Statistics for MINC volumes: A library to integrate voxel-based statistics for MINC volumes into the R environment. 
Supports getting and writing of MINC volumes, running voxel-wise linear models, correlations, etc.; correcting for 
multiple comparisons using the False Discovery Rate, and more. With contributions from Jason Lerch, Jim Nikelski, 
Matthijs van Eede and Daniel Cassel. Some additional information can be found here:

https://wiki.phenogenomics.ca/display/MICePub/RMINC

Dependencies:
-------------

RMINC depends on the following repository:
https://github.com/BIC-MNI/libminc
https://github.com/Mouse-Imaging-Centre/minc-stuffs

Installation:
-------------

The R_LIBS variable determines where the library is installed. By default it will be installed under /usr/share. 
If you want to install the library somewhere else, the R_LIBS environment variable should be set.

> export R_LIBS=/build/directory

The RMINC package currently depends on the MINC libraries to be installed. If these libraries are not installed in
a standard location, you will have to set the LD_LIBRARY_PATH (on a Mac, this path needs to be set by your default
shell profile):

export LD_LIBRARY_PATH=/path/to/minc/install/root/directory/lib:$LD_LIBRARY_PATH

The latest version of the software using the devtools package (R 3.1.1) from within R:

> install.packages("devtools")
> library(devtools)
> options(devtools.install.args = "--configure-args='--with-build-path=/path/to/minc/install/root/directory/'")
> install_git("https://github.com/mcvaneede/RMINC")

The latest version of the software using command line tools:

$ git clone https://github.com/mcvaneede/RMINC.git RMINC
$ cd RMINC
$ ./autogen.sh
$ cd ../
$ R CMD INSTALL RMINC /directory/where/sourcefiles/go --preclean --configure-args='--with-build-path=/install/directory/minc2'


Installation of a release:

Download the tarball from the Github RMINC website https://github.com/mcvaneede/RMINC/tree/master/releases
Install the package (example is for the tarball version 0.5):

> R CMD INSTALL RMINC_0.5.tar.gz --configure-args='--with-build-path=/install/directory/minc2'

Some notes on getting RMINC installed on a Mac
----------------------------------------------

Install latest version of 'minc-toolkit' from
http://packages.bic.mni.mcgill.ca/minc-toolkit/MacOSX/

Add the following set-up script and path to ~/.profile using an editor

. /opt/minc-itk4/minc-toolkit-config.sh
export LD_LIBRARY_PATH=/opt/minc-itk4/lib/:$LD_LIBRARY_PATH

Open a new terminal an then start R

library(devtools)
options(devtools.install.args = "--configure-args='--with-build-path=/opt/minc-itk4/'")
install_github('Mouse-Imaging-Centre/RMINC')