faq.txt

绝对经典,老外制作的功能强大的matlab实现PLS_TOOBOX

	Frequently Asked Question for PLS Program
	=========================================

Q:	Does PLSgui support ANT average binary data?

A:	Yes. The "load_ant.m" program in PLSgui is based on openlib
	library "cntopenlib.zip" and additional information "avr.txt"
	file that are released by ANT technical support.

	Since January 2004, ANT's average data file has been changed,
	and the history section is included in its header. This info
	is not included in the "cntopenlib.zip"; however, it is in the
	"avr.txt" file released by ANT's support people.

	Some people used "avr2asc" provided by ANT's EEProbe_3.3.120 
	to convert ANT's average data to plain text file. However, the
	disadvantage is that the "avr2asc" only supports new version
	of ANT's average data on Linux and Mac platforms, and does not
	work under MATLAB.

	Other programs relied on their "cntopenlib.zip" (e.g. Robert
	Oostenveld's "read_eep_avr" that is used by EEGLAB) can only
	support old version, and they are compiled in mex or dll file.
	You must first use "avrstrip" in EEProbe_3.3.120 to convert 
	your new version of ANT's average data to old version before
	you can use "read_eep_avr" to load them.

	The "load_ant.m" is the only explicit .m program so far (April,
	2007) that supports both old & new versions of ANT's average
	data file on any platform.


Q:	In my MEG data, the number of channels and their corresponding
	names do not match up with any of the pre-specified system. How
	can I read in my data when channel configuration and names do
	not match?

A:	Up to this version (5.0704231) We only have 4 scalp electrode
	location systems in PLSgui. They are the ones that we are using
	most frequently. There is a way to add any system by yourself,
	as long as you know the electrode names with their corresponding
	x and y locations. Since PLSgui will normalize your x and y
	location to Xmin/Xmax and Ymin/Ymax, you don't need to worry
	about the exact locations, and the relative ones will work.

	Here is the details of how to add a Standard 10-20 EEG System
	with 19 cap electrodes:

	1. First step: Put all electrode names on a piece of grid paper,
	   and make sure that they are spatially located appropriately.

	2. Second step: Select an origin for XY coordinates. You can
	   pick any point (on or off any electrode) as your origin. For
	   example, Cz is a good selection, the most lower left grid is
	   also a good selection.

	3. Third step: Use a ruler (or count the grid) to measure the
	   x and y location from the origin.

	4. Forth step: Pick any of the 4 PLSgui electrode systems for
	   your system. In PLSgui, each system is determined by a
	   "erp_loc*.mat" MATLAB file. So we have:
	   "erp_loc_besa148.mat", "erp_loc_egi128.mat",
	   "erp_loc_egi256.mat", and "erp_loc_ctf150.mat". The default
	   system for "Edit Channel Order" window is:
	   "erp_loc_besa148.mat". So, it will be convenient for you if
	   you pick this one.

	The whole idea to use your own system is to create an electrode
	systems MATLAB file with the same file name as the one used by
	PLSgui. Let's assume you picked "erp_loc_besa148.mat", once you
	save your own "erp_loc_besa148.mat" in the same folder as the
	one you will save session/datamat/result file, PLSgui will load
	your own "erp_loc_besa148.mat", instead of the one from PLSgui
	program folder.

	All 4 PLSgui electrode system MATLAB file in PLSgui contain two
	variables, one is char array "chan_nam", the number of rows is
	the number of channels and the number of columns is the longest
	length of the electrode names; the other one is double array
	"chan_loc", the number of rows is the number of channels and
	it only has two columns. Column 1 is for x values, and column 2
	is for y values. Now continue with this example:

	chan_nam=[
		'Fp1'
		'Fp2'
		'F7 '
		'F3 '
		'Fz '
		'F4 '
		'F8 '
		'T7 '
		'C3 '
		'Cz '
		'C4 '
		'T8 '
		'P7 '
		'P3 '
		'Pz '
		'P4 '
		'P8 '
		'O1 '
		'O2 ']

	chan_loc=[
		-3  10
		3   10
		-8  6
		-5  7
		0   8
		5   7
		8   6
		-10 0
		-7  0
		0   0
		7   0
		10  0
		-8  -6
		-5  -7
		0   -8
		5   -7
		8   -6
		-3  -10
		3   -10]

	%  Assume that your current directory is the one that
	%  you will save session/datamat/result file, then:
	%
	save erp_loc_besa148 chan_loc chan_nam

	Now you have your own system in "Edit Channel Order" window if
	you are under "ERP/BESAThetaPhi" system, and you can also pick
	channels that is used in the ERP data.


