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Vistasoft is a Matlab toolbox for analyzing Magnetic Resonance Imaging (MRI) data. Vistasoft tools span anatomical, functional, and diffusion analyses and include some sample data.

The software was written by a group of scientists who are now at various research facilities around the world. A history with Stanford (Wandell lab) links most of the contributors.

Certain Vistasoft functions rely on other open-source projects, including SPM, FSL, FreeSurfer, and MRTrix.

Resources

Our intention is to integrate information about Vistasoft here. This project is not complete, so that information about Vistasoft is still distributed across several sites.

• Wandell Lab
• Winawer Lab
• Mezer lab
• Yeatman lab
• Dumoulin lab

Quick links

• Getting Started
• Software overview
  • Git tips
  • Unit testing
  • [Remote Data](Remote data)
• Tutorials
• Anatomy
  • [ACPC alignment](ACPC alignment)
  • Segmentation
  • Alignment of functional to anatomical - Aligning various modalities to T1-anatomical
  • Flat
  • Visual maps from anatomy - Using the Benson Gear to define retinotopic maps from a T1 anatomy
  • Working with Freesurfer
• Functional MRI
  • [Retinotopy tutorial](Retinotopy Tutorial) - Traveling wave
  • [Population receptive fields](pRF methods)
• Diffusion weighted MRI
  • Initialization - dtiInit, dtiInitParams, ...
  • Automated Fiber Quantification
  • [Tensor Statistics] (http://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/Tensor_Statistics)
  • LiFE and Ensemble Tractography
  • Contrack
  • Other Diffusion MRI utilities
• Quantitative MR
  • mrQ - Quantitative T1 and PD mapping
• Visualization
  • Mesh - interactive cortical surface and overlay visualization
  • Quench - interactive fascicle visualization
  • DTIQuery - interactive visualization
  • Flattening Cortical flattening
• Reproducible research and data management
  • [Flywheel: A commercial venture to support reproducible research] (https://flywheel.io/)
  • [Project on scientific transparency: The code] (http://scitran.io)