### Archive

# Category: Software

## ScanHub

## 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…

## pyCoilGen

## Open BirdcageBuilder

## NMRduino

NMRduino is an affordable magnetic resonance prototyping and learning tool.

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

## EPTlib – A library for electric properties tomography

## Dafne

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

## CoilGen – an Open Source MR Coil Layout Generator

An automated and flexible algorithm for rapid prototyping of new MR gradient and shim coil designs.

## UKAT – UKRIN Kidney Analysis Toolbox

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

## DeLINEATE: Deep Learning In Neuroimaging

A Python toolbox that aims to make it easier for psychologists and neuroscientists to do “deep learning” analyses on their neuroimaging 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.

## ROAST: Realistic vOlumetric-Approach-based Simulator for Transcranial electric stimulation

## Halbach MRI Designer

## CoSimPy – A Python EM/Circuit Cosimulation Library

CoSimPy is a Python library designed to offer an interface between multi-port full-wave electromagnetic simulations and external circuitry analyses.

## Matlab toolboxes for medical image analysis

## SyneRBI

CCP SyneRBI is a collaborative computational project in synergistic reconstruction for biomedical imaging. Its main software package SIRF is an open-source framework for synergistic image reconstruction.

## B1 correction toolbox

## AFNI (Analysis of Functional NeuroImages)

## ThinWire – MRI Gradient Coil Design

MATLAB tool to design simple geometry gradient coils

## VeSPA – Versatile Simulation Pulses Analysis

Vespa allows users to design RF pulses, create spectral simulations and perform spectral data processing and analysis.

## OpenVnmrJ – Open Source variant of VnmrJ 4.2

OpenVnmrJ is the Open Source variant of the highly successful VnmrJ 4.2 acquisition and processing software

## HealthyPi

## 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),…

## Anser EMT – the first open-source electromagnetic tracking platform for image-guided interventions

The Anser project provides an open-source implementation for electromagnetic tracking (EMT) with particular application to image-guided interventions. This work provides implementation schematics for an EMT system which relies on low-cost acquisition and demodulation techniques using both National…

## 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

## Gradient Coil Design

A repository that contains many Matlab scripts used to design gradient MR coils.

## MIRT

The Michigan Image Reconstruction Toolbox (MIRT) is a collection of open source algorithms for image reconstruction (and related imaging problems) written in Mathwork’s MATLAB language.

## 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

## AxonPacking: Simulator of White Axons Arrangement

Here is a new random disks packing algorithm for numerical simulation of the white matter (axons, myelin sheaths and extra axonal space).

## Bilateral Breast Fusion Algorithms

The integrated models can be used for the study of Specific Absorption Rate (SAR) and thermal analysis in radio-frequency(RF) exposure. The following methodology has the potential to be applied on any patient-based whole-body breast models.

## 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.

## OpenICE – Medical device interoperability platform

OpenICE is an initiative to create a community implementation of an Integrated Clinical Environment. The initiative encompasses not only software implementation but also an architecture for a wider clinical ecosystem to enable new avenues of clinical research. OpenICE seeks to integrate an inclusive…

## 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.

## Direct signal control – Optimal B_{1}^{+} parallel transmission framework

Direct signal control provides reduced transmision field inhomogeneity allowing to recover regions of low signal without increasing imaging time or interecho spacing.

## Quantitative Magnetization Transfer MRI Optimization Toolbox

This toolbox optimizes the acquisition protocols for spoiled gradient echo qMT sensitivity against noise and also sensitivity-regularization for robustness of a qMT parameter-of-interest.

## 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.

## Ultimate intrinsic SNR in a uniform sphere

This program allows to calculate the ultimate intrinsic SNR at the center of a uniform dielectric sphere, which may be used, for example, as an absolute reference to assess the performance of head coils with spherical phantoms.

## 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.

## SequenceTree – Pulse sequence programming in a dynamic visual environment

A user friendly software environment for implementing MRI pulse sequences and, exporting them to actual MRI scanners.

## TOPPE – Rapid MR pulse sequence prototyping

TOPPE is a simple, modular framework for rapid prototyping of pulse sequences on General Electric MRI scanners.

## 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.

## GNU Octave – Scientific programming language

GNU Octave is a high-level language, primarily intended for numerical computations.

## Open fMRI – Sharing brain MRI data

OpenfMRI.org is a project dedicated to the free and open sharing of raw MRI datasets.

## Spinach – Simulating spin dynamics

Spinach is software library for simulation of spin dynamics in large spin systems. It supports NMR, EPR, DNP, MAS, PHIP, singlet state NMR and other forms of Magnetic Resonance spectroscopy.

## FreeSurfer

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

## Gadgetron

Gadgetron is an open source framework for medical image reconstruction. It consists of two main components: First, a modular, high performance framework for streaming data processing through a set of modules or “Gadgets”. Second, it provides a set of tool-boxes for common image reconstruction…

## ISMRMRD – Open MR data standard

The ISMRM Raw Data format is proposed as a common MR raw data format to promote collaborations and reproducible research by facilitating the sharing of data and data processing tools.

## gpuNUFFT – GPU based fast image reconstruction

gpuNUFFT is an open-source GPU Library for reducing computational time of non-linearly sampled 3D/2D MRI data with direct Matlab interface.

## 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.

## Berkeley Advanced Reconstruction Toolbox (BART)

The Berkeley Advanced Reconstruction Toolbox (BART) is a free and open-source image-reconstruction framework for Computational Magnetic Resonance Imaging. It consists of a programming library and a toolbox of command-line programs. The library provides common operations on multi-dimensional arrays,…

## PowerGrid

PowerGrid is an accelerated, open source, freely available toolkit for iterative reconstruction supporting non-Cartesian trajectories. Using high level compiler directives, GPU accelerated Fourier transform operators were implemented in a high level syntax designed to correlate with the popular Image…

## openEMS – A free and open electromagnetic field solver

openEMS is a free and open electromagnetic field solver using the FDTD method. Matlab or Octave are used as an easy and flexible scripting interface.

## Pulseq – Open-source pulse sequences

Open Source framework for the development and hardware-independent execution of MR pulse sequences for imaging and spectroscopy. MRI sequences can be programmed in MATLAB and executed on real hardware.

## gr-MRI: A Software Package for Magnetic Resonance Imaging Using Software-Defined Radios

gr-MRI is a software package using GNU Radio that enables the development of custom MRI spectrometers using off-the-shelf software-defined radios.

## Minimum Field Strength Simulator

A framework for simulating low-field proton-density weighted MRI acquisitions based on high-field acquisitions, which could be used to predict the minimum B0 field strength requirements for MRI techniques. This framework would be particularly useful in the evaluation of de-noising and constrained…

## JEMRIS

Open Source MRI sequence development and simulation environment

## MARIE – Magnetic Resonance Integral Equation Suite

A prototype MATLAB open source software for the fast electromagnetic analysis of MRI systems.