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FreeSurfer Release Notes

These Release Notes cover what's new in a release, and known issues. See the download and install page for the current stable release.

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

• Parallelization: a new flag was introduced which enables two forms of compute parallelization that significantly reduce the runtime. When the -parallel flag is specified at the end of the recon-all command-line, it will enable OpenMP parallelized code embedded in many of the binaries, namely affecting mri_em_register and mri_ca_register. By default, it instructs the binaries to use 4 processors (cores), meaning, 4 threads will run in parallel in some operations. This can be overridden by included the flag -openmp <num>, where <num> is the number of processors you'd like to use (ex. 8 if you have a 16 core machine). Note that this parallelization was introduced in v5.3, but many new routines were given OpenMP parallelization in v6. The other form of parallelization, a 'coarse' form, is that when the -parallel flag is specified, during the stages where left and right hemispheric data is processed, each hemi is run separately (and in parallel). This requires, of course, at least two cores available. Note that a couple of the hemi stages (eg. mris_sphere) make use of a tiny amount of OpenMP code, which means that for brief periods, as many as 8 cores are utilized (assuming the default settings). In general, though, a four core machine can easily handle those periods. Be aware that if you enable this -parallel flag on instances of recon-all running through a job scheduler (like a cluster), it may not make your System Administrator happy if you do not pre-allocate a sufficient number of cores for your job. As a point of reference, using a new-ish workstation (2015+), the recon-all -all runtime is just under 3 hours.

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)