Cholesky 3.0

• Disabled buggy matrix mode of anatLm
• Add explicit configuration file to civet.readCBRAIN
• Fixed segfault in minc.separation.sizes
• Add heat smoothing on surface meshes (thanks @DJFernandes)
• Improved numerical stability in effect size code

Cholesky-2.3

• Fixed mincLmer reinit (formula out of scope bug)
• Improved mac install notes (issue #261)
• Defaults RMINC_LABEL_DEFINITIONS to null instead of empty string
  (issue #259)
• anatGetAll fails faster if the label defs are broken (issue #260)
• civet.readCBrain now supports columnsToKeep to pass to flattening
  code
• Add environment variable to configure where test data is located, useful
  for systems where internet isn't available.
• Improvement to FDR threshold selection in launch_shiny_RMINC
• Code for reading in a matrix of minc files mincTable. Supports
  file backed matrices for when your files are too big for your computers
  memory.
• Fixed reading QC for CIVET 1.1.12 experiments
• Fixed and streamlined the continuous integration (travis) build scripts
• Fixed all outstanding R CMD check and test issues

Cholesky-2.2

• Improvements to vertex code (thanks @vfonov), now can
  read single columns from vertex data files
• Hedges G effect sizes (thanks @gdevenyi), currently
  for (minc/vertex/anat)Lm
• Better cortical figure layouting
• vertexAtlasApply for wrapping a common tapply pattern.

Cholesky-2.1

• Fix resource passing in mincLmer
• improve tag file handling
• allow dataPath passing in testbed
• convert RMINC github page to pkgdown (sweet)

Cholesky-2.0

• Rewrite parallel docs to reflect change to batchtools
• Add configuration passing for parallel functions
• Rewrite of anatGetAll for multi-mode. Subject specific
  atlases can be passed for computing summaries, useful
  for DTI with MAGeT
• Allow shinyRMINC to be run with mincSingleDim's
• Allow shinyRMINC to use an FDR object to select thresholds
• Add slider for dynamic upper limit setting in shinyRMINC
• Mention the MINC_FILE_CACHE_MB variable in the docs to help
  fix memory issues especially with parallel jobs
• Implements a transposed vertexApply for subject specific
  summaries
• Allows colour setting in vis2D
• Refactor 3D plotting code to improve legend placement
• Better symmetric palettes for 3D plots
• Fix the parallel memory variable for batchtools
• Adds a timeout for lsof to stop NFS issues killing RMINC
• Minor fix for new lmerTest
• Expose mincRandomize (WIP sharp edges expected)
• Nice new c++ API for working with minc volumes in RMINC
  internals.

Cholesky-1.0

• Converts parallel backend to batchtools. No more
  NFS file locks on hpf
• Improved vertexLmer df estimation robustness
• Configurable legend height in slice series plots
• Improved discrete legends in slice series plots
• mincTFCE preserves likeVolume
• Variety of miscellaneous bug fixes, see
  issue tracker for details.

Cholesky-0

• Adds hierarchical atlas features
• fixes pivoting bug in lm code
• Adds weighting option to anatLm/*Lmer
• Increases dplyr and lme4 version dependencies
• Adds symmetric colour palettes to 3D plotting

Besag

• Adds printer for anatModel
• Adds Model comparison with AIC, BIC, and AICc for lm/lmer models
• Lm/Lmer models now report their instance-wise log-likelihoods
• Adds colour lookup tables and interface function (thanks Yohan)
• Adds civet 2.0 and 2.1 reading support (from cbrain projects)
• Adds civet QC reading support
• Adds attribute preserving subsetting and merging for anatModels
• Adds hierarchy summarization for anatModels (anatSummarize)
• Adds Parallel mincAnova
• Adds adjustable output types for lmers so that lmer Anovas can
  be run (or random effects retrieved)
• Adds Minc and vertex TFCEs
• Adds randomization tests for vertex/mincLms
• Adds randomization tests for vertex/mincTFCEs
• Masks for mincLmer are now manadatory
• Adds vertexFindPeaks
• Fixes broken column selection in mincFDR

Pearson-4

• Fix banding bug in mincLm parallel with >6 cores.
• Improve file handle and file checks
• Add as.data.frame for anatMatrix
• Add print for anatModel.
• Better error when atlas omitted in anatGetAll

Pearson-3

• Fix left|right lateralization bug in anatGetAll
• Export vertexFDR related functions and update docs.
• Improve printing for numeric masks