faq.txt

绝对经典,老外制作的功能强大的matlab实现PLS_TOOBOX

	runs. In additon, for each condition, you must have at least 
	one valid onset (not -1) in one of your runs.


Q:	Why the results I obtained using Matlab 7 can not be loaded
	under earlier version of Matlabs?

A:	In order to load results generated using Matlab 7 on earlier
	versions of Matlab, a special Matlab 7 switch must be included
	during the saving process. Since such a switch is not coded in
	the package, a small program called 'matlab7to5.m' is included
	to covert the .mat files generated from Matlab 7 to be loaded
	on earlier versions of Matlab that are above Matlab 5.


Q:	I got "divide by zero" error when I tried to run Behavior PLS
	analysis, while there is no error when I ran task PLS.

A:	There are two reasons that could bring you into this trouble:

	1. You must have at least 3 subjects to do the behavior PLS.

	2. Values should not be all the same for behavior data. Even
	   if they are really all the same, you must add (or minus) a
	   slight difference (e.g. 1/1000) to make it work.


Q:	Is there any restriction on file name?

A:	Yes, but not many. There are 3 kinds of major files that will 
	be used in this program. They are session file, datamat file, 
	and result file.

	The 3 major files must be in the forms of:

		*_MODULEsession.mat
		*_MODULEdatamat.mat
		*_MODULEresult.mat

	You can replace MODULE with any of PET, ERP, fMRI, or BfMRI,
	depending what PLS are you working on, and the dialogbox will
	always prompt you with the correct MODULE.

	You can not insert your own string into the above forms and
	break it. However, you can always use your own string before 
	"_MODULE", which is called "prefix" in the program. I do not
	recommend you to use any blank space or symbol characters 
	like "+ - * / % ^ $ ' ..." etc. inside the string.

	In addition, you should not rename the filename manually by 
	yourself, since this will break the filename linkage stored
	inside the above major files.


Q:	When I opened the result file, it crashed and told me that the
	datamat file was unable to open. (No, the datamat file was not
	in the current directory.)

A:	In the early version of the PLSgui program, we used the stored
	'pls_data_path' variable to locate the files. However, this also
	caused trouble when people want to copy those datamat files from
	directory to directory, and even from one machine to the other.

	So, we decided to use the "current directory" rather than the 
	stored 'pls_data_path' variable for "Run PLS" window and "PLS 
	result" window. If you are not starting the program from the
	"current directory" where those datamat files sit, you can
	always change to "current directory" in the very first window
	by clicking "Change Current Working Directory" under "Tools"
	menu.


Q:	When I add or edit subject directory for ERP and PET, I saw an
	edit box called "Number of character for subject initial". What
	should I enter?

A:	For ERP and PET data, each subject has its own directory. The data
	files inside the subject directory stand for different conditions
	for this subject. The name of these files can be arbitrary; however,
	if you give "consistent naming across subjects", it will bring you
	convenience to match the conditions.

	Here is what the "consistent naming across subjects" means:

	1. All subject files consist two portions, subject initial portion
	   and condition name portion. e.g. SubjInit1_CondName1;
	2. Across all subject directories, the condition name portion
	   should be the same for the same condition;
	3. Within each subject directory, the subject initial portion
	   should be the same for all conditions of this subject;

	Here is how to make this feature work for you:

	1. Enter the length of the subject initials in the "Number of
	   Characters for subject initial" box. You can disable this
	   feature by leaving this value as -1.
	2. Click Add or Edit button in the same window (Edit Subject
	   Directory window), and a new window called Subject Directory
	   Detail will open.
	3. Select one of subjects that will be used in this datamat
	   group (Note: Remember that only select 1 subject this time).
	4. If you have "consistent naming across subjects", you will
	   notice that "File names are the same across subjects" check
	   box is checked. Uncheck it to disable this feature.
	5. Go to right hand side, select correct subject files that 
	   match the inputted conditions at their left side. Make sure
	   that no subject file can be duplicated.
	6. If you have multiple subjects in this datamat group, you
	   can now select the rest of subjects by holding Shift or Ctrl
	   key combination while selecting (Note: You can not do so 
	   before this step).
	7. Click Done button when you finish, and you return to "Session
	   Information" window.


