threeBrain - Your Advanced 3D Brain Visualization

A fast, interactive cross-platform, and easy to share 'WebGL'-based 3D brain viewer that visualizes 'FreeSurfer' and/or 'AFNI/SUMA' surfaces. The viewer widget can be either standalone or embedded into 'R-shiny' applications. The standalone version only require a web browser with 'WebGL2' support (for example, 'Chrome', 'Firefox', 'Safari'), and can be inserted into any websites. The 'R-shiny' support allows the 3D viewer to be dynamically generated from reactive user inputs. Please check the publication by Wang, Magnotti, Zhang, and Beauchamp (2023, <doi:10.1523/ENEURO.0328-23.2023>) for electrode localization. This viewer has been fully adopted by 'RAVE' <https://openwetware.org/wiki/RAVE>, an interactive toolbox to analyze 'iEEG' data by Magnotti, Wang, and Beauchamp (2020, <doi:10.1016/j.neuroimage.2020.117341>). Please check 'citation("threeBrain")' for details.

Last updated 4 days ago

brainecogelectroencephalographyieeglocalizationmri-brainneuroimagingtemplate-brains

8.20 score 43 stars 1 dependents 37 scripts 769 downloads

dipsaus - A Dipping Sauce for Data Analysis and Visualizations

Works as an "add-on" to packages like 'shiny', 'future', as well as 'rlang', and provides utility functions. Just like dipping sauce adding flavors to potato chips or pita bread, 'dipsaus' for data analysis and visualizations adds handy functions and enhancements to popular packages. The goal is to provide simple solutions that are frequently asked for online, such as how to synchronize 'shiny' inputs without freezing the app, or how to get memory size on 'Linux' or 'MacOS' system. The enhancements roughly fall into these four categories: 1. 'shiny' input widgets; 2. high-performance computing using the 'future' package; 3. modify R calls and convert among numbers, strings, and other objects. 4. utility functions to get system information such like CPU chip-set, memory limit, etc.

Last updated 2 months ago

cpp

7.96 score 13 stars 3 dependents 86 scripts 865 downloads

filearray - File-Backed Array for Out-of-Memory Computation

Stores large arrays in files to avoid occupying large memories. Implemented with super fast gigabyte-level multi-threaded reading/writing via 'OpenMP'. Supports multiple non-character data types (double, float, complex, integer, logical, and raw).

Last updated 3 months ago

arraybig-datamemory-mapout-of-memoryoutofmemorycpp

6.49 score 17 stars 3 dependents 10 scripts 796 downloads

readNSx - Read 'Blackrock-Microsystems' Files ('NEV', 'NSx')

Loads 'Blackrock' <https://blackrockneurotech.com> neural signal data files into the memory, provides utility tools to extract the data into common formats such as plain-text 'tsv' and 'HDF5'.

Last updated 5 months ago

data-formatsdbiieegieeg-dataneuroscience-datacpp

5.43 score 3 stars 1 dependents 7 scripts 356 downloads

raveio - File-System Toolbox for RAVE Project

Includes multiple cross-platform read/write interfaces for 'RAVE' project. 'RAVE' stands for "R analysis and visualization of human intracranial electroencephalography data". The whole project aims at providing powerful free-source package that analyze brain recordings from patients with electrodes placed on the cortical surface or inserted into the brain. 'raveio' as part of this project provides tools to read/write neurophysiology data from/to 'RAVE' file structure, as well as several popular formats including 'EDF(+)', 'Matlab', 'BIDS-iEEG', and 'HDF5', etc. Documentation and examples about 'RAVE' project are provided at <https://rave.wiki>, and the paper by John F. Magnotti, Zhengjia Wang, Michael S. Beauchamp (2020) <doi:10.1016/j.neuroimage.2020.117341>. For applications such as electrode localization, please check Zhengjia Wang, John F. Magnotti, Xiang Zhang, Michael S. Beauchamp (2023) <doi:10.1523/ENEURO.0328-23.2023>, or see 'citation("raveio")' for details.

Last updated 26 days ago

5.36 score 6 stars 1 dependents 115 scripts 269 downloads

ravetools - Signal and Image Processing Toolbox for Analyzing Intracranial Electroencephalography Data

Implemented fast and memory-efficient Notch-filter, Welch-periodogram, discrete wavelet spectrogram for minutes of high-resolution signals, fast 3D convolution, image registration, 3D mesh manipulation; providing fundamental toolbox for intracranial Electroencephalography (iEEG) pipelines. Documentation and examples about 'RAVE' project are provided at <https://rave.wiki>, and the paper by John F. Magnotti, Zhengjia Wang, Michael S. Beauchamp (2020) <doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for details.

