Software Image processing/visualization

FreeSurfer

Application

An open source software suite for processing and analysing human brain MRI images

Contributors

Bruce Fischl1, Martin Reuter1, Doug Greve1, Anastasia Yendiki1, Lilla Zollei1, Juan Eugenio Iglesias2

Contact

fischl@nmr.mgh.harvard.edu

Estimated cost

Free

Progress

Stable release, V 5.3.0 (require registration and license from Massachusetts General Hospital)

Resources

http://freesurfer.net/

FreeSurfer is a software package for analysis and visualization of structural and functional neuroimaging data

FreeSurfer has been developed for post-processing cross-sectional or longitudinal studies employing the following imaging modalities:

  • 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 morphometric differences
    • Hippocampus sub-field segmentation
    • Dedicated processing and statistics tools for longitudinal data analysis
  • Functional MRI: A set of tools for performing functional MRI data analyses on the cortical surface named “FreeSurfer Functional Analysis Stream” (FS-FAST) is provided.
  • Diffusion MRI: TRACULA is a tool for automated global probabilistic tractography with anatomical priors.
  • PET Partial Volume Correction (PVC) and Kinetic Modeling: PETSurfer is a tool for performing ROI-based, surface-based, and whole-brain analysis of PET data integrated with FreeSurfer anatomical analysis.
  • Combining with other modalities: FreeSurfer offers a range of tools for both within-subject and across-subject registration.

FreeSurfer can be controlled from the command line allowing for fully automatized post-processing. Alternatively, it has different graphical user interfaces (GUI) for data visualization, analysis and management.

Publications

Fischl, B. (2012). FreeSurfer. NeuroImage, 62(2), 774–781

Reuter, M., Schmansky, N.J., Rosas, H.D., Fischl, B. 2012. Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis. Neuroimage 61 (4), 1402-1418

Reuter, M., Fischl, B., 2011. Avoiding asymmetry-induced bias in longitudinal image processing. Neuroimage 57 (1), 19-21

Reuter, M., Rosas, H.D., Fischl, B., 2010. Highly Accurate Inverse Consistent Registration: A Robust Approach. Neuroimage 53 (4), 1181–1196

Fischl, B., Salat, D.H., Busa, E., Albert, M., Dieterich, M., Haselgrove, C., van der Kouwe, A., Killiany, R., Kennedy, D., Klaveness, S., Montillo, A., Makris, N., Rosen, B., Dale, A.M., 2002. Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain. Neuron 33, 341-355.

Dale, A.M., Fischl, B., Sereno, M.I., 1999. Cortical surface-based analysis. I. Segmentation and surface reconstruction. Neuroimage 9, 179-194

Fischl, B., Sereno, M.I., Dale, A.M., 1999a. Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system. Neuroimage 9, 195-207

Affiliations

1Massachusetts General Hospital, Harvard-MIT HST, A.A. Martinos Center, Laboratory for Computational Neuroimaging, Boston, MA, USA

2Translational Imaging Group, Medical Physics and Biomedical Engineering Department, London, England

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