Q:	I received a "Subject file name convention is not consistent"
	message when I try to edit a subject. However, all my subject
	file name convention are consistent. Is this a bug?

A:	No, it is not a bug. When you edit a subject with "File name
	are the same across subjects" checkbox selected, the program 
	expects that you are trying to use a different subject. You 
	should manually do the mapping between subject files and input
	conditions by yourself. If the mapping you selected does not 
	follow the other subjects you selected, the program will display
	such an error message. If you definitely need such a mapping, 
	then the "consistent naming across subjects" rule can not be 
	kept, and you will have to uncheck the "File name are the same 
	across subjects" checkbox.


Q:	All my subject files have consistent naming convention, and I
	also input the correct length in the "Number of Characters for
	subject initial" box. Why the "File names are the same across
	subjects" checkbox is grayed?

A:	Please check the following 2 possibilities:

	1. All files under any subject directory should follow the 
	   "consistent naming across subjects" rule. If one of them 
	   does not follow this rule (e.g. WS_FTP.LOG), the "File names
	   are the same across subjects" checkbox will be grayed.
	2. Don't let external program affects your subject initial. For 
	   example, there is a subject file with subject initial "S1" 
	   with length of 2 characters. When you normalize this file,
	   it may become nS1 with length of 3 characters. You will have
	   to rename the file name if this happened.


Q:	Does the length of the data file name matter?

A:	No. It can be any length. However, please make sure that subject
	initial portion should be the same length if you would like to
	use the "consistent naming across subjects" feature.


Q:	Does the letter case of the data file name matter?

A:	No. It is particularly designed for case insensitive. So you can call
	the first data file name "JSdata1", and the second "jsData2".


Q:	What can this PLS Program do?

A:	PLS indicates Partial Least Squares (PLS) analysis method. 
	It is based on the assumption that the focus of analysis 
	is on which aspects of the signal in one matrix are related 
	directly to signals in another matrix. 

	This PLS program is applied to neuroimaging data, such as 
	PET, ERP, Event Related fMRI and Blocked fMRI. It has been 
	used to identify the task-dependent changes in activity, 
	changes in the relations between brain and behaviour, and to 
	examine functional connectivity of one or more brain regions. 
	The similarities and differences in brain-behavior relations 
	can be identified from the resultant patterns.


Q:	What data should I prepare for analysis?

A:	The data can be obtained from PET, ERP, or fMRI scan images.
	For PET and ERP data, you put different condition of data for
	each subject into its corresponding directory. For fMRI data,
	you put each run of data into its corresponding directory.


Q:	I made some changes, but it disappeared. Why?

A:	Any changes you made on the edit box need to be recorded. This
	can be done by clicking "Enter" key on your keyboard, or simply
	click anywhere else on the window to let the focus switch off
	from this edit box. If you did not let the focus switch off from
	this edit box, the change will not be recorded.


Q:	What should I enter for "Edit Behavior Data"?

A:	For PET and ERP data, the number of rows for behavior data should be 
	the number of conditions times the number of subjects, in the order 
	of subjects in conditions:

		cond1/subj1
		cond1/subj2
		...
		cond2/subj1
		cond2/subj2
		...

	For fMRI data, the number of rows for behavior data should be either
	just the number of conditions, or the number of conditions times the
	number of runs, depending on whether you choose of "across run" or 
	"within run" when you create datamat. The order should be either all
	conditions, or runs in conditions:

		for across run:

		cond1
		cond2
		...

		for within run:

		Run1Cond1
		Run1Cond2
		...
		Run2cond1
		Run2Cond2
		...
		
	The column of the behavior data should correspond to the different 
	sets of the behavior measures.


Q:	When I exported data for behav analysis for PET module, I saw the 
	exported file name looks like "?_PET_grp?_behavdata.txt". For the 
	both E.R.fMRI and Blocked fMRI modules, however, it looks like 
	"_fMRI_grp?_subj?_behavdata.txt". Why the PET module does not 
	include the subject information?

