MFS – Magnetic Field Simulator
a Biot-Savart based versatile simulation software for industry, research, and education
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MagneticReadoutProcessing
Home OSI² e.V. News Projects Search Software Other MagneticReadoutProcessing ScanHubNEXUS Console Application MagneticReadoutProcessing is a Python library that makes it possible to store and further process raw data from magnetometers. The focus is on the processing of point clouds, on which the points are located on a circular path around a magnetic object to be [...]
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ScanHub
Home OSI² e.V. News Projects Search Software Simulations Reconstruction Image processing/visualization Lab software ScanHub UKF TractographyMagneticReadoutProcessing Application Open-source platform for MR acquisition control, data management and post-processing Contributors David Schote¹, Johannes Behrens¹, Christoph Dinh¹ Contact info@brain-link.de Estimated cost 0€ Progress under development GPL 3.0, BRAIN-LINK Commercial License Resources https://github.com/brain-link ScanHub is a cloud-based platform designed [...]
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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…
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pyCoilGen
Home OSI² e.V. News Projects Search Hardware Coils Software Simulations pyCoilGen Open BirdcageBuilderUKF Tractography Application Python based tool for generating MR coil layouts. It generates a connected, non-overlapping wire path for a given surface mesh or meshes and target field. Contributors Kevin Meyer, Philipp Amrein¹ Contact kevin@belapena.com Estimated cost Free Progress Stable Resources https://github.com/kev-m/pyCoilGen https://pycoilgen.readthedocs.io/en/stable/index.html [...]
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Open BirdcageBuilder
Home OSI² e.V. News Projects Search Hardware design Software Open BirdcageBuilder NMRduinopyCoilGen Application Calculates first-pass capacitances to aid in construction and simulation of birdcage coils. Contributors Douglas Brantner1,2, Giuseppe Carluccio1,2, Chih-Liang Chin3, Christopher Collins1,2 Contact douglas.brantner@nyulangone.org Estimated cost Free Progress Beta 0.0.8, AGPL 3.0 License – Working, results validated against previous versions; need to update [...]
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NMRduino
NMRduino is an affordable magnetic resonance prototyping and learning tool.
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DL+DiReCT – Direct Cortical Thickness Estimation using Deep Learning-based Anatomy Segmentation and Cortex Parcellation
Home OSI² e.V. News Projects Search Software Image processing/visualization DL+DiReCT – Direct Cortical Thickness Estimation using Deep Learning-based Anatomy Segmentation and Cortex Parcellation Parallel transmission implant safety testbedNMRduino Application DL+DiReCT combines a deep learning-based neuroanatomy segmentation and cortex parcellation with a diffeomorphic registration technique to measure cortical thickness from T1-weighted magnetic resonance images. Contributors Michael [...]
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EPTlib – A library for electric properties tomography
Home OSI² e.V. News Projects Search Software Reconstruction EPTlib – A library for electric properties tomography 8-channel transmit/receive RF coil for 3TWireless reference implant Application EPTlib is a C++ library collecting electric properties tomography methods. It includes a terminal application for a simple ready-to-use adoption of the implemented methods. Contributors Alessandro Arduino¹ Contact a.arduino@inrim.it Estimated [...]
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Dafne
Dafne (Deep Anatomical Federated Network) is a collaborative platform to annotate MRI images and train machine learning models
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CoilGen – an Open Source MR Coil Layout Generator
An automated and flexible algorithm for rapid prototyping of new MR gradient and shim coil designs.
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UKAT – UKRIN Kidney Analysis Toolbox
UKAT is a vendor agnostic framework for the analysis of quantitative renal MRI data.
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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
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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.
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ROAST: Realistic vOlumetric-Approach-based Simulator for Transcranial electric stimulation
Home OSI² e.V. News Projects Search Software Simulations ROAST: Realistic vOlumetric-Approach-based Simulator for Transcranial electric stimulation Halbach MRI DesignerVirtual MRI Scanner Application A fully-automated, easy-to-use toolbox for simulating and optimizing transcranial electrical stimulation Contributors Yu (Andy) Huang1 Maximilian Nentwich2 Takfarinas Medani3 Dalton Bermudez4 June Kang5 Contact andypotatohy@gmail.com Estimated cost Free Progress Stable release v3.0 GPL-3.0 [...]
