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= FreeSurfer Release Notes =
These Release Notes cover what's new in a release, and known issues. See [[PreviousReleaseNotes|previous release notes]] for older versions.

== Stable v6.0 ==
'''''Date: TBD'''''

=== What's New ===
 * Brain networks (cognitive components) estimated from 10449 Experiments and 83 tasks in the Brainmap database are released in MNI152 and fsaverage space:
  * Wikipage: [[BrainmapOntology_Yeo2015]]
  * There are three sets of data (networks+auxiliary information) that are released: (1) Probability that a task would recruit a component (csv files), (2) Probability that a component would activate a voxel/vertex, (3) quantitative measures of functional specificity and flexibility (i.e., whether a voxel/vertex specializes for a specific cognitive component or supports multiple components).
  * The volumetric maps + csv files are found in average/Yeo_Brainmap_MNI152/. See Yeo_Brainmap_MNI152_README in directory for more details.
  * The surface maps are found in the subjects/fsaverage/label directory. See Yeo_Brainmap_fsaverage_README in directory for more details.
 * Substructure Segmentation:
  * New hippocampal subfields generation - See HippocampalSubfields
  * New brainstem substructures generation - See BrainstemSubstructures
 * Longitudinal:
  * New dedicated longitudinal pipeline for subfield segmentation - See LongitudinalHippocampalSubfields
  * New longitudinal pipeline for tractography 
  * Fix for time point addition (see bug in 5.3)
 * Matlab Linear Mixed Effects Tools:
  * Updated Matlab LME tools to newer Matlab versions
  * Allow missing Parallel Toolbox (process sequentially)
  * minor improvements to F-test
 * recon-all now produces aseg.mgz (subcortical atlas) with Hi-Res data (<1mm).  the -hires flag is still necessary to include with recon-all when hi-res data is input.  changes to mri_normalize, mri_em_register and mri_watershed were made to support this feature.
 * Improved accuracy of ?h.cortex.label
 * Improved prevention of surfaces from crossing into the contralateral  hemisphere
 * Adding the 'fs_update' script which allows users to update binaries or other elements of the freesurfer installation.
 * Adding the 'fs_tutorial_data' script which provides a means for downloading the data for completing the Self:Tutorials.
 * bbregister now uses the FS mri_coreg program by to initialize BBR. FSL or SPM/matlab are no longer needed. mri_coreg is based on spm_coreg and gives very similar results as to when spmregister is run.
 * mri_fdr -- command line program to compute and apply the false discovery rate algorithm

=== Known Issues ===