gaozhy

Dynamic_brain_connectivity_analysis

This repository covers our developed algorithms and techniques for dynamic brain connectivity analysis.

cocoanCORE

Core tools for Cocoan Lab

Development-of-brain-module-dynamics

control_costs

Reliability_Multilayer_Networks

Code for Yang, et al., 2020, "Reliability of dynamic network reconfiguration: impact of code implementation, parameter selection, scan duration, and task condition."

layerfMRI-toolbox

DeepPrep

DeepPrep: An accelerated, scalable, and robust pipeline for neuroimaging preprocessing empowered by deep learning

IEM-tutorial

tutorial and example scripts for implementing inverted encoding model analysis framework

neuraldynamics

Behavioral and processed fMRI data and analysis codes: Large-scale neural dynamics in a shared low-dimensional state space reflect cognitive and attentional dynamics

adaptation-manifolds

awesome-neural-geometry

A curated collection of resources and research related to the geometry of representations in the brain, deep networks, and beyond

dynamax

State Space Models library in JAX

Matlab_functions

Custom Matlab code that may (or may not) be useful

misc-code

Random snippets of useful and not-so-useful code.

lipsia

lipsia3.0

TaskFCRemoveMeanActivity

Code for running simulations and data analysis from: Cole MW, Ito T, Schultz D, Mill R, Chen R, Cocuzza C (2019). "Task activations produce spurious but systematic inflation of task functional connectivity estimates". NeuroImage. doi:10.1016/j.neuroimage.2018.12.054 https://authors.elsevier.com/a/1YNWs3lc~r3Jbx

ashs

Automatic Segmentation of Hippocampal Subfields

CREx_fMRI

Scripts on Matlab to facilitate the fMRI data processing using SPM12 software

fmri_misc

misc-fmri-code

Just small functions for preprocessing, analysis, etc. of fMRI data.

exgauss

Simple toolbox for fitting the ex-Gaussian distribution to response time data

GLMsingle

A toolbox for accurate single-trial estimates in fMRI time-series data

word_cloud

A little word cloud generator in Python

TDLM

methods & simulation code to measure sequential replay

glum

High performance Python GLMs with all the features!

MAGeTbrain

Multiple Automatically Generated Templates brain segmentation algorithm

minc-bpipe-library

Library of bpipe implemented commands commonly applied to minc datafiles, suitable for importing into other pipelines

hippodeep_pytorch

quick segmentation of the hippocampus from T1 MRI images. (pytorch version)

surfplot

A package for publication-ready brain surface figures

rica

Rica (Reports for ICA) provides an app to visualize ICA components and perform manual classification in an interactive way