Software platform for clinical neuroimaging studies

Preprocessing pipeline on Brain MR Images through FSL and ANTs, including registration, skull-stripping, bias field correction, enhancement and segmentation.

This repository contains the files that generate Andy's Brain Book on ReadTheDocs.

ICA-AROMA Software Package: a data-driven method to identify and remove head motion-related artefacts from functional MRI data.

Small Animal Magnetic Resonance Imaging via Python.

FSL-R Interface package

Probabilistic Threshold-Free Cluster Enhancement of Neuroimages

A re-implementation of FSL's Brain Extraction Tool in Python

The project is used to do preprocessing on brain MR images by using Nipype.

Tools for dealing with neuroimaging data in the BIDS structure

Code for performing static, dynamic and real-time shimming using external and internal MRI shim coils

Introduction to dMRI

Preprocessing Pipelines for EEG (MNE-python), fMRI (nipype), MEG (MNE-python/autoreject) data

PNH segmentation pipelines based on nipype

FSL Anatomical Labels for MNI Vector/ROI

Utility MATLAB functions and wrappers for fMRI data analysis, mostly based in SPM12

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

A volumetric version of the HCP-MMP1 atlas conveniently imported in FSL. This repo was used in Bedini, M., Olivetti, E., Avesani, P., & Baldauf, D. (2023). Accurate localization and coactivation profiles of the frontal eye field and inferior frontal junction: an ALE and MACM fMRI meta-analysis. Brain Structure and Function, 1-21.

A collection of ILINK linker configurations that simplifies project setup for flash libraries on IAR Embedded Workbench for Renesas RL78

A Matlab-based software package for preprocessing the resting-state fMRI data