Showing 37 of total 37 results (show query)
bjw34032
oro.nifti:Rigorous - 'NIfTI' + 'ANALYZE' + 'AFNI' : Input / Output
Functions for the input/output and visualization of medical imaging data that follow either the 'ANALYZE', 'NIfTI' or 'AFNI' formats. This package is part of the Rigorous Analytics bundle.
Maintained by Brandon Whitcher. Last updated 6 months ago.
105.1 match 2 stars 7.70 score 764 scripts 38 dependents
muschellij2
neurobase:'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects
Base package for 'Neuroconductor', which includes many helper functions that interact with objects of class 'nifti', implemented by package 'oro.nifti', for reading/writing and also other manipulation functions.
Maintained by John Muschelli. Last updated 1 months ago.
65.0 match 5 stars 8.49 score 486 scripts 7 dependents
dfsp-spirit
freesurferformats:Read and Write 'FreeSurfer' Neuroimaging File Formats
Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' <http://freesurfer.net/> formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.
Maintained by Tim Schรคfer. Last updated 6 months ago.
brainbrain-atlasbrain-surfacescurvdtifileformatsfreesurferlabelmeshmghmrineuroimagingparcellationresearchsurfacevoxel
49.3 match 23 stars 8.07 score 25 scripts 8 dependents
jonclayden
RNifti:Fast R and C++ Access to NIfTI Images
Provides very fast read and write access to images stored in the NIfTI-1, NIfTI-2 and ANALYZE-7.5 formats, with seamless synchronisation of in-memory image objects between compiled C and interpreted R code. Also provides a simple image viewer, and a C/C++ API that can be used by other packages. Not to be confused with 'RNiftyReg', which performs image registration and applies spatial transformations.
Maintained by Jon Clayden. Last updated 24 days ago.
medical-imagingnifti-formatzlibcpp
22.6 match 48 stars 10.43 score 522 scripts 56 dependents
nandp1
nser:Bhavcopy and Live Market Data from National Stock Exchange (NSE) & Bombay Stock Exchange (BSE) India
Download Current & Historical Bhavcopy. Get Live Market data from NSE India of Equities and Derivatives (F&O) segment. Data source <https://www.nseindia.com/>.
Maintained by Nandan Patil. Last updated 4 months ago.
bhavbhavcopybhavcopy-downloaderfinancial-datamarket-datanational-stock-exchangensense-stock-dataoption-pricingoptionchainrseleniumstock-prices
12.5 match 8 stars 7.61 score 76 scripts
martin3141
spant:MR Spectroscopy Analysis Tools
Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Maintained by Martin Wilson. Last updated 1 months ago.
brainmrimrsmrshubspectroscopyfortran
10.3 match 25 stars 8.52 score 81 scripts
cran
nifti.io:Read and Write NIfTI Files
Tools for reading and writing NIfTI-1.1 (NII) files, including optimized voxelwise read/write operations and a simplified method to write dataframes to NII. Specification of the NIfTI-1.1 format can be found here <https://nifti.nimh.nih.gov/nifti-1>. Scientific publication first using these tools Koscik TR, Man V, Jahn A, Lee CH, Cunningham WA (2020) <doi:10.1016/j.neuroimage.2020.116764> "Decomposing the neural pathways in a simple, value-based choice." Neuroimage, 214, 116764.
Maintained by Timothy Koscik. Last updated 4 years ago.
47.2 match 1.70 scoremuschellij2
freesurfer:Wrapper Functions for 'Freesurfer'
Wrapper functions that interface with 'Freesurfer' <https://surfer.nmr.mgh.harvard.edu/>, a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'Freesurfer' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'Freesurfer' command and returns an R object of class 'nifti' or necessary output.
Maintained by John Muschelli. Last updated 3 months ago.
8.8 match 10 stars 7.69 score 55 scripts 1 dependents
dipterix
ieegio:File IO for Intracranial Electroencephalography
Integrated toolbox supporting common file formats used for intracranial Electroencephalography (iEEG) and deep-brain stimulation (DBS) study.
Maintained by Zhengjia Wang. Last updated 4 days ago.
bci2000brainbrainvisiondbsedfelectrophysiologyephysfreesurferieegneuroimagingneuroscienceniftinwb-format
11.0 match 5.65 score 10 scripts 1 dependentsmuschellij2
fslr:Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')
Wrapper functions that interface with 'FSL' <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>, a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'FSL' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'FSL' command and returns an R object of class 'nifti' if desired.
