Common Docker Image for the Dosenbach and Greene Labs

Alcohol study DTI Analyses

A sample neuroimaging pipeline for the fMRI data collected by the Aging Brain Cohort.

Repository containing files associated with ENIGMA diffusion weighted image preprocessing protocol and instructional video series. Designed by Ryan Cali for the 2022 ReproNim Fellowship Project and the Imaging Genetics Center at the University of Southern California. Questions? Reach out to the author: rcali@loni.usc.edu

Why should radiologists rely on eyesight alone, when computer vision and amazing open-source processing frameworks are already available. This respository hosts the full bash-based pipeline, whilst there is a minimal python+webui implementation also available open-source

A simple script to deface (with use of fsl_deface) multiple T1/T2-weighetned files prepared according to the BIDS standard.

An API to interactively run the AlignEM-SWiFT software on the Lonestar6 supercomputer.

Deployment repository for the VUMC Picture tool, responsible for orchestrating the installation and setup of the PICTURE project's core components. This repository automates the deployment process for seamless integration across all related repositories within the PICTURE project.

Pipeline for Cortical and Subcortical SC and FC

pipeline to calculate T1/MPRAGE ratio of MRI images. Adapted from KUL_T1T2FLAIRMTR_ratio.sh https://github.com/treanus/KUL_NIS

Pipeline computing volumes statistics for different brain lobes according to a atlas.

Optional components for TFCE_mediation (https://github.com/trislett/TFCE_mediation)

A Whole-Brain 3D Myeloarchitectonic Atlas: Mapping the Vogt-Vogt Legacy to the Cortical Surface

Analysis of the NYU Slow Flanker dataset, investigating neural correlates of selective attention and response inhibition in the Eriksen Flanker task using neuroimaging tools.

Gnome Nautilus scripts for right click handy nifti manipulations

brainlife app - runs AFNI's skullstrip function on NIfTI files

BIDS raw dataset (also on OpenNeuro)

Batch download the BigBrain slices and more

This repository hopes to house techniques, thoughts, and insights, into neuroimaging.

Code snippets for preprocessing DTI/MRI neuroimaging data