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In this lesson, we will demonstrate a series of potentially useful tools to visualize neuroimaging data and make the manual quality control process a lot easier.

The list of tools we will attempt to cover are:

  • SPM visualizer (cross-platform)
  • xjView toolbox for SPM (cross-platform)
  • FSLeye visualizer (Linux/Mac Only. Windows with Linux VM)
  • MRICron, MRICronGL (cross-platform)
  • ITKSnap (cross-platform)
  • MNI Display (Linux)
  • 3D Slicer (cross-platform)

Prerequisites

  • Ability to navigate computer folders in Windows/Mac/Linux.
  • Open terminals and invoke commands.
  • Concept of 3D volume file as a 3D matrix.
  • Optional: MatLab (for SPM, xjView related visualization).
  • Optional: FSL (for fsleye).