GenichiS

torchio

Medical imaging toolkit for deep learning

dynamax

State Space Models library in JAX

CBIG

HCPpipelines

Processing pipelines for the HCP

HMM-MAR

Toolbox for segmentation and characterisation of transient connectivity

ANTsPyNet

Pre-trained models and utilities for deep learning on medical images in Python

nobrainer

A framework for developing neural network models for 3D image processing.

pythresh

Outlier Detection Thresholding

ciftify

The tools of the Human Connectome Project (HCP) adapted for working with non-HCP datasets

dyconnmap

A dynamic connectome mapping module in python.

xcp_d

Post-processing of fMRIPrep, NiBabies, and HCP outputs

ColeAnticevicNetPartition

Public release of The Cole-Anticevic Brain-wide Network Partition (CAB-NP)

cifti-matlab

MATLAB code for reading and writing CIFTI connectivity files

rsHRF

rsHRF: A Toolbox for Resting State HRF Deconvolution and Connectivity Analysis (MATLAB)

ciftiTools

ciftiTools R package

brainSurfer

MATLAB toolbox for visualizing brain data on surfaces.

rsfMRI-VAE

Pytorch implementation of 'Representation Learning of Resting State fMRI with Variational Autoencoder'

CuBIDS

Curation of BIDS (CuBIDS): A sanity-preserving software package for processing BIDS datasets.

fmriprep-denoise-benchmark

Benchmark denoising strategies available from fmriprep.

fMRI-Matlab

Matlab Wrapper of Surface-based Analysis. Custom Matlab functions for running analyses with FreeSurfer, CoSMoMVPA, HCP pipeline (and SamSrf)...

hcp_extras

A bunch of scripts I've been writing to get hcp built tools to work on none hcp data

DeepWMH

DeepWMH: Annotation-free white matter hyperintensity (WMH) lesion segmentation tool using deep learning.

bidsconvertr

NHB_Taylor2023

pfc-toolkit

The Precomputed Functional Connectome Toolkit

BOLDLagMapping_Deperfusioning

Extraction and removal of the time-lag structure within 4D blood oxygenation level dependent (BOLD) signal MRI data

HCP-fMRI-Analysis

Data analysis of fMRI scans provided by the Human Connectome Project. Analysis focuses on comparison of brain activity while tools are being presented during task compared to activity in similar task while other stimuli are presented.

HCP-rsfMRI-connectivity-and-network-analysis