Pearson-0

Many bug-fixes, and speed-ups, with an emphasis on more parallel functionality

• Mixed effects for all
  • added vertex and anatLmer variants along with degrees of freedom
    estimation and FDR correction
• Major parallelism updates
  • offload configuration to BatchJobs, see ?configureMincParallel
  • provide graceful exit and cleanup if interrupted
• Parallelize all the things (for local and queued systems)
  • mincLm (+ minor performance improvement)
  • vertexLmer
  • vertexApply
  • anatLmer
  • anatGetAll
• Explanation of parallel use and implementation in
  RMINC/documentation/RMINC_parallelism.html
• vertexApply behaves more like apply, no longer requires a quoted function string
  accepting a function name and an arbitrary number of additional arguments
• MincLmer returns the full volume matrix as opposed to the masked subset
• Peak finding: Find local optima in a minc volume subject to constraints
• anatGetAll rewrite:
  • 10-15x faster for method = "labels" (and parallelizable)
  • More informative errors
  • no minc-stuffs dependency
  • atlas name no longer required for method = "labels"
  • pretty printing
• File and vector masks for vertex operations (apply, lmer)
• Simple single volume and matrix TFCE interfaces, randomization tests
  complete but inadequately tested
• Mesh->Graph conversion (via igraph) opens surface oriented graph algorithms
• thresholds method for FDR (mincQValues) objects to retrieve matrix of thresholds
  and a summary to tabulate N significant tests per threshold
• maskFile(obj) and maskFile(obj) <- "mask.mnc" methods for getting/setting masks
• likeVolume(obj) and likeVolume(obj) <- "vol.mnc" methods for getting/setting likeVolumes
• simple civet QC reader civet.readQC
• Surface transparency for surface renderings with add_opacity
• Decrease mincGetVolume verbosity
• File handle problem detection with many files.