Last updated 11 days ago

fftw3cpp

5.14 score 3 stars 1 dependents 19 scripts 475 downloads

ieegio - File IO for Intracranial Electroencephalography

Integrated toolbox supporting common file formats used for intracranial Electroencephalography (iEEG) and deep-brain stimulation (DBS) study.

Last updated 9 days ago

bci2000brainbrainvisiondbsedfelectrophysiologyephysfreesurferieegneuroimagingneuroscienceniftinwb-format

5.04 score 10 scripts 505 downloads

shidashi - A Shiny Dashboard Template System

A template system based on 'AdminLTE3' (<https://adminlte.io/themes/v3/>) theme. Comes with default theme that can be easily customized. Developers can upload modified templates on 'Github', and users can easily download templates with 'RStudio' project wizard. The key features of the default template include light and dark theme switcher, resizing graphs, synchronizing inputs across sessions, new notification system, fancy progress bars, and card-like flip panels with back sides, as well as various of 'HTML' tool widgets.

Last updated 12 months ago

4.67 score 9 stars 1 dependents 35 scripts 194 downloads

ravedash - Dashboard System for Reproducible Visualization of 'iEEG'

Dashboard system to display the analysis results produced by 'RAVE' (Magnotti J.F., Wang Z., Beauchamp M.S. (2020), Reproducible analysis and visualizations of 'iEEG' <doi:10.1016/j.neuroimage.2020.117341>). Provides infrastructure to integrate customized analysis pipelines into dashboard modules, including file structures, front-end widgets, and event handlers.

Last updated 3 months ago

4.39 score 1 stars 45 scripts 58 downloads

rave - R Analysis and Visualization of 'ECOG/iEEG' Data

R Analysis and Visualization of 'ECOG/iEEG' Data RAVE provides cross-platform analysis and visualizations for neuroscience 'ECoG/iEEG' data by "just clicking buttons". This package include: (a) pre-processing of 'ECoG/iEEG' raw data into 'HDF5' format (a cross-platform data format that can be used for R, Matlab, Python, Java and C/C++); (b) 'ECoG/iEEG' epoch and visualizations in real time; (c) Users can write customized analysis as R packages and easily insert into RAVE for interactive visualizations. (d) 3D viewers driven by 'WebGL'.

Last updated 8 months ago

4.14 score 23 stars 10 scripts

rpyANTs - An Alternative Advanced Normalization Tools ('ANTs')

Provides portable access from 'R' to biomedical image processing toolbox 'ANTs' by Avants et al. (2009) <doi:10.54294/uvnhin> via seamless integration with the 'Python' implementation 'ANTsPy'. Allows biomedical images to be processed in 'Python' and analyzed in 'R', and vice versa via shared memory. See 'citation("rpyANTs")' for more reference information.

Last updated 2 months ago

antsbrainieegmrineuroimagingnormalizationpythonregistration

4.13 score 1 stars 1 dependents 8 scripts 260 downloads

rpymat - Easy to Configure an Isolated 'Python' Environment

Aims to create a single isolated 'Miniconda' and 'Python' environment for reproducible pipeline scripts. The package provides utilities to run system command within the 'conda' environment, making it easy to install, launch, manage, and stop 'Jupyter-lab'.

Last updated 1 years ago

3.78 score 1 stars 4 dependents 9 scripts 306 downloads

ravemanager - Manage 'RAVE' Packages

Manages installation, upgrade, and removal of packages and corresponding dependence for the project 'RAVE' (R Analysis and Visualization for 'iEEG').

Last updated 9 days ago

2.74 score 1 scripts

spfda - Function-on-Scalar Regression with Group-Bridge Penalty

Implements a group-bridge penalized function-on-scalar regression model proposed by Wang et al. (2020) <arXiv:2006.10163>, to simultaneously estimate functional coefficient and recover the local sparsity.

Last updated 3 years ago

function-on-scalar-regressionregularization-methodssparse

2.70 score 224 downloads

ravebuiltins - Builtin Modules for `RAVE`

This package provides builtin modules for `RAVE`. It aims at analyze and visualize `iEEG` data from different perspectives.

Last updated 2 years ago

1.78 score 3 stars

niivuer - 'NiiVue' for R

What the package does (one paragraph).

Last updated 5 months ago

1.70 score

rnwb - 'Neurodata' Without Borders in R

Supports 'Neurodata' Without Borders ('NWB') format in R.

Last updated 1 years ago

1.70 score 4 scripts

rutabaga - Simple R Tools for Analysis and Visualizations

Provides functions (R, C++) to speed up array calculations. Includes various tools for prettier visualizations via R base plots.

Last updated 3 years ago

1.70 score 2 scripts