Packaging FreeSurfer

FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. It contains a fully automatic structural stream for processing cross sectional and longitudinal data. Packaging of FreeSurfer for Debian is a part of our general efforts to provide comprehensive neuro-imaging research support.


The majority of FreeSurfer 5.1.0 has been released under seems to be DFSG-compliant FOSS license terms on 24 May 2011. We have started working on packaging. Following has been done

  • modularization of the FreeSurfer distribution into code and data components
  • FreeSurfer 5.1.0 FOSS code made available from our FreeSurfer GitHub repository (temporarily taken offline)
  • debian/patches contains a series of patches primarily to
    • rely on system-provided libraries where applicable
    • in general replace static inclusion with dynamic linking thus greatly decreasing size of distributed binaries and making deployment more modular


FreeSurfer packaging

  • Collect and provide all required libraries to link against
  • Decide on further separation in to binary packages
  • Decide on how to ship “freesurfer-cuda” (depends on non-free materials, so cannot be build by the source in Debian main component)
  • Investigate possibility to deprecate/replace functionality dependent on antique libraries which might have been or soon will be removed from Debian (e.g. xview)



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