fsl

atlasBREX: Automated averaged template-derived brain extraction in animal MRI

A modified FSL version for use with Slurm

General utility scripts, documentation, and analysis tutorials for Smith Lab.

Reproduce BRATS preprocessing for a given patient (needed: 4 modalities T1, T2, T1c and FLAIR, optional: segmentation).

Scripts for processing brain image data

Code to create structural connectivity matrix from preprocessed DWI and structural MRI data.

Guide to perform ANTs registration on ASL data into the MNI-152 template.

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

lnifmri_prep is a set of plain bash scripts to automate preprocessing and QC of fMRI data.

Code snippets for preprocessing DTI/MRI neuroimaging data

Alcohol study DTI Analyses

Explore the neural basis of cognitive control with this repository's in-depth analysis of the Flanker Dataset using fMRI. Using bash scripting to streamline preprocessing and ROI analysis, while incorporating R scripts to explore brain region activity during the task.

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

Single-subject diffusion MRI workflow with MRtrix3 and FSL: DTI, CSD, probabilistic tractography, SIFT, and quantitative QC.