Search Results for "mri"
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Showing 74 open source projects for "mri"
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x-unet
Implementation of a U-net complete with efficient attention
Implementation of a U-net complete with efficient attention as well as the latest research findings. For 3d (video or CT / MRI scans). -
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TorchIO
Medical imaging toolkit for deep learning
...These transforms include typical computer vision operations such as random affine transformations and also domain-specific ones such as simulation of intensity artifacts due to MRI magnetic field inhomogeneity (bias) or k-space motion artifacts. TorchIO is a Python package containing a set of tools to efficiently read, preprocess, sample, augment, and write 3D medical images in deep learning applications written in PyTorch, including intensity and spatial transforms for data augmentation and preprocessing. Transforms include typical computer vision operations such as random affine transformations and also domain-specific ones such as simulation of intensity artifacts due to MRI magnetic field inhomogeneity. -
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MIRT.jl
MIRT: Michigan Image Reconstruction Toolbox (Julia version)
MIRT.jl is a collection of Julia functions for performing image reconstruction and solving related inverse problems. It is very much still under construction, although there are already enough tools to solve useful problems like compressed sensing MRI reconstruction. Trying the demos is a good way to get started. The documentation is even more still under construction. -
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VoxelMorph
Unsupervised Learning for Image Registration
...Once the model has been trained, it can rapidly compute the transformation required to register new image pairs, significantly reducing computational time compared to classical registration algorithms. The framework supports both supervised and unsupervised learning approaches and is commonly used in medical imaging applications such as MRI alignment, anatomical analysis, and longitudinal studies. -
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AWS X-Ray SDK for Ruby
The official AWS X-Ray Recorder SDK for Ruby
...It has experimental support for JRuby 9.2.0.0 (still forthcoming). To install the Ruby gem for your project, add it to your project Gemfile. You must also add either the Oj or JrJackson gems, for MRI and JRuby respectively, for JSON parsing. The default JSON parser will not work properly, currently. The SDKs included with X-Ray are part of a tightly integrated instrumentation solution offered by AWS. The AWS Distro for OpenTelemetry is part of a broader industry solution in which X-Ray is only one of many tracing solutions. You can implement end-to-end tracing in X-Ray using either approach, but it’s important to understand the differences in order to determine the most useful approach for you. -
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Mongoid
Ruby ODM framework for MongoDB
Mongoid is the officially supported ODM (Object-Document-Mapper) framework for MongoDB in Ruby. This Mongoid community organization is a group of open-source contributors around the Mongoid ODM not affiliated with the company, MongoDB. Mongoid is customarily configured through a mongoid.yml file that specifies options and clients. The simplest configuration is as follows, which configures Mongoid to talk to a MongoDB server at “localhost:27017” and use the database named “mongoid”. If you... -
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Doctor Dok
Doctor Dok is an AI based medical data framework
Store, manage, and understand your medical history in one secure place that only you can access. Built to protect your privacy with full end-to-end encryption. Convert all your Blood Tests, MRI Scans, TK Scans, Visit reports, and Hospital Admission Reports to JSON, safely store in the cloud, and discuss, annotate, and translate them with AI. Doctor Dok is a secure storage, digitization, sharing, and AI discovery platform for all your family and/or folder health data. All health history - digitalized - accessible anywhere from Mobile or Desktop. ... -
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Resque
Ruby library for creating background jobs and processing them
...Resque is heavily inspired by DelayedJob (which rocks) and comprises three parts, a Ruby library for creating, querying, and processing jobs, a Rake task for starting a worker which processes jobs, a Sinatra app for monitoring queues, jobs, and workers. Resque workers can be distributed between multiple machines, support priorities, are resilient to memory bloat / "leaks," are optimized for REE (but work on MRI and JRuby), tell you what they're doing, and expect failure. -
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ODIN
develop, simulate and run magnetic resonance sequences
ODIN is a free software framework for rapid prototyping of magnetic resonance imaging (MRI) sequences. The sequences can be tested, simulated and executed on scanner hardware from different manufacturers. -
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iElectrodes
intracranial electrodes localization toolbox
iElectrodes is a free and open-source Matlab® toolbox to obtain intracranial electrode coordinates from MRI and CT images. Precise and reliable localization can be achieved fast and in a semiautomatic way with minimal user intervention. The toolbox works with ECoG (subdural grids and strips) and SEEG (depth) electrodes. The new GridFit algorithm can precisely localize high-density electrodes (up to 3mm). Brain parcellations (atlas) and surfaces can be imported to aid 2D and 3D visualization and anatomical localization can be done in native or normalized space. ... -
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Iso2Mesh - A 3D Mesh Generation Toolbox
A 3D surface and volumetric mesh generator for MATLAB/Octave
A simple yet powerful mesh generator based on MATLAB/GNU Octave language, creating finite-element mesh from surfaces or arbitrary 3D volumetric images (such as MRI/CT scans) with fully automatic workflows. -
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SimPET
A web platform for the MC simulation of realistic brain PET data
SimPET (http://www.sim-pet.org) is an open, efficient, and user‐friendly online platform for the generation of synthetic brain PET datasets. The platform offers the ability to generate realistic activity and attenuation maps from patient's PET/CT and MRI images. These maps can then be simulated, and sinograms and simulated images can be downloaded. More advanced features can be obtained by using the SimPET scripts: https://github.com/txusser/brainviset_simset https://github.com/txusser/simpet (New version pre-alpha) You can also upload your own phantoms to simulate. Currently the platform incorporates MC models for the GE Advance, GE Discovery ST and Siemens mCT. ... -
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KMedicalImageScreener1
A Medical Scanner for Computer Aided Detection of MRI Scans
This app is JSP that has been tested for use in Computer Aided Detection of MRI scans in the cranial and abdominal areas for cancer detection. There was one case study completed with a very high accuracy rate of over 95% on test data. This app is provided as-is under the GNU License with Accrediation. Let me know what you think, Diana -
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MELAGE is a neuroimaging software developed for visualizing and processing medical images, both Ultrasound and Magnetic Resonance Images (MRIs). Specially it has been prepared for neuroimaging of newborns, it is a versatile platform that allows the visualization of many types of medical images. It allows to load two, three and four-dimensional images of both techniques and in the case of 3D images it allows the simultaneous visualization of the three orthogonal planes which facilitates the...