A:	For PET module, each datamat (and session file) represents a group 
	that already contains subjects. However, for fMRI, each datamat (and
	session file) represents a subject. So, for fMRI, we need behavior 
	measure of each subject in the group in order to add it into datamat
	(from session profile). For PET, we need behavior measure of each 
	group.


Q:	Can I rename the session / datamat / result files manually? Why the
	corresponded session file also changed its name, after I save as 
	fMRI datamat into another file name?	

A:	We do not recommend you to change name manually. For fMRI, there is 
	some internal processing between session / datamat files. That's why 
	the session file name will be changed after you saved datamat file 
	into another name.


Q:	After deselect the conditions, why the behavior data I loaded before 
	running analysis get lost (or still use the one from datamat)?

A:	Because the rows of behavior data is determined by the conditions you
	selected. So, you need to load behavior data after you deselect the
	conditions.


Q:	When I generate fMRI datamat, I got something like this: Scans 147 for 
	the condition 3 of run1 are not included due to out of bound. Do you 
	have any idea what this means?

A:	When you enter onset data, make sure they are in the range. 
	In most case, you encounter this problem because the onset 
	data you input exceeds the maximum range. The minmum value
	is started from 0. However, The maximum value you can enter is: 
	Number_of_Scans - Temporal_Window_Size_if_fMRI - 1. E.g.: If you 
	have 180 files, and window size is 8, the maximum value in onset 
	data is 171.


Q:	What is the lag number? Is there anywhere I can enter lag values?

A:	In E.R.fMRI, lag number is the index of the temporal window, and it
	starts from 0. You decide the temporal window size in "Generate ST 
	Datamat" window. The unit of temporal window size is scan, and its
	default value is 8. In "LagXYZ" field of result window, you can 
	enter lag value, as well as XYZ coordinates in voxel.


Q:	In our lab we use AFNI in the processing of fMRI data but I would
	like to use the PLS program to analyse an event-related dataset 
	and further progress to conducting a functional connectivity 
	analysis.  My problem is that the PLSgui seems to need separate 
	image files for every time volume (a separate image file for every
	'scan' in a run), however, using AFNI, the raw 2D timeseries is 
	transformed into a 3D dataset, upon which the motion correction,
	edge-detection and spatial normalisation processing steps are 
	carried out.  Can the PLSgui read in this entire timeseries or 
	must the time volumes be somehow extracted from this file?

A:	If your AFNI 3D dataset is conformed with NIFTI standard, PLSgui
	can read it directly. Otherwise, you can use an AFNI utility called
	"AFNItoANALYZE" to convert it to Analyze Format.


Q:	Can I use Analyze image with different orientation?

A:	Yes, a new feature has been added to the version of Octobor 29,2004.
	This allows people to use Analyze images in any orientation for PET, 
	E.R.fMRI and Blocked fMRI. In "Create Datamat" window, a new button 
	named "Check image orientation" is added beside the "Create" button.
	Once you click this button, the 3-View of one of the subject images 
	will be displayed in the "Change Image Orientation" window, and you 
	can re-orient it by click the "Re-orient" button. Once you click the 
	"Re-orient" button, it will ask you to input the orientation of the 
	CURRENT DISPLAYED image. If you did not get the correct orientation, 
	you can do as many times as you want to make it standard Analyze 
	orientation, i.e. from Left to Right in X orientation, from Back to 
	Front in Y, and from Bottom to Top in Z. If you closed the "Change 
	Image Orientation" window, you can re-open it by click the "Check 
	image orientation" button in "Create Datamat" window again.

	For people that already generated the result file in wrong orientation 
	but did not correct it during creating datamat, we provided axial view 
	of "Convert Orientation" (under "Image Rotation" menu in the result 
	window) only for PET and Blocked fMRI. However, we do not recommend
	people to use this limited patch. Instead, we recommend people to use 
	the feature in "Create Datamat" window to correct the orientation 
	during creating datamat.