Welcome


Welcome to the FreeSurferWiki. The FreeSurferWiki is the central documentation and download source for FreeSurfer, a software application developed at the Martinos Center for Biomedical Imaging by the Laboratory for Computational Neuroimaging.

FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.

FreeSurfer provides many anatomical analysis tools, including: representation of the cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from the rest of the brain, skull stripping, B1 bias field correction, nonlinear registration of the cortical surface of an individual with a stereotaxic atlas, labeling of regions of the cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures and much more ...

Software


Documentation


Overview of FreeSurfer

MRI Sequences

Troubleshooting

Some of Our Tools

More Details about FreeSurfer Processing

Sharing What You Learned

Citing FreeSurfer

Acknowledgements


http://www.nih.gov/

http://www.ncrr.nih.gov/

http://www.nbirn.net/

http://www.ninds.nih.gov/NINDS

http://www.na-mic.org/ NAMIC

http://www.nibib.nih.gov/

http://www.nitrc.org/projects/freesurfer/

Publications

When citing Freesurfer, here is some boilerplate text.



Methods


Published material describing the methods used in FreeSurfer (please cite our software!, see also boilerplate text):

surface reconstruction

inter-subject spherical averaging

thickness measurement

cortical parcellation

subcortical segmentation

longitudinal processing

tracts constrained by underlying anatomy (TRACULA)

optical coherence tomography

positron emission tomography

related methodological papers

history


Citations


Published material citing Freesurfer:

(If you have a citation you would like to include in this list please e-mail your request to vinke[at]nmr.mgh.harvard.edu)

cortical thickness

cortical surface area

local gyrification index (LGI)

clinical biomarkers

volumetric

white matter

longitudinal

tracts constrained by underlying anatomy (TRACULA)

cortical region localization

cortical surface shape and folding analysis

surface-based analysis (SBA)

ROI-based analysis

SBA vs. VBM

diffusion analysis

CBF - cerebral blood flow

cortical flat-patches

FS-FAST

validation / evaluation

FreeSurferWiki (last edited 2014-06-14 23:10:49 by AllisonStevens)