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

Batch download the BigBrain slices and more

Create a neuroimaging environment on the cloud

A tool for automatically segmenting white matter lesions on human brain MRI images

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

A modified FSL version for use with Slurm

Common Docker Image for the Dosenbach and Greene Labs

Software for use at the University of Arizona SCAN Lab

Prisma preprocessing (AFNI)

Scripts and pipeline for the handling of scripts from DICOMS to 4DFP and then analysis.

Singularity image to download data from XNAT servers.

A simple and intuitive wrapper for FSL tools.

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

Scripts for MRI preprocessing

Preprocessing pipeline for region of interest selection, linear and non-linear registrations, ICA-based noise rejection, spatial smoothing, and more.

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

runs AFNI's 3dQwarp function over a NIfTI file

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

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.