Maintained by John Muschelli. Last updated 1 months ago.
fslfslrneuroimagingneuroimaging-analysisneuroimaging-data-science
6.3 match 41 stars 8.01 score 420 scripts
jrad1
nifti.pbcor:Parcel-Based Correlation Between NIfTI Images
Estimate the correlation between two NIfTI images across random parcellations of the images (Fortea et al., under review). This approach overcomes the problems of both voxel-based correlations (neighbor voxels may be spatially dependent) and atlas-based correlations (the correlation may depend on the atlas used).
Maintained by Joaquim Radua. Last updated 8 months ago.
49.0 match 1.00 score
mandymejia
ciftiTools:Tools for Reading, Writing, Viewing and Manipulating CIFTI Files
CIFTI files contain brain imaging data in "grayordinates," which represent the gray matter as cortical surface vertices (left and right) and subcortical voxels (cerebellum, basal ganglia, and other deep gray matter). 'ciftiTools' provides a unified environment for reading, writing, visualizing and manipulating CIFTI-format data. It supports the "dscalar," "dlabel," and "dtseries" intents. Grayordinate data is read in as a "xifti" object, which is structured for convenient access to the data and metadata, and includes support for surface geometry files to enable spatially-dependent functionality such as static or interactive visualizations and smoothing.
Maintained by Amanda Mejia. Last updated 2 months ago.
5.4 match 47 stars 8.90 score 176 scripts 4 dependentsmandymejia
templateICAr:Estimate Brain Networks and Connectivity with ICA and Empirical Priors
Implements the template ICA (independent components analysis) model proposed in Mejia et al. (2020) <doi:10.1080/01621459.2019.1679638> and the spatial template ICA model proposed in proposed in Mejia et al. (2022) <doi:10.1080/10618600.2022.2104289>. Both models estimate subject-level brain as deviations from known population-level networks, which are estimated using standard ICA algorithms. Both models employ an expectation-maximization algorithm for estimation of the latent brain networks and unknown model parameters. Includes direct support for 'CIFTI', 'GIFTI', and 'NIFTI' neuroimaging file formats.
Maintained by Amanda Mejia. Last updated 3 days ago.
5.8 match 10 stars 6.35 score 25 scripts
angelgar
voxel:Mass-Univariate Voxelwise Analysis of Medical Imaging Data
Functions for the mass-univariate voxelwise analysis of medical imaging data that follows the NIfTI <http://nifti.nimh.nih.gov> format.
Maintained by Angel Garcia de la Garza. Last updated 5 years ago.
7.5 match 9 stars 4.85 score 78 scriptsbjw34032
oro.pet:Rigorous - Positron Emission Tomography
Image analysis techniques for positron emission tomography (PET) that form part of the Rigorous Analytics bundle.
Maintained by Brandon Whitcher. Last updated 3 years ago.
11.0 match 1 stars 2.70 score 7 scriptsmandymejia
fMRItools:Routines for Common fMRI Processing Tasks
Supports fMRI (functional magnetic resonance imaging) analysis tasks including reading in 'CIFTI', 'GIFTI' and 'NIFTI' data, temporal filtering, nuisance regression, and aCompCor (anatomical Components Correction) (Muschelli et al. (2014) <doi:10.1016/j.neuroimage.2014.03.028>).
Maintained by Amanda Mejia. Last updated 10 days ago.
5.8 match 2 stars 5.10 score 35 scripts 4 dependentscran
fmri:Analysis of fMRI Experiments
Contains R-functions to perform an fMRI analysis as described in Polzehl and Tabelow (2019) <DOI:10.1007/978-3-030-29184-6>, Tabelow et al. (2006) <DOI:10.1016/j.neuroimage.2006.06.029>, Polzehl et al. (2010) <DOI:10.1016/j.neuroimage.2010.04.241>, Tabelow and Polzehl (2011) <DOI:10.18637/jss.v044.i11>.
Maintained by Karsten Tabelow. Last updated 8 months ago.
6.3 match 2 stars 4.47 score 99 scripts 1 dependents
benwu233
BSPBSS:Bayesian Spatial Blind Source Separation
Gibbs sampling for Bayesian spatial blind source separation (BSP-BSS). BSP-BSS is designed for spatially dependent signals in high dimensional and large-scale data, such as neuroimaging. The method assumes the expectation of the observed images as a linear mixture of multiple sparse and piece-wise smooth latent source signals, and constructs a Bayesian nonparametric prior by thresholding Gaussian processes. Details can be found in our paper: Wu et al. (2022+) "Bayesian Spatial Blind Source Separation via the Thresholded Gaussian Process" <doi:10.1080/01621459.2022.2123336>.
Maintained by Ben Wu. Last updated 2 years ago.
4.0 match 4 stars 4.30 score 5 scripts
bbuchsbaum
neuroim:Data Structures and Handling for Neuroimaging Data
A collection of data structures that represent volumetric brain imaging data. The focus is on basic data handling for 3D and 4D neuroimaging data. In addition, there are function to read and write NIFTI files and limited support for reading AFNI files.
