= Partial Least Squares (PLS) =
''Authors: Golia Shafiei''

This tutorial explains the concept of Partial Least Squares (PLS) analysis in general, which was first introduced to the neuroimaging community in 1996 (McIntosh et al., 1996). In addition, we illustrate how to use PLS process on a sample data in Brainstorm.

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== License ==
PLS is a free toolbox developed at [[https://www.rotman-baycrest.on.ca/index.php?section=84|Baycrest, University of Toronto]]. The PLS code is written entirely in MATLAB (Mathworks Inc) and can be downloaded from https://www.rotman-baycrest.on.ca/index.php?section=345. To cite PLS Toolbox, please see the “References” section of this tutorial.

== Introduction ==
Partial Least Squares (PLS) analysis is a multivariate statistical technique that is used to find the relationship between two blocks of variables. PLS has various applications and types (Krishnan et al., 2011); however, the focus of this tutorial is on Mean-Centered PLS analysis, which is a common type of PLS while working with neuroimaging data. In this type of PLS analysis, one data block is neural activity (e.g. MEG measurements/source data here) while the other one is the experiment design (e.g. different groups/conditions).

PLS analysis is based on extracting the common information between the two data blocks by finding a correlation matrix and linear combinations of variables in both data blocks that have maximum covariance with one another. In the example provided here, we find a contrast between different conditions as well as patterns of brain activity that maximally covary with that specific contrast.

For this purpose, we take the neural activity as one data block, matrix X, where the rows of matrix X are observations (participants/trials) nested in conditions or groups, and the columns of X are variables (time scales nested within sources). The other data block, matrix Y, is a matrix of dummy coding that corresponds to experimental design (different groups or conditions) (Krishnan et al., 2011).

PLS analysis first calculates a mean-centered matrix using matrices X and Y. Then, singular value decomposition (SVD) is applied on the mean-centered matrix. The outcome of PLS analysis is a set of latent variables that are in fact linear combinations of initial variables of the two data blocks that maximally covary with the corresponding contrasts (Krishnan et al., 2011, Mišić et al., 2016). More specifically, each latent variable consists of a set of singular values that describe the effect size, as well as a set of singular vectors, or ''weights'', that define the contribution of each initial variable to the latent variables (Mišić et al., 2016).

Finally, the statistical significance of a latent variable is defined by a p-value calculated from permutation test. In addition, bootstrapping is used to assess the reliability of each original variable (e.g. a source at a time point) that contributes to the latent variable. Bootstrap ratios are calculated for each original variable for this purpose. Bootstrap ratio is the ratio of the weights to the standard errors estimated from bootstrapping. Therefore, the larger the magnitude of a bootstrap ratio, the larger the weight (i.e. contribution to the latent variable) and the smaller the standard error (i.e. higher stability) (McIntosh and Lobaugh, 2004, Mišić et al., 2016). Bootstrap ratio can be equivalent to a z-score if we have an approximately normal bootstrap distribution (Efron and Tibshirani, 1986).

PLS analysis was explained in general in this section. However, this tutorial assumes that the users are already familiar with basics of PLS analysis. If PLS is new to you or if you want to read more about PLS and its applications in details, please refer to the articles introduced in “References” section.

== Download and installation ==
==== Code ====
In order to run PLS process in Brainstorm, you must install the PLS Toolbox on your computer:

 * Download it from here: http://pls.rotman-baycrest.on.ca/source/Pls.zip
 * Unzip the file on your computer (not in any of the Brainstorm folders)
 * Add this new folder to your MATLAB path (with all its subfolders).

==== Data ====
The dataset used to illustrated the method comes from the tutorial [[Tutorials/VisualGroup|MEG visual tutorial: Group analysis]]. It consists in simultaneous MEG/EEG recordings of 19 subjects performing a  simple visual task on a large number of famous, unfamiliar and scrambled  faces. The detailed presentation of experiment is available in the [[http://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle|MEG visual tutorial: Single Subject]]. We repackaged only the few files need this PLS demonstration to make it more accessible, the only difference with the original tutorial is that the sources are not normalized with respect with their baselines (no Z-score).''' '''

 * Go to the [[http://neuroimage.usc.edu/bst/download.php|Download]] page, download the file '''TutorialPLS.zip'''.
 * Unzip this file in your Brainstorm database folder (brainstorm_db).
 * In Brainstorm, menu File > Load protocol > Load from folder > Select '''brainstorm_db/TutorialPLS'''

== Running PLS ==
There are two PLS processes available in Brainstorm:

 * You can run PLS analysis for __only two conditions__ through the Process2 tab at the bottom of the Brainstorm window.
 * You can also run PLS analysis for __more than two conditions__ through the Process1 tab at the bottom of the Brainstorm window. This option is explained in the “Advanced” section of this tutorial.