Q:	I am not using MATLAB in MS Windows platform now. When I click
	"How to use this window?" under help menu, I only get "To learn
	how to configure your Web browser type 'help docopt'" message in
	MATLAB command window. When I did so using MATLAB in MS Windows
	platform, I can see that the help is nicely opened in my default
	web browser. Does it mean that this menu can only be used in 
	MATLAB in MS Windows?

A:	This menu should work on both Windows and Unix (Linux). I have
	not tested it on other OS.

	However, you could still encounter error (the message in your
	question is automatically displayed by MATLAB) because of the
	following reasons:

	1. You are using MATLAB version 5. It does not have a MATLAB
	   desktop, and it uses the current terminal for commands.

	2. You specified -nodesktop or -nojvm when you launch MATLAB.

	3. You do not have any web browser in your system, or you did
	   not specified properly in "docopt.m" file. In latter case,
	   please type 'help docopt'.

	In any case, in fact, I recommand PLS user to manually open your
	favorate web browser, and view our PLSgui User's Guide from PLS
	web site:

	http://www.rotman-baycrest.on.ca/pls/UserGuide.htm


Q:	Why the figures in UserGuide.htm can not be displayed?

A:	Because those figures took hundreds of kilobytes of the space, I
	have to leave them in our website. As long as your computer have
	internet access, you will be able to see them properly, even if
	you browse "UserGuide.htm" that is on your local computer.


Q:	I wrote a batch file to create fMRI datamat. I have 5 conditions
	and 2 runs. Since I set "across_run" keyword to "0" (merging data
	within each run), I will have 10 conditions. I listed all 10 after
	10 "cond_name" keywords. When I run the batch, I got error message
	saying "Index exceeds matrix dimensions".

A:	You can only list your 5 conditions after 5 "cond_name" keywords.
	This is because the program will expand your 5 conditions in your
	2 runs to something like Run1Cond1, Run1Cond2, Run2Cond1, etc.


Q:	I preprocessed my data in FSL, where left is R and right is L. I
	then entered the normalised, slicetime- and motioncorrected data
	into a PLS analysis. When we now look at the results, where is 
	left and right? As in FSL?

A:	Let's use command: nii = load_nii('filename.nii'), where 
	"filename.nii" is the one from FSL:

	1. If you find nii.filetype is 0, it means that the image 
	   orientation is as is in the data. 

	2. If filetype is not 0, and there is no "rot_orient" & 
	   "flip_orient" field under "nii.hdr.hist", it means that
	   your data is already in RAS, and my NIFTI package did not
	   convert your data. 

	3. If file type is not 0, and there is "nii.hdr.hist.rot_orient"
	   or "nii.hdr.hist.flip_orient", it means that your data has 
	   been converted to RAS (Left is L) by NIFTI package.


Q:	What should the contents of the input file for "multiple voxel 
	extraction"? I created a text file with 1 XYZ coordinate per row.
	However, I keep getting an error message.

A:	That's the correct contents. However, please make sure that the 
	XYZ coordinates should be in unit of millimeter. (Note, we did
	use absolute voxel location before 15-SEP-2006. You can use 
	script "xyz2xyzmm.m" to easily convert absolute voxel location
	to voxel location with unit of millimeter.)


Q:	When I use the multiple voxel extraction, does it output the
	baseline-adjusted values or the raw image values?

A:	It outputs the baseline-adjusted value (from *datamat.mat), and
	there is no raw image values kept. If you need raw image values,
	you have to load images by yourself, and extract only the voxels
	indexed by the XYZmm file you provided.


