### Archive

# Category: Image processing/visualization

## UKF Tractography

Tracing multiple crossing/kissing fibers while estimating the underlying microstructural parameters is a hard tractography problem. We solve this problem using an unscented Kalman filter based tractography algorithm, where model parameters (and thereby the associated microstructural measures) and…

## DL+DiReCT – Direct Cortical Thickness Estimation using Deep Learning-based Anatomy Segmentation and Cortex Parcellation

## Dafne

Dafne (Deep Anatomical Federated Network) is a collaborative platform to annotate MRI images and train machine learning models

## UKAT – UKRIN Kidney Analysis Toolbox

UKAT is a vendor agnostic framework for the analysis of quantitative renal MRI data.

## Virtual MRI Scanner

Virtual Scanner is an end-to-end hybrid Magnetic Resonance Imaging (MRI) simulator/console designed to be zero-footprint, modular, and supported by open-source standards.

## Matlab toolboxes for medical image analysis

## AFNI (Analysis of Functional NeuroImages)

## 3D Slicer

Software application and development platform for medical image visualization, analysis, quantification, segmentation, and registration. Supports all imaging modalities, wide range of data types (surface and volumetric meshes, textured surface scans, spectrum data, points, lines, curves, tables, etc.),…

## hMRI-toolbox

The hMRI-toolbox is an easy-to-use open-source and flexible tool, for qMRI data handling and processing. It allows the estimation of high-quality multi-parameter qMRI maps (longitudinal and effective transverse relaxation rates R1 and R2*, proton density PD and magnetisation transfer MT saturation),…

## Water/Fat Separated MR Thermometry

## QMRITools – Mathematica Toolbox for quantitative MRI data

QMRITools is written in Mathematica using Wolfram Workbench and Eclipse and contains a collection of tools and functions for processing quantitative MRI data.

## MRILab – GPU accelerated MRI simulator

An efficient and versatile numerical MRI simulator with GPU parallel acceleration

## Yarra

Yarra is a simple and open software framework for Siemens MRI systems to facilitate data transfer for offline processing of computationally expensive algorithms.

## AxonDeepSeg: Axon Segmentation Toolbox

Segment axon and myelin from microscopy data, extract statistics and compare histology with MRI

## Pulseq-GPI / IMR-framework

Python-based and UI-based pulse sequence design.

## AnalyzeNNLS

A MatLab ROI-based analysis suite for multiecho MRI data. AnalyzeNNLS creates a T2 distribution from the averaged decay data.

## TAPAS – Translational Algorithms for Psychiatry – Advancing Science

A collection of software tools developed to support clinical neuromodeling, particularly computational psychiatry, computational neurology, and computational psychosomatics.

## DIPY – Diffusion imaging in Python

A software for computational neuroanatomy with focus on diffusion magnetic resonance imaging (dMRI) analysis. It implements a broad range of algorithms for denoising, registration, reconstruction, tracking, clustering, visualization, and statistical analysis of MRI data.

## Spinal Cord Toolbox – Image processing for multiparametric MRI

Spinal Cord Toolbox is a comprehensive software for the processing and analysis of multiparametric MRI data of the spinal cord.

## qMRLab – Quantitative MRI under one umbrella

An open-source software for quantitative MR image analysis.

## Blind Source Separation of Diffusion MRI

A diffusion model-free framework with echo time dependence for free-water elimination and brain tissue microstructure characterization.

## High dynamic range processing for local contrast-enhancement in MRI

A high dynamic range image processing algorithm which can offer enhanced contrast and feature preservation for multichannel and multisequence MRI.

## Hybrid MRI‐Ultrasound scannerless real‐time imaging

This project proposes a hybrid system based on a single‐element ultrasound transducer and an MR scanner to help boost temporal resolution in real‐time MRI.

## FID-A – Advanced MR spectroscopy processing and simulation

Advanced toolbox for design and analysis of radiofrequency (RF) pulses, and processing of magnetic resonance spectroscopy data.

## R-project – Statistical computing

R is a state-of-the-art statistical computing software with powerful graphic possibilities.

## ODIN – Object-Oriented Development Interface for NMR

ODIN is a C++ software framework to develop and simulate magnetic resonance sequences.

## FreeSurfer

FreeSurfer is a software package for analysis and visualization of structural and functional neuroimaging data

## SimpleElastix – Easy image registration

SimpleElastix is a user-friendly command line based program that registers (matches/aligns) images in C++, Python, Java, R, Ruby, Octave, C#, Lua and Tcl.