Search Results for "brain ct mri"
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Showing 41 open source projects for "brain ct 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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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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ITKSnap
View 3D Images (also work with DICOM MRI images)
This software is used to view the 3D DICOM images. It is highly used to view 3D Medical Images (Human Brain, etc.). The official website for this software is: http://www.itksnap.org/ -
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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. ... -
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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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DcmStoreService
A lightweight and robust Dicom server to archive medical images
Dicom storage service - DcmStoreService is a lightweight and robust package for implementing the Dicom Storage SCP Service. The application (C++ compiled x86/x64) runs on computer as automatic MS Windows system service (24 hrs). It has a variety of customizable options. -
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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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Adult MRI ihMTR, MWF, angle brain atlas
Atlas averaging brain myelin-sensitive MRI data from 17 healthy adults
Averaged inhomogeneous magnetization transfer, magnetization transfer and myelin water fraction and white matter fibre angle brain MRI atlases in MNI space. -
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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. ... -
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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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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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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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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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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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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
...The data itself is for internal access only during project development. 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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QuantitativeT2
Glioblastoma in mouse brain analyzed by QuantitativeT2
This video clip shows the analysis of a normal mouse brain by QuantitativeT2, a software tool recently developed by TS Ali (more information can be found at: Ali T, Bjarnason T, Senger DL, Dunn JF, Joseph JT, Mitchell J; Quantitativet2: interactive quantitative t2 mri witnessed in mouse glioblastoma. J. Med. Imag. 0001;2(3):036002. doi:10.1117/1.JMI.2.3.036002.). It is written in XCode. -
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DRAMMS
A Deformable Medical Image Registration Toolbox
...Released by Section of Biomedical Image Analysis (SBIA) at the University of Pennsylvania. Some typical applications of DRAMMS include, -- Cross-subject registration of the same organ (can be brain, breast, cardiac, etc); -- Mono- and Multi-modality registration (MRI, CT, histology); -- Longitudinal registration (pediatric brain growth, cancer development, mouse brain development, etc); -- Registration under missing correspondences (e.g., vascular lesions, tumors, histological cuts). DRAMMS runs in command line in UNIX/Mac OS, It accepts Nifti/ANALYZE/MetaImage image formats. ... -
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MatrixUser
A Multi-functional GUI-based Program for Image Processing and Analysis
The MatrixUser project is moving to GitHub, the latest version can be obtained from https://leoliuf.github.io/MatrixUser/ Most of the medical images (e.g. CT, MRI, PET, etc.) comprises multiple frames which represent slices, phases, timing etc. from the same imaging object. Those images can be saved as multidimensional matrices in Matlab thanks to Matlab's powerful support of multidimensional data representation. However, within Matlab, most of image manipulation functions are limited or tailored for processing two-dimensional matrix. ... -
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METAlab GTG
Matlab toolbox to run a GLM on graph theoretic properties in MRI data
This Matlab toolbox runs a GLM on graph theoretic network properties in brain networks. The GLM accepts continuous & categorical between-participant predictors and categorical within-participant predictors. Significance is determined via non-parametric permutation tests. The toolbox allows testing of both fully connected and thresholded networks (based on a range of thresholds). The toolbox also provides a data processing path for resting state fMRI data. Several options for partialing...