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Halbach MRI Designer
Home OSI² e.V. News Projects Search Software Halbach MRI Designer MRI distortion phantomROAST: Realistic vOlumetric-Approach-based Simulator for Transcranial electric stimulation Application Create a Halbach MRI Magnet from parametric definitions Contributors Benjamin Menküc1, Lukas Winter2, Thomas O'Reilly3 Contact benjamin.menkuec@fh-dortmund.de Estimated cost Free Progress Stable release v0.2 Resources https://github.com/menkueclab/HalbachMRIDesigner This tool can create an OpenSCAD geometry of [...]
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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.
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Matlab toolboxes for medical image analysis
Home OSI² e.V. News Projects Search Software Image processing/visualization Matlab toolboxes for medical image analysis SyneRBIMRI Compatible Wireless Sensors Application Image registration and segmentation, diffusion-MRI reconstruction and tractography, tissue thickness measurement, etc. Contributors Iman Aganj1 Contact iaganj@mgh.harvard.edu Estimated cost Free Progress Stable release (BSD-3-Clause) Resources https://nmr.mgh.harvard.edu/~iman/software These tools are useful for the following neuro- and [...]
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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.
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B1 correction toolbox
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AFNI (Analysis of Functional NeuroImages)
Home OSI² e.V. News Projects Search Software Image processing/visualization AFNI (Analysis of Functional NeuroImages) ThinWire – MRI Gradient Coil DesignHalbach array magnet for in vivo imaging Application Software for Analysis and Visualization of Functional Magnetic Resonance Neuroimages Contributors Robert Cox¹ Contact robertcox@mail.nih.gov Estimated cost Free Progress Software: released Resources https://afni.nimh.nih.gov/ AFNI (Analysis of Functional NeuroImages) is [...]
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ThinWire – MRI Gradient Coil Design
MATLAB tool to design simple geometry gradient coils
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VeSPA – Versatile Simulation Pulses Analysis
Vespa allows users to design RF pulses, create spectral simulations and perform spectral data processing and analysis.
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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
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HealthyPi
Home OSI² e.V. News Projects Search Other hardware (non-MR) Software HealthyPi 3D SlicerOpenVnmrJ – Open Source variant of VnmrJ 4.2 Application An open-source, multi-parameter, full fledged human body vital sign monitoring HAT for Raspberry Pi as well as standalone use. Contributors Ashwin Whitchurch¹ Contact ashwin@protocentral.com Estimated cost Total price: 250$ Progress Hardware: released Software: released [...]
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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.),…
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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),…
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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…
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Water/Fat Separated MR Thermometry
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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.
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MRILab – GPU accelerated MRI simulator
An efficient and versatile numerical MRI simulator with GPU parallel acceleration
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Gradient Coil Design
A repository that contains many Matlab scripts used to design gradient MR coils.
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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.
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Yarra
Yarra is a simple and open software framework for Siemens MRI systems to facilitate data transfer for offline processing of computationally expensive algorithms.
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AxonDeepSeg: Axon Segmentation Toolbox
Segment axon and myelin from microscopy data, extract statistics and compare histology with MRI
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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).
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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.
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Pulseq-GPI / IMR-framework
Python-based and UI-based pulse sequence design.
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AnalyzeNNLS
A MatLab ROI-based analysis suite for multiecho MRI data. AnalyzeNNLS creates a T2 distribution from the averaged decay data.
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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.
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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.
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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…
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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.
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qMRLab – Quantitative MRI under one umbrella
An open-source software for quantitative MR image analysis.
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Blind Source Separation of Diffusion MRI
A diffusion model-free framework with echo time dependence for free-water elimination and brain tissue microstructure characterization.
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Direct signal control – Optimal B1+ 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.
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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.
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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.
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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.
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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.
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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.
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TOPPE – Rapid MR pulse sequence prototyping
TOPPE is a simple, modular framework for rapid prototyping of pulse sequences on General Electric MRI scanners.
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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.
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R-project – Statistical computing
R is a state-of-the-art statistical computing software with powerful graphic possibilities.
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ODIN – Object-Oriented Development Interface for NMR
ODIN is a C++ software framework to develop and simulate magnetic resonance sequences.
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GNU Octave – Scientific programming language
GNU Octave is a high-level language, primarily intended for numerical computations.
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Open fMRI – Sharing brain MRI data
OpenfMRI.org is a project dedicated to the free and open sharing of raw MRI datasets.
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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.
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FreeSurfer
FreeSurfer is a software package for analysis and visualization of structural and functional neuroimaging data
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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…
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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.
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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.
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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.
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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,…
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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…
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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.
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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.
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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.
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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…
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JEMRIS
Open Source MRI sequence development and simulation environment
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MARIE – Magnetic Resonance Integral Equation Suite
A prototype MATLAB open source software for the fast electromagnetic analysis of MRI systems.