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FreeSurfer Release Notes
These Release Notes cover what's new in a release, and known issues.
See also DownloadAndInstall, and BugReporting.
Stable v3.0.1
13 March 2006BR
Stable release version 3.0.1 is a bug-fix release.
What's New
- FIX_VERTEX_AREA no longer need be set in the environment outside of recon-all.
- In tkmedit, while loading a functional overlay or time course, the registration file name is now read properly.
- The FSFast utility mkanalysis-sess.new now accepts only sequence names matching "TR " (instead of all occurrences of TR).
Known Issues
- No known issues at this time.
Be sure to read about the changes to recon-all, detailed below, and also read about the new [wiki:FsAverage fsaverage] subject.
Stable v3.0
5 March 2006BR
Stable release version 3.0 is a major release containing many new features over the prior stable release (version 2.2).
Important! The [wiki:recon_2dall recon-all] script has been updated. Please read the ReconAllChanges page which describes these changes! Users of prior 'dev' releases should also take note of the changes.
COR file format is no longer accepted by recon-all. mgz file's have replaced this old format.
brainmask.mgz has replaced what was the brain volume. You should visualize and make all edits to brainmask.mgz and not to brain.mgz
- recon-all will now save all your changes by default. Any manual changes/edits to the talairach, setting of control points, edits to volumes etc will be saved and used by default and you must specify when you wish to ignore these changes.
Data processed with an older release should make use of the -legacy flag in [wiki:recon_2dall recon-all].
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). Note: this requires the use of the new average subject [wiki:FsAverage fsaverage] because the surface registration changes.
Improved automation - The need to conduct manual edits to account for skull-stripping and cutting-plane problems is reduced. The topology fixer is much better at handling temporal lobe strands. Overall, greater than 90% of hemispheres processed by recon-all do not require manual intervention.
Improved GUI tools - The GUI tools tkmedit and tksurfer incorporate many usability improvements requested by the user-base.
New cortical parcellation - 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. [wiki:FsAverage $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 [wiki:SetupConfiguration 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
Make sure to run "setenv FIX_VERTEX_AREA" if using any commands outside of recon-all, particularly the mri_glmfit and mri_surfcluster programs. To be safe, you can just add the line "setenv FIX_VERTEX_AREA" into FreeSurferEnv.csh or your .cshrc file. This will only affect those downloading the new version. This will automatically be done for those in the Martinos Center.
- In tkmedit, while loading a functional overlay or time course, the registration file name may not be read properly. A workaround is to load the overlay or time course from the command line (see ["tkmedit"] for details).
The surface registration curvature target has changed with the new automatic filling of ventricles and basal ganglia. Do not mix newly reconstructed subjects with those that used the old target. For new data recons, display overlay maps on the new average subject [wiki:FsAverage fsaverage]. For older data, use average7.
There are some changes in the way that mri_surfcluster and mri_glmfit computes cluster sizes and how these interact with the average subject (and average7) see the notes [wiki:FsAverage fsaverage] for more detail.