MFS – Magnetic Field Simulator
a Biot-Savart based versatile simulation software for industry, research, and education
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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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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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Dafne
Dafne (Deep Anatomical Federated Network) is a collaborative platform to annotate MRI images and train machine learning models
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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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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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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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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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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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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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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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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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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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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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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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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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FreeSurfer
FreeSurfer is a software package for analysis and visualization of structural and functional neuroimaging data
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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.