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FreeSurfer Release Notes

These Release Notes cover what's new in a release, and known issues. See previous release notes for older versions.

Stable v6.0-beta

16 November 2016

Freesurfer version 6.0-beta is a beta release to the Freesurfer community to help identify bug fixes and other unknown issues before the release of Freesurfer version 6.0

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
• 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

• Fixed the libcrypt issue with OpenSuse linux platforms

Known Issues

• On Ubuntu platforms, you may encounter the error "freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory." Freeview will work fine if you install libjpeg62-dev and run:

sudo apt-get install libjpeg62-dev

• 'recon-all -make all' may fail when it reaches the step requiring the '?h.white.preaparc' file. (Will be fixed in final v6 release)