jcaballeroi

multishell-qspace-gradients

Generate a ready-to-import gradient table for a multi-shell DWI acquisition using Emmanuel Caruyer et al., 2013 uniform schemes in a Siemens scanner.

along-tract-stats

A MATLAB toolbox for performing along-tract analysis of diffusion tensor imaging (DTI) MRI tractography data.

connectir

Fast and memory efficient approach for connectome-wide association studies in R and C++. Uses custom implementation of multivariate distance matrix regression to associate brain and behavior.

MDMR_fMRI

bambi

BAyesian Model-Building Interface (Bambi) in Python.

pval_adjust

Adjust p-values for multiple comparisons

Psychtoolbox-3

Psychophysics Toolbox Version 3 (PTB-3) is a free set of Matlab and GNU Octave functions for vision and neuroscience research.

FastSurfer

PyTorch implementation of FastSurferCNN

MRIcroGL

v1.2 GLSL volume rendering. Able to view NIfTI, DICOM, MGH, MHD, NRRD, AFNI format images.

dcm2niix

dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC

surf-ice

GLSL surface rendering source code. Compiled versions available from NITRC. Loads 3DS, CTM, DXF, FreeSurfer, GII (GIfTI), GTS, LWO2, MS3D, MZ3, NV (BrainNetViewer), OBJ, OFF, PLY, STL, VTK. Tractography formats include BFloat, PDB, TCK, TRK, and VTK. Also NIfTI format voxelwise images.

BCBToolKit

This repository contains only the scripts and java files but cannot be cloned to run analyses. Please visit http://toolkit.bcblab.com if you want to use the BCBtoolkit.

DPABI

DPABI: a toolbox for Data Processing & Analysis of Brain Imaging

gifti

MATLAB/Octave GIfTI Library

HCPpipelines

Processing pipelines for the HCP

workbench

Connectome Workbench

fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

ANTs

Advanced Normalization Tools (ANTs)

gramm

Gramm is a complete data visualization toolbox for Matlab. It provides an easy to use and high-level interface to produce publication-quality plots of complex data with varied statistical visualizations. Gramm is inspired by R's ggplot2 library.

fieldtrip

The MATLAB toolbox for MEG, EEG and iEEG analysis

cifti-matlab

MATLAB code for reading and writing CIFTI connectivity files

bids-matlab

MATLAB / Octave tools for BIDS datasets

BrewerMap

[MATLAB] The complete palette of ColorBrewer colormaps. Simple selection by scheme name and map length.

cmap

Perceptually uniform colormaps for MATLAB, compiled from multiple sources.

DeepLabCut

Official implementation of DeepLabCut: Markerless pose estimation of user-defined features with deep learning for all animals incl. humans