scitran-apps

Generate montage from NIfTI

mrtrix3preproc runs the mrTrix3 preprocessing pipeline in the diffussion data. It uses FSLs topup when the optional inverted phase encoding files are found, otherwise uses the eddy tool. It performs some other denoising steps, and it can normalize or align to acpc the data

FMRIB's Automated Segmentation Tool

FSL's Brain Extraction Tool (BET)

Gannet analysis of edited MRS data

Vistasoft (mrDiffusion) preprocessing pipeline for diffusion MR data

AFNI-based brain warping based on D99 Macaque Atlas warp scripts

AFQ Pipeline Gear using Flywheel SDK

dtiPrep quality assurance algorithm

Calculate the RMSE between a tensor fit from dtiInit and the diffusion weighted imaging data