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fastMRI
A large open dataset + tools to speed up MRI scans using ML
...It includes reference implementations for key MRI reconstruction architectures such as U-Net and Variational Networks (VarNet), along with example scripts for model training and evaluation using the PyTorch Lightning framework. The project also releases several fully anonymized public MRI datasets, including knee, brain, and prostate scans. -
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Region-based spatial normalization
Region-based spatial normalization (RBSN) for functional MRI.
Region-based spatial normalization (RBSN) for functional MRI. He, Hengda, and Qolamreza R. Razlighi. "Landmark‐guided region‐based spatial normalization for functional magnetic resonance imaging." Human Brain Mapping (2022). -
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CineTracker
CineTracker GUI for motion tracking of cine MRI
CineTracker GUI for motion tracking of cine MRI Developed by Liam Lawrence and Angus Lau, Sunnybrook Health Sciences Centre -
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fog
The Ruby cloud services library
Whether you need compute, dns, storage, or a multitude of other services, fog provides an accessible entry point and facilitates cross-service compatibility. Just getting started working with cloud resources? You are not alone, and having so many complicated options makes it hard to know where to start. fog delivers the knowledge of cloud experts to you, helping you to bootstrap your cloud usage and guiding you as your own expertise develops. By coding with fog from the start you avoid... -
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plastimatch
Volumetric image processing software
Plastimatch is an open source software for image computation. Our main focus is high-performance volumetric registration of medical images, such as X-ray computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET). -
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These are plugins to Fiji (ImageJ) originally developed at Nuclear Medicine at Beth Israel, Boston MA. Pet_Ct_Viewer is for PET/SPECT - CT/MRI studies showing fusion of the modalities. Read_BI_Studies is for BI database activities. See http://petctviewer.org
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VR Neuroanatomy
Explore and dissect a complete brain model in VR
Understanding the anatomy of complex organs such as the human brain can be a challenge for students, so there is a definite advantage given to students who can experience the structures in a spatial way through real or virtual experiences. Since 2016, the Marquette Visualization Lab has been utilizing a dataset of 3 and 7 Tesla MRI scans from the Structural Informatics Group at University of Washington to visualize the structures of the brain in their Cave, utilizing the Unity game engine and 10 stereoscopic 3D projectors. Most MRI scans are presented as a volumetric rendering, but this dataset is unique because it was fully labelled and parcellated, allowing lab users to not only view the structures of the brain, but also virtually dissect it in a large scale, collaborative virtual reality environment. ... -
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Relative Overestimation VOP
VOP compression for MRI with overestimation control
**** This work is outdated! For better compression and speed use these: ***** https://sourceforge.net/projects/enhanced-sar-compression/ Virtual Observation Points SAR compression. Contains multiple Algorithms: Compression according to Eichfelder et al. and Lee et al. The Lee algorithm is enhanced by including overestimation control to reduce maximum relative overestimation. All algorithms are implemented in Matlab and were optimized for enhanced speed. Needs Matlab R2016b at least.... -
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Pediatric MRI Myelin+Diffusion Atlas
MRI atlas for myelin and diffusion distribution in pediatric brain.
Atlas is described in this paper: https://onlinelibrary.wiley.com/doi/full/10.1111/jon.12689. Structural template, myelin water fraction, fractional anisotropy, mean diffusivity, radial diffusivity and axial diffusivity atlases for children aged 9-10 years are provided for free download for pediatric neuroimaging applications. -
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Camino is a free, open-source software package for simulation, analysis and reconstruction of Diffusion MRI data. Download the latest version of the code by clicking the "Code" tab and then "Download Snapshot". The green download button will get the latest major change (updated less frequently). For tutorials and more information, visit http://camino.org.uk. CAMINO IS A RESEARCH TOOL ONLY AND SHOULD NOT BE USED FOR CLINICAL PURPOSES.
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Myelin water atlas
Normative myelin water atlas for myelin distribution in the brain
Normative myelin water atlas was created by co-registering and averaging myelin images in MNI space from 50 healthy brains to depict the population mean and variability of the myelin content in the brain. The myelin images of individual subjects were acquired using myelin water imaging. Details about myelin water imaging technique and its analysis can be found here: https://mriresearch.med.ubc.ca/news-projects/myelin-water-fraction/. The created myelin water atlas with its standard deviation...