Both of these two processes work in a similar way:

 * '''Input: '''the      input files are the source data from different conditions. Number of observations/trials per      condition must be the same for all conditions. Make sure you have enough observations/trials per condition in order to get meaningful results from statistical tests.
  * '''Note: You can also run PLS analysis on sensor level data (channel data). However, the results will not be as meaningful and useful as the ones from source level data.'''
 * '''Output: '''               the output files include bootstrap ratios and p-values for all latent variables. In addition, you can look at the contrast between conditions (groups and/or experimental tasks) for each latent variable. The output files are explained in details in the following sections.

We will continue with explaining the PLS process for only two conditions from now and we will leave PLS process for more conditions for the Advanced section of this tutorial.

=== File selection ===
 * Select the process2 tab at the bottom of Brainstorm window.
 * Drag      and drop '''16 source files''' from '''Group_analysis/Faces-MEG''' to      the left (Files A).
 * Drag      and drop '''16 source files''' from '''Group_analysis/Scrambled-MEG'''      to the right (Files B).
 * Note that the number of files in each window (“A” and “B”) must be the same.<<BR>> <<BR>> {{attachment:select_files.gif}}

=== Process options ===
 * In Process2, click on [Run].
 * Select process '''Test > Partial Lest Squares (PLS). '''This opens the '''Pipeline editor''' window with the PLS process for two conditions.<<BR>><<BR>> {{attachment:pipeline1.gif}}

 * '''“Condition      1” and “Condition 2”''': Name of the two input      conditions: “Condition 1” and “Condition 2” are related to files in      windows “A” and “B” of “Process2” tab, respectively. We can use “Faces”      and “Scrambled Faces” as the condition names here.

 * '''Number      of Permutations''': Indicates the      number of permutations you want to run in PLS.
 * '''Number of Bootstraps''':      Indicates the number of bootstraps you want to run in PLS.
 * '''Sensor types or name''': Indicates the type of sensors that has been used for source      localization (e.g. MEG or EEG). This will occur in the result file name as      well.

Run the process when the options are set. The process will take some time depending on the number of files, number of permutations and number of bootstraps. The results are then saved in '''Group Analysis > Intra-Subject''' folder.

=== Results ===
 * Output files include contrast between conditions, p-value of the latent variable and bootstrap ratios:<<BR>><<BR>> {{attachment:results_overview.gif}}

<<BR>>

 * '''PLS : Contrast: '''You can first look at the contrast between two conditions: Double-click on the contrast file. The contrast is shown in the form of time series; however, the x-axis is not actual time. In fact, the integer numbers on time axis show the number of conditions (e.g. 1 for condition 1 or “Faces” and 2 for Condition 2 or “Scrambled Faces”) and the non-integer ones should be ignored.<<BR>><<BR>> {{attachment:contrast.gif}}

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 * '''PLS: p-value for latent variable:''' if you double click on this files, you will see a table containing the p-value of the latent variable that is related to the contrast shown above. A significant latent variable means the contrast observed between two conditions is also significant.
 * Note: You will see two numbers in the table for p-value of the latent variable when you run PLS for two conditions. Ignore the second one.<<BR>><<BR>> {{attachment:p_value.gif}}

<<BR>>

 * '''PLS: Bootstrap ratio: '''This file is saved in the format of source maps. Double-click on the file and open it. The colormap shows bootstrap ratios for each source at each time point. There are some important points you should keep in mind when working with bootstrap ratios:
 * Bootstrap ratios show how reliably each source is contributing to the observed contrast and latent variable at each time point. A bootstrap ratio larger than 2.58 is considered reliable. Therefore, adjust the amplitude of bootstrap ratios to 25%-26% to be able to see the reliable signals. For this, choose “Surface” tab from Brainstorm window and adjust the “Amplitude”.<<BR>><<BR>> {{attachment:bootstrap_ratio.gif||width="660",height="261"}}

 * Do not display absolute values of the signals. Make sure “Absolute Values” is not selected in the colormap menu for this figure. The sign of bootstrap ratio is important since positive bootstrap ratios express the contrast as is, while bootstrap ratios with negative values express the opposite contrast.

