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3d-printing-of-brain-regions

Goal is to arrive at a pipeline that takes an MRI scan of a human or animal brain, processes and segments it, and produces a collection of 3d printable files that clip together.

ants

Advanced Normalization Tools (ANTs)

asdlangoutcomebloodgexfmripls

atlasreader

Python interface for generating coordinate tables and region labels from statistical MRI images

automaticanalysis

Automatic analysis

barzilaystress

Code used to produce stress analysis results

bctpy

brain connectivity toolbox for python

brainsforpublication

Code and documentation for the Brains for Publication proposal for the 2016 OHBM Hackathon

brainstools

A suite of tools for medical image processing focused on brain analysis

bspmview

MATLAB program for viewing 3D fMRI statistical images

cbig

cntk

Microsoft Cognitive Toolkit (CNTK), an open source deep-learning toolkit

code

Various matlab scripts for analysis of Freesurfer and fMRI data. Also contains analysis for epigenitc data and longitudinal head circumference in autism

corticostriatal_holmes

devrhesuslmd

Non-human primate brain development gene expression

dti_preprocess

dynamicnetworks

Interpret dynamic functional connectivity in brain imaging by comparing methods

easy_lausanne

Easy creation of Lausanne2008 atlases

enigma

ENIGMA TOOLBOX is an open-access repository for data sharing, neuroimaging analysis, and visualization of ENIGMA datasets

enigmaanxiety

ENIGMA anxiety study

eyetrack

Perform dual-angle video-oculography calibration for magnetic eye tracking

fmriprep

fMRIprep is a functional magnetic resonance image pre-processing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to differences in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.

froudist-walsh-et-al-elife-2018

Code to reproduce the figures in Froudist-Walsh, Browning, Young, Murphy, Mars, Fleysher and Croxson, "Macro-connectomics and microstructure predict dynamic plasticity patterns in the non-human primate brain", eLife, 2018. Note that raw imaging data will be uploaded to PRIME-DE (Milham et al., Neuron, 2018) upon publication.

gretna

A Graph-theoretical Network Analysis Toolkit in MATLAB

hcp_mri-behavior

Code for predicting individual differences in behavioral variables (e.g., intelligence, personality) from resting-state fMRI functional connectivity, using data from the Young Adult Human Connectome Project

hmm-fmri

HMM with HRF

hmm-mar

Toolbox for segmentation and characterisation of transient connectivity

human-analysis-examples

Starter Human Brain Atlas Analysis Code

imagem

MATLAB version of ImageJ

itk

Insight Segmentation and Registration Toolkit -- Official Repository