at King Abdullah University of Science and Technology (KAUST). I improved the existing MRI denoising algorithm using SCSA significantly.

ODGD

Diffusion-Weighted MRI often suffers from signal attenuation due to long TE, sensitivity to physiological motion, and dephasing due to concomitant gradients (CGs). These challenges complicate image interpretation and may introduce bias in quantitative diffusion measurements. Motion moment-nulled diffusion-weighting gradients have been proposed to compensate motion, however, they frequently result in high TE and suffer from CG effects. In this work [1], we present a novel Optimed Diffusion-weighting Gradient waveform Design (ODGD) method for diffusion-weighting gradient waveform design for any diffusion-weighting direction that seeks to overcome the limitations of previous methods. The proposed ODGD method consists of: 1) a constrained optimization formulation that minimizes the TE for a given b-value subject to both, moment-nulling and/or CG-nulling constraints, and 2) a quadratic optimization algorithm that directly solves the formulation without introducing approximations.

Multi-scaleSR_For_MRI_Blur

使用一种更深更宽的多尺度神经网络来进行核磁共振图像的去除伪影操作

Motion-Compensated-Dynamic-MRI-Reconstruction-with-Local-Affine-Optical-Flow-Estimation

DiST

Codes and example scripts for "Wong, R.K.W., T.C.M. Lee, D. Paul, and J. Peng. Fiber direction estimation, smoothing and tracking in diffusion MRI (2016). AOAS, 10(3): 1137-1156

DCE-MRI_Regularization_MRM

Code to the paper: M. Bartoš, P. Rajmic, M. Šorel, M. Mangová, O. Keunen and R. Jiřík. Spatially regularized estimation of the tissue homogeneity model parameters in DCE-MRI using proximal minimization. Magnetic Resonance in Medicine. 2019; 82: 2257-2272. https://doi.org/10.1002/mrm.27874. Pre-print available at http://www.utko.feec.vutbr.cz/~rajmic/papers/Bartos_etal_RegularizedDCEMRI_web.pdf.

pyAFQ

Automated Fiber Quantification ... in Python

AFQ

Automated Fiber Quantification

ksvd-sparse-dictionary

Learn atoms of a sparse dictionary using the iterative K-SVD algorithm, written in Python.

noise_estimate

Potts_DTI

Codes for "A Spatial Bayesian Semiparametric Mixture Model for Positive Definite Matrices with Applications to Diffusion Tensor Imaging" Copyright (C) 2018 Zhou Lan (zlan@ncsu.edu) - All Rights Reserved

dti-error

Calculate the RMSE between a tensor fit from dtiInit and the diffusion weighted imaging data

GHOSTDR

Development repository for the GHOST data reduction software.

supervised_blur_kernel_estimation

If you have the original image and the blurred image, you can use this code to estimate the blur kernel.

General-Cross-Validation-denoising-Forward

This repository contains MATLAB scripts and sample data for applying denoising method presented in: "Automatic noise-removal/signal-removal based on general cross-validation thresholding in synchrosqueezed domain and its application on earthquake data"

PCA_denoising

The PCA denoising matlab algorithm used in the publication "Principal component analysis for fast and model-free denoising of multi b-value diffusion-weighted MR images" by Oliver J Gurney-Champion et al. in physics in medicine and biology in 2019.

Image-denoising-code

This is MATLAB script for image denoising using total-variation and Nesterov's 1st order method

NGMeet

Matlab Code for: "Non-local Meets Global: An Integrated Paradigm for Hyperspectral Denoising. Arvix. Dec 2018"

AST-NLS

Matlab Code for Image Denoising via Bandwise Adaptive Modeling and Regularization Exploiting Nonlocal Similarity

nlbayes.m

Matlab version of the NL-Bayes image denoising algorithm

fmri_denoising

Collection of Matlab functions for denoising fMRI data

MP-PCA-Denoising

Matlab implementation of Marchenko Pastur denoising (Veraart et al, NeuroImage 142 (2016) 394–406)

Wavelet-decomposition-and-Filter-bank

The wavelet transform and its applications in image denoising

medical_image_denoising

Demo Matlab software package for 3D MRI image denoising

SNN

Matlab code implementation the modified Non Local Means and Bilateral filters, as described in I. Frosio, J. Kautz, Statistical Nearest Neighbors for Image Denoising, IEEE Trans. Image Processing, 2018. The repository also includes the Matlab code to replicate the results of the toy problem described in the paper.