Here is a short list of some multivariate analysis tools that are designed for variable selection and inferential analyses while relating two or more high dimensional data sets. They seem like appropriate tools for imaging genomic analyses, e.g., identifying genotype-phenotype (and even endophenotype) relationships by joint analysis of high throughput behavioral, imaging and genome wide data.

* PMA: Penalized Multivariate Analysis, http://cran.r-project.org/web/packages/P...
* mixOmics: Omics Data Integration Project, http://cran.r-project.org/web/packages/m...
* MExPosition: Multi-table multivariate analysis with the singular value decomposition, http://cran.r-project.org/web/packages/M...
* ade4 and FactoMineR also include multi-table multivariate techniques (http://cran.r-project.org/web/packages/a... http://cran.r-project.org/web/packages/F...)
* Partial Least Squares correlation approaches (symmetric analyses; via Rotman mostly for 2 table analyses): http://www.rotman-baycrest.on.ca/index.p...
* Partial Least Squares regression in R (asymmetric analyses): http://cran.r-project.org/web/packages/p...