 * You can display the results at different time points using contact sheet. <<BR>><<BR>> {{attachment:contact_sheet.gif||width="660",height="481"}}

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 * You can also define regions of interest as usual: OFA (Occipital Face Area), V1.<<BR>><<BR>> {{attachment:ROI.gif||width="660",height="283"}}

== More than two conditions ==
You can run PLS for more than 2 conditions through Process1 tab. However, you should be careful when arranging the files in this option. We will use the same dataset to illustrate how to use this option in Brainstorm.

 * Select the Process1 tab at the bottom of Brainstorm window.
 * Drag      and drop '''16 source maps''' from  '''Group_analysis/Famous-MEG''' to the Process1 window.
 * Drag      and drop '''16 source maps''' from '''Group_analysis/Scrambled-MEG''' to the Process1 window under the      previous source maps.
 * Finally,      drag and drop '''16 source maps''' from '''Group_analysis/Unfamiliar-MEG''' at      the end of previous files.
 * Make sure you have the same number of files for each condition.
 * '''Note: '''PLS processes the data in “subject in condition” format. Therefore, all files from the same condition must be placed in the process window at once and files from the second condition must be added to the end of first condition, and so on for the rest of the conditions.<<BR>><<BR>> {{attachment:select_files2.gif||width="660",height="428"}}

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Run process '''Test > Partial Least Squares (PLS) – More than Two Condition'''.

 * Define the number of conditions and the number of subjects/trials per condition.
 * The other options are the same as explained above.<<BR>><<BR>> {{attachment:pipeline2.gif}}
 * The process will take some time. The results are displayed in the same way as before; however, you may have more bootstrap ratio files for different latent variables depending on the number of conditions you have. In this example, we have 2 latent variables.<<BR>><<BR>> {{attachment:results_overview2.gif}}

<<BR>>

 * Check the p-values first to detect the significant latent variables. Each latent variable will have a p-value that indicates whether the related effect (or contrast) is significant or not. In this example, only latent variable 1 (LV1) is significant.<<BR>><<BR>> {{attachment:p_value2.gif}}

<<BR>>

 * Open the contrast file and focus on the contrasts (effects) related to the significant latent variables. LV1 (green) is the significant latent variable in this example, which discriminates condition 2 (scrambled faces) from the other conditions (famous faces and unfamiliar faces).<<BR>><<BR>> {{attachment:contrast2.gif}}

<<BR>>

 * Keep the bootstrap ratio files for significant latent variables and delete the rest. Bootstrap ratios should be interpreted in the same way as it was explained above. Bootstrap ratio of a latent variable (e.g. LV(x) ) shows the pattern of brain activity that corresponds to the contrast defined by the same latent variable ( LV(x) ).

== References ==
 1. Efron B, Tibshirani R (1986). "Bootstrap methods for standard errors, confidence intervals and other measures of statistical accuracy." ''Stat. Sci. 1'', 54– 77.
 1. Krishnan A, Williams LJ, McIntosh AR, Abdi H (2011). "Partial Least Squares (PLS) methods for neuroimaging: a tutorial and review." ''Neuroimage, 56(2)'', 455-475.
 1. McIntosh AR, Bookstein F, Haxby J, Grady C (1996). "Spatial pattern analysis of functional brain images using partial least squares." ''Neuroimage 3'', 143–157.
 1. McIntosh AR, Lobaugh NJ (2004). "Partial least squares analysis of neuroimaging data: applications and advances." ''Neuroimage 23'', S250–S263.
 1. Mišić B, Dunkley BT, Sedge PA, Da Costa L, Fatima Z, Berman MG, ... & Pang EW (2016). "Post-traumatic stress constrains the dynamic repertoire of neural activity." ''The Journal of Neuroscience, 36(2)'', 419-431.

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