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  * [[attachment:FreeSurfer_Suggested_Morphometry_Protocols.pdf|Suggested Morphometry Protocols for Optimal FreeSurfer Reconstruction|&do=get]]
  * [[http://adni.loni.usc.edu/methods/documents/mri-protocols/|Alternative Morphometry Protocols, from ADNI]]
  * [[attachment:FreeSurfer_Suggested_Morphometry_Protocols.pdf|Suggested morphometry protocols for optimal FreeSurfer reconstruction|&do=get]]
  * [[http://adni.loni.usc.edu/methods/documents/mri-protocols/|Alternative morphometry protocols, from ADNI]]


FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging.

Our tools

Structural MRI

FreeSurfer provides a full processing stream for structural MRI data, including:

  • Skull stripping, B1 bias field correction, and gray-white matter segmentation
  • Reconstruction of cortical surface models (gray-white boundary surface and pial surface)
  • Labeling of regions on the cortical surface, as well as subcortical brain structures
  • Nonlinear registration of the cortical surface of an individual with a stereotaxic atlas
  • Statistical analysis of group morphometry differences

For more information, see:

Functional MRI

Diffusion MRI

  • TRActs Constrained by UnderLying Anatomy (TRACULA): TRACULA is a tool for automated probabilistic tractography with anatomical priors. It reconstructs a set of major white-matter pathways by incorporating prior information on the structural segmentation labels that each pathway goes through or next to, at every point long the pathway's trajectory. It includes a specialized stream for processing longitudinal diffusion MRI data.


  • Registration tools: FreeSurfer offers a range of tools for both within-subject and across-subject registration.

FreeSurferWiki (last edited 2021-07-12 14:00:49 by AndrewHoopes)