- How to display PLS results of Event Related fMRI data

All the PLS Result data are saved in any of the '*fMRIresult.mat' files.
The result window will provide you a convenient way to display the Brain
LV image and Bootstrap Ratio image (if bootstrap number is greater than
0, and you can toggle between Bootstrap Ratio image and Brain LV image by 
selecting the View menu.)

	From 'File' menu, you can choose:

	1. Load Background Image
	2. Load PLS Result
	3. Save BLV Result to IMG File
	4. Save BS Ratio to IMG File (if bootstrap)

	From 'Windows' menu, you can choose:

	1. Singular Value Plot
	2. Canonical Brain Scores Plot
	3. Design LV and Design Scores Plot (for task analysis result)
	4. Response Function Plot (for task analysis result)
	5. Brain Scores vs. Behavior Data Plot (for behavior test result)
	6. Datamat Correlations Plot (for behavior test result)
	7. Contrasts Information (for non-rotated task analysis)
	8. Create Brain LV Figure
	9. Create Bootstrap Ratio Figure (if bootstrap)

	From 'Report' menu, you can choose:

	1. Set Cluster Report Option
	2. Load Cluster Report
	3. Create Cluster Report



- About Color Bar and Color in Result Image

The color in result image represent its value compared with threshold
value. If the absolute value is below the threshold, it will be shown
in gray. The maximum value will be shown in saturated red, which is
located in the upper part of color bar, while the minimum value will be 
shown in dark blue, which is located in the lower part of color bar.

** After adjust any of the above value, press "PLOT" button to update
   the display.



- About the Control Panel

The control panel is located at the left of the result window. On top
of the control panel, it displays the name of result file.

LV index: By default, it display the result on LV1, you can update the
'LV index:' field to display results on other latent variable.

First Slice: First slice in the image to be shown

Last Slice: Last slice in the image to be shown

Step: Incremented steps between two display slices

Threshold: threshold is calculated based on 95 percentile of the brain 
LV or bootstrap ratio. You can always update this field to change the 
threshold.

Curr. Value: clicking on any voxel on brain LV image, this field will
display the current value on the clicked voxel.

approx. P Value: clicking on any voxel on bootstrap ratio image, this 
field will display approximate P value of the bootstrap ratio.

Min Value or Ratio: any data lower than this value will be set to this 
value.

Max Value or Ratio: any data higher than this value will be set to this 
value.

XYZ: clicking on any voxel on result image, this field will display the
coordinate of the clicked voxel in [x y slice#].

XYZ(mm): it displays the clicked voxel coordinate in respect to the 
origin voxel coordinate in mm unit. Usually, the origin voxel coordinate
is written in image header file. If the it is not indicated in the image
header file, or the origin in the image header file contains 0, it will 
then be set to middle of the brain.



- Background Template File and Background Image

Both background template and background image contains 1 brain volume of
image data, which provides the basic brain physical structure that can
contrast out the activity brain area we try to display.



- Save BLV Result (or BS Ratio) to IMG File

Save the volume of current LV of index Brain LV or BS Ratio data.



- Singular Values Plot

This is a bar graph window. Through its view menu, you can choose to 
display Observed Singular Values, Percent Crossblock Covarience, and
Permuted Singular Value if if permutation number is greater than 0.



- Design LV and Design Score Plot

In this window, it displays Design LV and Design Scores in different
conditions, and Brain Scores vs. Design Scores. Different displays are 
switched via view menu. All the displays correspond to a LV vector. The
default LV is LV #1, and you can select other LVs in the left Display
LVs panel in this window.



- Response Function Plot

This window plots the activity of a particular voxel. When you click 
this menu, the plot window will be popped up behind the main result 
window. By clicking any voxel, the response function window will plot 
the detail information about voxel activity.



- Canonical Brain Scores Plot

This window plots the brain scores for individual and average stimulus
in each condition. When you click this menu, the Canonical Brain Scores
window will open. Choose one of LV and click Plot button, and the result
will be displayed. This feature is helpful to identify the timepoints 
where the maximal effects are present.




- Brain Score vs Behavior Data, and Correlation Bar Plot

If the result is from Behavior test, the Brain Score vs Behavior Data
menu is available in the window menu instead of Design LV and Design 
Scores Plot. It displays the Brain Score vs Behavior Data for all the
conditions. User can change the number of subplot through 'Change Plot
Dimension' menu under 'Option' menu. User can also choose 'Show Per LV
Plot' to have a montage like plot.

If there is any bootstrap loop in the Behavior test, user can also view
the Correlation Bar Plot by choosing 'Show Correlation Plot' under 'View'
menu.



- Datamat Correlation plot

This window plots the correlation between datamat and behavior data for 
each behavior measures and their average for each condition. When you 
click this menu, the plot window will be popped up behind the main result
window. By clicking any voxel, the datamat correlation window will plot 
the detail information just mentioned.



- Cluster Report

A cluster is defined as a connected volume in the brain. If the cluster 
size is smaller than the minimum cluster size you defined in the cluster
report option, it will not be count. If the distance between two cluster
peak is shorter than the minimum distance you defined in the cluster
report option, they are only counted as one cluster. In cluster report
option, you can also re-define the origin location of the brain.

The cluster report window will display the cluster#, peak voxel location,
and cluster size etc. You can also save cluster report into a .mat file, 
and the cluster_info struct will give more information for clusters.

By clicking 'Cluster Mask' submenu under Report menu, you can also turn on
(or turn off) the cluster mask on the result display image. Because the 
cluster report is calculated on fly and not saved in the result file. You
must first Load or Create a cluster report for each different scenario,
and you can close the report window afterwards. If you did not do so, the
program will prompt you to do so.

You have to Load or Create cluster report again if you changed display
threshold, min.value, max.value, or switching among axi/sagi/coro views.
However, if you just change LV Index, FirstSlice/Step/LastSlice, or even
change betweem BLV to BSR views, you do no need to load/create report
again if you already did so in this scenario. Anyway, program will prompt
you to do so if there is such a need.

In some resolution, you may want to enlarge or reduce the size of Cluster
Mask marker. You can change this value by click Set Cluster Report Options
submenu under Report menu. The current display will not be updated, you 
can let it be updated by click (uncheck) the Cluster Mask submenu, and 
click (check) it again.