RMINC

Statistical Tools for Medical Imaging NetCDF (MINC) Files

Tools for reading, writing, analyzing, and visualizing MINC neuroimaging files with R. Supports voxel-wise linear models, mixed-effects models, correlations, ANOVA, FDR correction, TFCE, ROI-based anatomy analysis, surface-based vertex statistics, and parallel execution.

Unix only (Linux, macOS). Requires R >= 4.0. No native Windows support (WSL may work — see INSTALL).

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Table of Contents

• Features
• Installation
  • System Requirements
  • Troubleshooting
• Quick Example
• Dockerized Testing
• Tutorials
• Getting Help
• Development
• License

Features

Capability	Key functions
Voxel-wise linear models	mincLm, mincAnova, mincTtest, mincWilcoxon
Correlations & summaries	mincCorrelation, mincMean, mincSummary
Mixed-effects models	mincLmer, mincLmerEstimateDF, mincLogLikRatio
Surface / vertex statistics	vertexLm, vertexLmer, vertexTFCE
ROI / anatomy analysis	anatLm, anatLmer, hanatLm (hierarchical atlases)
Multiple comparisons	mincFDR, mincTFCE, mincRandomize
I/O	mincGetVolume, mincWriteVolume, mincArray
Visualization	mincPlotSliceSeries, mincTriplanarSlicePlot (2D), rgl (3D), hanatView
Parallel execution	pMincApply, qMincApply, mincLm(parallel = ...)

Installation

The easiest way to install is with devtools from the develop branch:

devtools::install_github(
  "Mouse-Imaging-Centre/RMINC@develop",
  upgrade_dependencies = FALSE
)

System Requirements

RMINC depends on the MINC C library. You have two options:

1. minc-toolkit-v2 (recommended): Download binary installers from http://bic-mni.github.io/ or build from source at https://github.com/BIC-MNI/minc-toolkit-v2. This provides the MINC library plus command-line tools.

2. libminc from source: If the toolkit is not found, RMINC's configure will attempt to build libminc for you. This requires CMake (> 2.6), git, and the HDF5 development headers.

Debian / Ubuntu:

sudo apt-get install libhdf5-dev cmake git lsof autoconf automake libtool

macOS (Homebrew):

brew install hdf5 cmake autoconf automake libtool

macOS note: RMINC's compiled backend needs a Fortran compiler. Apple's default clang does not include one — install gcc via Homebrew (brew install gcc libssh2 libgit2 libomp zlib) or gfortran directly, and point R at it via ~/.R/Makevars. See the INSTALL file for the exact FLIBS/LDFLAGS setup and detailed instructions.

Troubleshooting

If configure cannot find MINC, set the install prefix via an environment variable:

export MINC_TOOLKIT=/opt/minc/1.9.18

Or pass the path at install time from R:

devtools::install_github(
  "Mouse-Imaging-Centre/RMINC@develop",
  args = "--configure-args='--with-build-path=/opt/minc/1.9.18'",
  upgrade_dependencies = FALSE
)

Quick Example

Fit a voxel-wise linear model across a set of MINC volumes. The response column in data holds MINC file paths; the model is fit independently at every voxel:

library(RMINC)

# `gf` is a data frame whose `volumes` column holds MINC file paths
fit <- mincLm(volumes ~ group, data = gf)

# Output columns: "F-statistic", "R-squared", beta coefficients,
# t-statistics, "logLik". Write the whole-model F-statistic (column 1):
mincWriteVolume(fit, output.filename = "group_Fstat.mnc", column = 1)

Function-level documentation is available in R via ?mincLm, ?mincLmer, ?vertexLm, ?anatLm, etc.

Dockerized Testing

Build the test image:

docker build -t rminc-test .

Run checks and tests (mount the source directory):

docker run -v $(pwd):/RMINC rminc-test              # check + tests (default)
docker run -v $(pwd):/RMINC rminc-test check          # R CMD check --as-cran only
docker run -v $(pwd):/RMINC rminc-test test            # tests only
docker run -v $(pwd):/RMINC rminc-test test mincLm     # filtered tests
docker run -v $(pwd):/RMINC rminc-test shell           # interactive bash shell

Tutorials

• Voxel-wise Statistics (somewhat out of date)
• How RMINC Parallel Works
• RMINC 2D Visualization
• Visualizing 3D Objects with RMINC
• Analyzing Anatomy with Hierarchical Atlases

Getting Help

Function documentation is available through R's ? interface (e.g. ?mincLm). The MICePUB wiki has additional background and usage notes. Report bugs or request features at the issues page.

Development

The develop branch is where active development happens; the master branch may lag behind. Contributions via pull requests to develop are welcome.

The C/C++ backend is built with Rcpp and autoconf — src/Makevars is generated from src/Makevars.in, and RcppExports.{R,cpp} are auto-generated by Rcpp. Do not edit these files directly.

After editing R source containing roxygen comments, regenerate documentation and the NAMESPACE with:

roxygen2::roxygenise()

License

RMINC is released under the BSD 3-Clause License.