Maintained by Bradley Buchsbaum. Last updated 4 years ago.
2.9 match 6 stars 5.64 score 48 scripts
michaelhallquist
ggbrain:Create Images of Volumetric Brain Data in NIfTI Format Using 'ggplot2' Syntax
A 'ggplot2'-consistent approach to generating 2D displays of volumetric brain imaging data. Display data from multiple NIfTI images using standard 'ggplot2' conventions such scales, limits, and themes to control the appearance of displays. The resulting plots are returned as 'patchwork' objects, inheriting from 'ggplot', allowing for any standard modifications of display aesthetics supported by 'ggplot2'.
Maintained by Michael Hallquist. Last updated 25 days ago.
3.3 match 2 stars 5.03 score 18 scripts
ktabelow
qMRI:Methods for Quantitative Magnetic Resonance Imaging ('qMRI')
Implementation of methods for estimation of quantitative maps from Multi-Parameter Mapping (MPM) acquisitions (Weiskopf et al. (2013) <doi:10.3389/fnins.2013.00095>) and analysis of Inversion Recovery MRI data. Usage of the package is described in Polzehl and Tabelow (2023), "Magnetic Resonance Brain Imaging", 2nd Edition, Chapter 6 and 7, Springer, Use R! Series. <doi:10.1007/978-3-031-38949-8>. J. Polzehl and K. Tabelow (2023), "Magnetic Resonance Brain Imaging - Modeling and Data Analysis Using R: Code and Data." <doi:10.20347/WIAS.DATA.6> provides extensive example code and data.
Maintained by Karsten Tabelow. Last updated 11 days ago.
3.4 match 4.81 score 36 scripts
jeffreydurieux
CICA:Clusterwise Independent Component Analysis
Clustering multi-subject resting state functional Magnetic Resonance Imaging data. This methods enables the clustering of subjects based on multi-subject resting state functional Magnetic Resonance Imaging data. Objects are clustered based on similarities and differences in cluster-specific estimated components obtained by Independent Component Analysis.
Maintained by Jeffrey Durieux. Last updated 8 months ago.
3.6 match 2 stars 4.15 score 2 scriptsjonclayden
RNiftyReg:Image Registration Using the 'NiftyReg' Library
Provides an 'R' interface to the 'NiftyReg' image registration tools <https://github.com/KCL-BMEIS/niftyreg>. Linear and nonlinear registration are supported, in two and three dimensions.
Maintained by Jon Clayden. Last updated 6 months ago.
image-registrationmedical-imagingtransformationscppopenmp
1.9 match 43 stars 7.64 score 50 scripts 5 dependentsmartin3141
fmriqa:Functional MRI Quality Assurance Routines
Methods for performing fMRI quality assurance (QA) measurements of test objects. Heavily based on the fBIRN procedures detailed by Friedman and Glover (2006) <doi:10.1002/jmri.20583>.
Maintained by Martin Wilson. Last updated 5 years ago.
3.4 match 2 stars 4.00 score 8 scriptsbjw34032
oro.dicom:Rigorous - DICOM Input / Output
Data input/output functions for data that conform to the Digital Imaging and Communications in Medicine (DICOM) standard, part of the Rigorous Analytics bundle.
Maintained by Brandon Whitcher. Last updated 1 years ago.
1.9 match 1 stars 6.35 score 188 scripts 8 dependentsmuschellij2
cifti:Toolbox for Connectivity Informatics Technology Initiative ('CIFTI') Files
Functions for the input/output and visualization of medical imaging data in the form of 'CIFTI' files <https://www.nitrc.org/projects/cifti/>.
Maintained by John Muschelli. Last updated 5 years ago.
1.9 match 3 stars 5.76 score 96 scripts
ggseg
ggsegExtra:Extra Utilities for the 'ggseg' and 'ggseg3d' Plotting Tools
Contains functions to create new data sets compatible with the 'ggseg' and 'ggseg3d' packages for plotting brain segmentations through R. Requires several external software to be installed on the system for atlas creations to work, and most of these are not available for windows. But atlas creation tools exist for 2d simple features data, and also 3d tri-surface mesh plots. Also has a list of compatible data sets and functions for easy installation of these.
Maintained by Athanasia Mo Mowinckel. Last updated 3 years ago.
2.0 match 55 stars 4.59 score 70 scripts
jdwor
vesselr:Gradient and Vesselness Tools for Arrays and NIfTI Images
Simple functions for calculating the image gradient, image hessian, volume ratio filter, and Frangi vesselness filter of 3-dimensional volumes.
