User Guide

Partial Least Squares (PLS), which was first introduced to the neuroimaging community in 1996 (McIntosh et al., 1996), has proven to be a robust method for describing the relationship between signal changes in brain and a set of exogenous variables (i.e. task demands, performance, or activity in other brain regions).

PLS Applications include a Graphic User Interface - GUI application and a Command-Line computation application. Both applications must be kept under the same parent folder, and their folder names (i.e. plsgui and plscmd) can not be changed.

If you would like to use GUI interface, path to plsgui folder must be manually added in MATLAB command window. When you run PLS analysis, computation part in plscmd folder will automatically be called internally. You only need to type plsgui, and a GUI interface will be driven by messages from your mouse and keyboard inputs. As an alternative, you can also run GUI interface unattendedly with Batch Process.

Command-Line PLS (see Appendix B) pls_analysis is the core computation application of PLS. All PLS computations in the GUI will resort to pls_analysis application. If you would like to use Command-Line PLS alone, you can manually add a path to plscmd folder in MATLAB command window. However, keep in mind that its result is only part of GUI result, and cannot be displayed under GUI interface.

This User Guide only intends to show HOW to use PLS Applications for those users who have already understood the PLS method. If PLS is new to you and you want to know WHY PLS Applications are designed this way, please refer to the relevant articles listed at the bottom.