Search Results for "mri" - Page 2
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Showing 101 open source projects for "mri"
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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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emruby
emscripten'ed MRI
emruby is a project that integrates the mruby lightweight Ruby interpreter into emulation and embedded environments, enabling scripting capabilities within systems that require high performance and low memory usage. It is designed to allow developers to embed Ruby-based scripting into applications such as emulators or other performance-sensitive software, providing flexibility without sacrificing efficiency. By leveraging mruby, emruby enables dynamic behavior, configuration, and... -
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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**** This work is outdated!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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Java_RMI_PiMonteCarlo
MRI service for Pi computation with Monte Carlo
There are two versions: one with a single thread in client and other multithread. This is just an exercice of a master. -
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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... -
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Deep Learning for Medical Applications
Deep Learning Papers on Medical Image Analysis
Deep-Learning-for-Medical-Applications is a repository that compiles deep learning methods, code implementations, and examples applied to medical imaging and healthcare data. The project addresses domain-specific challenges like segmentation, classification, detection, and multimodal data (e.g. MRI, CT, X-ray) using state-of-the-art architectures (e.g. U-Net, ResNet, GAN variants) tailored to medical constraints (small datasets, annotation costs, class imbalance). It includes Jupyter notebooks, model architectures, data preprocessing pipelines, and evaluation scripts specific to medical imaging tasks. The repository may also contain domain-specific modules: loss functions like Dice, focal loss, metrics such as sensitivity/recall/IoU, and visualization utilities for overlaying segmentation masks. -
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CorThiZon
Cortical Thickness of brain by Zones
CorThiZon is a Matlab toolbox. MRI 3D T1 images are treated to estimate cortical thickness by zones in native and normalized space. It uses a Laplace-based technique following brain segmentation. Results can be easily reported in Excel files for further statistical analysis. If you use this toolbox, please reference: ‘Early diagnostic of Alzheimer’s disease using cortical thickness: impact of cognitive reserve', Querbes O, Aubry F, Pariente J, Lotterie JA, Démonet JF, Duret V, Puel M, Berry I, Fort JC, Celsis P, Alzheimer’s Disease Neuroimaging Initiative, Brain, 2009 Aug, 132(Pt 8):2036-47 A footnote giving the link to: http://sourceforge.net/projects/corthizon/ will be appreciated. -
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Dielectric shimming design tool for MRI
Design of high-permittivity pads to tailor the magnetic RF field
In MRI, a homogeneous magnetic RF field is of great importance to acquire equally weighted contrast images. In high-field MRI, however, the RF field is inhomogeneous. Dielectric materials, in the form of flexible pads, are an effective method to tailor the magnetic RF field. These pads are placed on the body and induce a secondary magnetic field because of its high permittivity, such that the magnetic field distribution can be improved. -
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In this Project, a human head voxel model is developed for use in CST Studio commercial software pack using an improved voxel set extracted from MRI images of a human head. The proposed voxel model contains 256x256x128 voxel elements with dimensions of 1.1x1.1x1.4 mm. Moreover, the dispersive dielectric properties of head tissues, as well as their density and thermal conductivity, are embedded. This head voxel model was presented at the ICEE2017 conference. If you find this tool useful, please consider citing the following article: https://doi.org/10.1109/IranianCEE.2017.7985315
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RBF Python Scripts
Collection of python scripts, mostly DICOM or MRI related
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AnalyzeNNLS
MRI Multiple Echo T2 Analysis
Users load multiecho MRI data and draw ROIs. AnalyzeNNLS creates a T2 distribution from the averaged decay data. Regional fractions and geometric T2 times can be determined. Please reference: Bjarnason TA, Mitchell JR. JMR 206:200-4 (2010). Temporal Phase Correction included in version 2.5. If you use this functionality, please reference: Bjarnason TA, Laule C, Bluman J, Kozlowski P. -
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PreclinicalNeuroMRI
Tools for preclinical MRI mostly diffusionMRI
A collection of tools for preclinical brain and spinal cord MRI -
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PyVE
PyVE is image analysis and visualization environment
PyVE is image analysis and Visualization Environment focused at clinical use. At the core of it there is a powerful viewer for displaying 3D datasets (MRI, PET, CT) based on VTK. It all comes precompiled allowing painless access to Python (2.x), the ITK toolkit for image analysis, numpy/scipy for numerical calculations, Qt and PyQt4 for the development Graphical User Interfaces. It is what you need for fast prototyping and development of more complex projects. -
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Eye
Process monitoring tool. Inspired from Bluepill and God
Process monitoring tool. Inspired from Bluepill and God. Requires Ruby(MRI) >= 1.9.3-p194. Uses Celluloid and Celluloid::IO. Eye is an image processing and analysis library for quickly analyzing image patterns and features, often used in computer vision tasks. -
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MRiLab
A Numerical MRI Simulation Platform
...The main MRiLab simulation platform combined with those toolboxes can be applied to customize various virtual MR experiments which can serve as a prior stage for prototyping and testing new MR technique and application. If you find MRiLab useful for your work, please cite this paper: Fast Realistic MRI Simulations Based on Generalized Multi-Pool Exchange Tissue Model. IEEE Transactions on Medical Imaging. 2016. doi: 10.1109/TMI.2016.2620961 -
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3DimViewer
3DimViewer is a lightweight 3D viewer of medical DICOM datasets.
3DimViewer is a lightweight 3D viewer of medical DICOM datasets that is distributed as open source software. The viewer is multiplatform software written in C++ that runs on Windows, Mac OS X and Linux systems. 3DimViewer source codes are available on Bitbucket (https://bitbucket.org/3dimlab/3dimviewer). Video tutorials can be found on YouTube (https://www.youtube.com/playlist?list=PLCvwUmKRw9ZO4YexLKEXmw_2jPo-kXVRn). -
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CVDdb
Cerebrovascular Disease database
...Development is by the BRAINS imagebank team : (http://www.brainsimagebank.ac.uk/, Job et al., 2016) Job et al., 2016. A brain imaging repository of normal structural MRI across the life course: Brain Images of Normal Subjects (BRAINS). http://dx.doi.org/10.1016/j.neuroimage.2016.01.027 Das et al, 2011. LORIS: a web-based data management system for multi-center studies. Frontiers in Neuroinformatics (5:37). -
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DTI-density
Seeding resolution dependence of diffusion tensor MRI visualizations
While visualizing the diffusion tensor MRI (DTI) dataset using streamtubes, the unit (1x1x1) resolution in full volume seeding approach has been used as default parameters and the resulting tractography contains very dense geometries that causes visual complexity impeding the exploration of DTI visualizations. However, questions like "if the unit seeding resolution is optimal for visualizing either whole brain model or tract-of-interest (TOI)", "if not, what the optimal choice of seeding should be", and especially, "how quantitatively the choice of the fiber tracking parameter, seeding resolution, connects with the informativeness and meaningfulness of DTI visualizations". ... -
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Stereo-display-dti
Effects of display factors on diffusion tensor MRI visualizations
This project was launched to further study other factors beyond those during the data processing - display factors such as screen size and stereo/mono characteristics. With this study, we expected to verify the hypothesis that, given the dense information in DTI streamtube visualization, enlarging screen and/or employing stereo would enhance the visualization of DTI dataset as a whole by improving user's task performance.