Maintained by Jordan D. Dworkin. Last updated 8 years ago.
2.9 match 2 stars 3.00 score 4 scripts
openjusticeok
ojoutils:A Collection of Nifty Functions and Objects for OJO Analysts
We find ourselves repeating the same simple tasks or running a series of R commands over and over again. No more!
Maintained by Brancen Gregory. Last updated 1 months ago.
2.9 match 2.90 score 2 scriptscran
RIA:Radiomics Image Analysis Toolbox for Medial Images
Radiomics image analysis toolbox for 2D and 3D radiological images. RIA supports DICOM, NIfTI, nrrd and npy (numpy array) file formats. RIA calculates first-order, gray level co-occurrence matrix, gray level run length matrix and geometry-based statistics. Almost all calculations are done using vectorized formulas to optimize run speeds. Calculation of several thousands of parameters only takes minutes on a single core of a conventional PC. Detailed methodology has been published: Kolossvary et al. Circ: Cardiovascular Imaging. 2017;10(12):e006843 <doi: 10.1161/CIRCIMAGING.117.006843>.
Maintained by Marton Kolossvary. Last updated 1 years ago.
2.3 match 7 stars 3.24 scoremuschellij2
stapler:Simultaneous Truth and Performance Level Estimation
An implementation of Simultaneous Truth and Performance Level Estimation (STAPLE) <doi:10.1109/TMI.2004.828354>. This method is used when there are multiple raters for an object, typically an image, and this method fuses these ratings into one rating. It uses an expectation-maximization method to estimate this rating and the individual specificity/sensitivity for each rater.
Maintained by John Muschelli. Last updated 4 years ago.
1.8 match 1 stars 3.70 score 8 scripts
kangjian2016
brainKCCA:Region-Level Connectivity Network Construction via Kernel Canonical Correlation Analysis
It is designed to calculate connection between (among) brain regions and plot connection lines. Also, the summary function is included to summarize group-level connectivity network. Kang, Jian (2016) <doi:10.1016/j.neuroimage.2016.06.042>.
Maintained by Jian Kang. Last updated 6 years ago.
1.7 match 3.70 score 5 scripts
tractor
tractor.base:Read, Manipulate and Visualise Magnetic Resonance Images
Functions for working with magnetic resonance images. Reading and writing of popular file formats (DICOM, Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive visualisation; flexible image manipulation; metadata and sparse image handling.
Maintained by Jon Clayden. Last updated 7 hours ago.
brain-imaginggraph-algorithmsparcellationtractography
0.8 match 28 stars 6.79 score 35 scripts 1 dependentsjonclayden
divest:Get Images Out of DICOM Format Quickly
Provides tools to sort DICOM-format medical image files, and convert them to NIfTI-1 format.
Maintained by Jon Clayden. Last updated 11 days ago.
conversiondicommedical-imagingopenjpeg2cpp
0.5 match 14 stars 7.09 score 30 scriptsktabelow
dti:Analysis of Diffusion Weighted Imaging (DWI) Data
Diffusion Weighted Imaging (DWI) is a Magnetic Resonance Imaging modality, that measures diffusion of water in tissues like the human brain. The package contains R-functions to process diffusion-weighted data. The functionality includes diffusion tensor imaging (DTI), diffusion kurtosis imaging (DKI), modeling for high angular resolution diffusion weighted imaging (HARDI) using Q-ball-reconstruction and tensor mixture models, several methods for structural adaptive smoothing including POAS and msPOAS, and a streamline fiber tracking for tensor and tensor mixture models. The package provides functionality to manipulate and visualize results in 2D and 3D.
Maintained by Karsten Tabelow. Last updated 6 months ago.
1.7 match 2.20 score 16 scriptsmuschellij2
gifti:Reads in 'Neuroimaging' 'GIFTI' Files with Geometry Information
Functions to read in the geometry format under the 'Neuroimaging' 'Informatics' Technology Initiative ('NIfTI'), called 'GIFTI' <https://www.nitrc.org/projects/gifti/>. These files contain surfaces of brain imaging data.
Maintained by John Muschelli. Last updated 3 years ago.
0.5 match 4 stars 6.99 score 82 scripts 10 dependentscran
ARIbrain:All-Resolution Inference
It performs All-Resolutions Inference (ARI) on functional Magnetic Resonance Image (fMRI) data. As a main feature, it estimates lower bounds for the proportion of active voxels in a set of clusters as, for example, given by a cluster-wise analysis. The method is described in Rosenblatt, Finos, Weeda, Solari, Goeman (2018) <doi:10.1016/j.neuroimage.2018.07.060>.
Maintained by Livio Finos. Last updated 7 years ago.
1.1 match 1 stars 2.78 score 2 dependents