FreeSurfer Release Notes

These Release Notes cover what's new in a release, and known issues.

Download and installation instructions [wiki:DownloadAndInstall are found here].

Bug reporting instructions [wiki:BugReporting are found here].

Stable v3.0

Stable release version 3.0 is a major release containing many new features over the prior stable release (version 2.2). Data processed using stable v2.2 or earlier is not compatible with this new release.

Important! The [wiki:recon_2dall recon-all] script has been updated. Please read the page [https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllChanges https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllChanges] which describes these changes! Users of prior 'dev' releases should also take note of the changes.

What's New

Sub-cortical segmentation - Each MRI volume voxel is assigned one of 37 possible neuroanatomical labels, including left and and right caudate, putamen, pallidum, thalamus, lateral ventricles, hippocampus, and amygdala. The labeling allows for volumetric measurement of these structures. The segmentation information also improves the ability to create a filled white-matter volume.
Automated filling of ventricles and basal ganglia - Improves the ability to create a filled white-matter volume (which is used in the surface creation process).
Improved skull stripping/cutting plane definition - The need to conduct manual edits to account for skull-stripping and cutting-plane problems is reduced.
New cortical parcellation (Desikan-Killiany) - A neuroanatomical label is assigned to each location on the cortical surface model based on probabilistic information estimated from a manually labeled training set.
Surface-based GLM analysis - Utilities for conducting group analysis studies with GLM.
Multiple comparison correction for surface analysis - False discovery rate (FDR), permutation and Monte Carlo simulations.
New average subject. $FREESURFER_HOME/subjects/fsaverage. Keeps info about average surface area.
Average subject customization. Make your own average subject from your cohort.
Extensive testing - The recon-all processing stream has been tested against several hundred subjects, different pulse-sequence types, and different MRI system platforms.
Online tutorial of the Freesurfer work-flow - This release is compatible with the [wiki:FsTutorial on-line tutorial]. Tutorial data must be downloaded separately.
Simplified distribution download and installation - The critical library and toolkit dependencies (MNI, FSL, GSL, Tcl/Tk/Tix/BLT, and Qt) are included to ease installation. These third-party open-sourced packages can be removed if they are already installed on the target system (although full Freesurfer functionality is no longer assured). For Mac OS X, a GUI installation package is provided.
Compatible with all mouse pads.
Now Y2K compliant!

Known Issues

There are no known issues at this time. Issues will be listed here as they are discovered.