- How to run PLS Analysis on Blocked fMRI data

To run PLS analysis on Blocked fMRI data, you will need to have both 
session file and datamat file ready. Each session file and the 
corresponding datamat file represents one subject. All the subjects 
should have the same conditions.

Click 'Add' button, and you will get a Select Session Profiles window. 
Select session files from 'Files' panel, and click '>>' button to 
transfer them into 'Selected Session Profiles' panel. Then, click 'DONE'
when complete.

For task PLS analysis, if the 'Group Analysis' check box is checked, the
rows of the datamats from selected sessions will be averaged to form a 
single row to represent the same condition in the same group. If more
than 1 group is selected, the 'Group Analysis' check box can not be 
unchecked.

For behavior PLS analysis, we never not do average among the selected 
sessions. All session subjects in the same group will be treated as one
group. We also treated each run as one subject to prevent the loss of 
statistical meaning. All the groups will then be stacked together to 
form a 'Stacked Datamat' for analysis.

TIPS -

Since session subjects in different groups are belonging to different 
groups, and we have to provide enough subjects to make the statistical 
calculation meaningful, we must input at least 3 session files for each
group.



- Deselect Menu

Once you have added Session into group(s), you can click 'Deselect'
menu in the menu bar. There are two items: 'Deselect Conditions' and
'Modify Behavior Data'. Click 'Deselect Conditions' first, and select
which conditions you want to analyze. If you are doing Behavior analysis,
you can modify the behavior data right before clicking the 'Run' button.
However, you need to make sure the row order of behavior data, which 
should be in the form of 'subject-in-condition'. Also, make sure you
modify behavior data after you select the conditions.



- PLS Option

Mean-Centering Task PLS perform grand mean across tasks. i.e. Datamat
for each group are subtracted from the grand mean for each condition. The
PLS result should be very similar to that of using Helmert Matrix.

If you run Behavior PLS, you may also include Posthoc Data File. This 
will give you another result for further analysis.

Recently, we have added a "non-rotated" Task PLS Analysis, wherein a priori
contrasts are used to restrict the patterns derived from PLS. You need to
choose 'Non-Rotated Task PLS" and provide a contrasts file in order to run
this analysis. The contrast file can be generated from the contrast window
in the "Contrast" menu



- About computation parameters

You can run Permutation and Bootstrap to randomly swap and/or replace
the datamat rows with a number of times you designated in this frame.
The Number of Permutation is usually from 300 to 500 (the higher the 
better but longer), and the Number of bootstrap is usually set to 100.
For group analysis, there must be at least 3 subjects in each group.
For nongroup analysis, there must be at least 3 subjects (or repetitions)
for each conditions.