Showing 10 of total 10 results (show query)
dipterix
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://rave.wiki>, 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.
Maintained by Zhengjia Wang. Last updated 12 days ago.
brainecogelectroencephalographyieeglocalizationmri-brainneuroimagingtemplate-brains
44 stars 8.26 score 38 scripts 1 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 Schäfer. Last updated 7 months ago.
brainbrain-atlasbrain-surfacescurvdtifileformatsfreesurferlabelmeshmghmrineuroimagingparcellationresearchsurfacevoxel
23 stars 8.07 score 25 scripts 8 dependents
muschellij2
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 2 months ago.
fslfslrneuroimagingneuroimaging-analysisneuroimaging-data-science
41 stars 8.01 score 420 scripts
cwatson
brainGraph:Graph Theory Analysis of Brain MRI Data
A set of tools for performing graph theory analysis of brain MRI data. It works with data from a Freesurfer analysis (cortical thickness, volumes, local gyrification index, surface area), diffusion tensor tractography data (e.g., from FSL) and resting-state fMRI data (e.g., from DPABI). It contains a graphical user interface for graph visualization and data exploration, along with several functions for generating useful figures.
Maintained by Christopher G. Watson. Last updated 1 years ago.
brain-connectivitybrain-imagingcomplex-networksconnectomeconnectomicsfmrigraph-theorymrinetwork-analysisneuroimagingneurosciencestatisticstractography
188 stars 7.86 score 107 scripts 3 dependentsdfsp-spirit
fsbrain:Managing and Visualizing Brain Surface Data
Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.
Maintained by Tim Schäfer. Last updated 4 months ago.
3dbraindtifreesurfermeshmrineuroimagingresearchsurfacevisualizationvoxel
68 stars 6.49 score 15 scriptsdipterix
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 10 days ago.
bci2000brainbrainvisiondbsedfelectrophysiologyephysfreesurferieegneuroimagingneuroscienceniftinwb-format
5.68 score 10 scripts 1 dependents
ropensci
tacmagic:Positron Emission Tomography Time-Activity Curve Analysis
To facilitate the analysis of positron emission tomography (PET) time activity curve (TAC) data, and to encourage open science and replicability, this package supports data loading and analysis of multiple TAC file formats. Functions are available to analyze loaded TAC data for individual participants or in batches. Major functionality includes weighted TAC merging by region of interest (ROI), calculating models including standardized uptake value ratio (SUVR) and distribution volume ratio (DVR, Logan et al. 1996 <doi:10.1097/00004647-199609000-00008>), basic plotting functions and calculation of cut-off values (Aizenstein et al. 2008 <doi:10.1001/archneur.65.11.1509>). Please see the walkthrough vignette for a detailed overview of 'tacmagic' functions.
Maintained by Eric Brown. Last updated 5 years ago.
mrineuroimagingneuroscienceneuroscience-methodspetpet-mrpositronpositron-emission-tomographystatistics
5 stars 4.76 score 23 scriptsdipterix
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.
Maintained by Zhengjia Wang. Last updated 2 days ago.
antsbrainieegmrineuroimagingnormalizationpythonregistration
1 stars 4.48 score 8 scripts 2 dependents
martin3141
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.
2 stars 4.00 score 8 scriptsdfsp-spirit
regfusionr:Registration Fusion in R
Implementation of the 'Wu et al. 2018' registration fusion method in R.
Maintained by Tim Schäfer. Last updated 3 years ago.
freesurferfsaveragemni152mni305mrineuroimagingregistrationregistration-fusionvoltosurf
5 stars 2.40 score 1 scripts