Q:	In E.R.fMRI and Blocked fMRI datamat create window, what does 
	the "Normalize data with ref.scans" check box mean?

A:	This check box is checked by default to remove the low frequency
	noises and scale the data. The formula for this check box is very
	simple:

		dataset = (dataset - ref_dataset) * 100 ./ ref_dataset

	In this way, activity for each event is expressed as a %change 
	from the reference scan (i.e., baseline) similar to what is done 
	for ERP, where activity is expressed as a change from prestimulus 
	baseline.

	Please keep this check box checked unless you have a good reason 
	not to do so.


Q:	Also in E.R.fMRI and Blocked fMRI datamat create window, when the
	"Single Subject Analysis" check box was checked, the red words
	"Number of onset must be same" were presented in the bottom of
	this window, however,when this check box was not checked, session
	session file could be created successfully. Why?

A:	For single subject analysis, we actually treat each onset as 
	a "subject" (in the sense of our "subject-in-condition-in-group" 
	format). This is why we need you to keep onset number same, 
	because the number of "subject" should be the same for each 
	"condition" in each group.

	If you uncheck the single subject analysis, all the onsets for 
	each condition will be averaged together, so there is no need to
	keep onset number same.


Q:	I have three conditions (positive, negative and neutral) and I 
	want to compare the effect of positive vs neutral, if the 
	"Mean-Centering PLS" is cheked, how do I "deselect" conditions
	in the window of "PLS Analysis"?

A:	Click "Deselect Conditions" under "Deselect" menu, and deselect
	the "nagative" condition.


Q:	What does the "Non-Rotated Task PLS" check box in "PLS Analysis"
	window means?

A:	In "Non-Rotated Task PLS", we directly used crossblock between 
	the contrast data and the task mean of your fMRI data as brainlv,
	and directly used sum of squre of the crossblock for singular 
	value. There is no PCA computation involved, and there is no need
	to do procrustean rotation for the result. This is why we call it
	"Non-Rotated Task PLS".


Q:	If the "Non-Rotated Task PLS" check box is checked, how do I 
	design the contrast?

A:	Click "Contrast" menu in PLS analysis window. Click "Using Helmert
	Matrix" under the "File" menu of the contrast window. The freedom 
	of contrast is number of conditions minus 1. For example, if you 
	have 3 conditions, you can have 2 contrast. You can either take 
	the Helmert Matrix value in the text box, or re-enter your own 
	contrast value (e.g. [-1 1 2], [1 -2 3] etc.). At the end, you 
	have to go to "File" menu to save your contrast data into a file,
	and this file name will be entered into the "Contrast Data File"
	in the PLS analysis window (you can only enter file name under 
	"Non-Rotated Task PLS" option.


Q:	I have completed a group analysis with seven subjects under three
	conditions(positive, negtive and neutral) using Helmert contrast, 
	when showing the result, how could I find the the values of latent
	vectors for design contrast?

A:	Click "Design Scores and LVs Plot" in the "Windows" menu of the 
	result display window. The Design Scores for each latent variable
	reflect the impact of your contrast data.


Q:	In my result the "Brain LV" view is very different from the 
	"Bootstrap Ratio" view with default threshold, and which view do
	I prefer to support my experiment result?

A:	The "Bootstrap Ratio" view gives you a "stability map", so you can
	focus on the high positve (or negative) voxels in the "Bootstrap 
	Ratio" view. However, "Brain LV" view is the one to support your 
	experiment result. The positive (negative) value should be 
	consistent with the one in Design Scores plot.


Q:	I have more than one runs in my MRI study. However, for some
	runs, I do not have all the conditions. How should I fill out
	the onset field?

A:	If you want to exclude certain conditions for certain runs, 
	you can simply put a -1 for the onset field, (and put a 1 for
	the length of Blocked fMRI). Then choose "Merge data of each 
	condition: across all runs" to create a datamat. Please ignore 
	the command line message saying "Scans -01 not included due 
	to out of bound". You can not choose "Within each run only", 
	since you do not have all the conditions filled for every