Welcome to the SOTNIR handbook!

This handbook is a resource for those carrying out neuroimaging projects.

This resource contains quickstart guides, example scripts, and standardised workflows, developed in Southampton.

Contributors are credited on each page.

Important

This site is under construction and active development. Contents of this site are subjected to change. You can be a part of this project as well! If you would like to contribute to this handbook, please contact Nathan (N.Huneke@soton.ac.uk), Ara (A.Varatharaj@soton.ac.uk), or Kai (Y.Zou@soton.ac.uk)

Getting started

• Linux Workstations
• Unix Basics

Undertaking a Neuroimaging Project in Southampton

• Trainings and Certifications
• Research MRI Scanners
• High Performance Computing
• Cloud Computing

File conversion

• Convert from DICOM to NIfTI
• Pseudonymise your dataset

Sharing Neuroimaging Data

• Brain Imaging Data Structure (BIDS)
• DataLad: Distributed Data Management

functional MRI

• Nordic Neuro Lab (NNL)
  • Configuring NNL Equipment with Your PC
  • NNL SyncBox Configuration with PsychoPy
• PsychoPy
  • psychopy-mri-emulator
• fMRI Analysis
  • fMRI Preprocessing with fMRIPrep
  • FMRIB Software Library (FSL)
  • Quality Assurance Checks
  • Functional Connectivity Analysis with CONN

diffusion MRI

• dMRI Analysis
  • Diffusion Tensor Imaging: An Introduction
  • DTI Preprocessing with FSL
  • DTI Analysis with FSL

Quantitative Susceptibility Mapping

• QSM Analysis