SOTNIR handbook

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)
  • PsychoPy
  • fMRI Analysis
    • fMRI Preprocessing with fMRIPrep
    • FMRIB Software Library (FSL)
    • Quality Assurance Checks
    • Functional Connectivity Analysis with CONN

diffusion MRI

  • dMRI Analysis

Quantitative Susceptibility Mapping

  • QSM Analysis
SOTNIR handbook
  • fMRI Analysis
  • View page source

fMRI Analysis

Contributors: Nathan TM Huneke, Yukai Zou
Maintainers: Nathan TM Huneke

Under construction

Sections

  • fMRI Preprocessing with fMRIPrep
    • Beginner’s Guide to fMRI Preprocessing
    • Running fMRIPrep
  • FMRIB Software Library (FSL)
    • fMRI Analysis with FEAT
    • Using FSL on Iridis Open OnDemand
    • FSLeyes: a brief intro
    • Brain Extraction Tool (BET)
    • (Optional) FSLUTILS
  • Quality Assurance Checks
    • Standard deviation and Signal to Noise ratio maps
    • Using MRIQC for Quality Assurance
  • Functional Connectivity Analysis with CONN
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© Copyright 2021, Huneke NTM, Varatharaj A, Zou K.

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