whatsnew.txt

绝对经典,老外制作的功能强大的matlab实现PLS_TOOBOX

			1) list of number of subjects in groups
			2) number of conditions
			3) number of samples
			4) switch to control whether the boot_order
			   includes an original un-resampled order

Version 3.0501171  January 17, 2005
	1.	Reversed the change made in Version 3.0412081 on December
		8, 2004, because the "rri_boot_samples.m" only return the
		boot samples with specific different subjects. I need to
		modify "rri_boot_order.m" in order to include more other
		different subjects. So, it is correct to have 81 bootstrap
		samples for 5 subjects with 3 minimum different subjects
		in version before December 8, 2004.
	2.	Added a feature to let user choose the "percentage of
		minimum different subject number". By default, bootstrap
		must include at least 50% (i.e. half of the subjects).
		The percentage can go from 30 to 70 percent.
	3.	Input parameters for both "rri_boot_order" and "rri_perm_
		order" are now the same: 1. list of number of subjects in
		groups; 2. number of conditions; 3. number of samples.

Version 3.0501111  January 11, 2005
	1.	Command line PLS program is released. The result is the
		same as the PLSgui, but it is more simplified because we
		restrict the datamat in "subject-in-condition-in-group"
		format. By taking away the fancy result rendering part 
		and complicated subject stacking part (especially for 
		fMRI and Blacked fMRI), the code is much easy to read
		Unused codes are properly removed and the codes are
		detailly commented. It can be used to validate PLSgui
		result, or might be of interest to some other people 
		who may want to port it to other platform.
	2.	Added bootsamp/permsamp to boot_result/perm_result for
		all the modules.

Version 3.0501101  January 10, 2005
	1.	The boot order in the following scenario was incorrect:
		fMRI/BfMRI mean-center/no-rotate with any datamat created
		under "with each run only" option. It has been fixed now.
	2.	Fixed several bugs like posthoc file validating etc.

Version 3.0501061  January 6, 2005
	1.	In fMRI and Blocked fMRI session edit window, the
		Run Information contents are checked when DONE
		button or previous (next) button is clicked.

Version 3.0412081  December 8, 2004
	1.	Using Uril's "rri_boot_samples.m" to generate bootstrap
		order. For 5 subjects with 3 minimum different subjects,
		there will be 60 bootstrap samples, instead of 81.

Version 3.0412061  December 6, 2004
	1.	For "Multiple Voxel Extraction" under "Windows" menu
		of PET, fMRI and Blocked fMRI module, it now reports
		any entry in the voxel location file that is not
		inside the brain region.

Version 3.0411221  November 22, 2004
	1.	When creating datamat for PET, fMRI or Blocked fMRI,
		user is now allowed to consider all voxels as brain
		region, by select "Consider all voxels as brain"
		checkbox bedises the threshold editbox in "Create
		Datamat" window.
	2.	For fMRI and Blocked fMRI, Onsets field and/or Length
		field are checked to make sure they are not empty or
		not match when "Done" button is clicked in "Run Info"
		window.

Version 3.0411191  November 19, 2004
	1.	Fixed a bug of saving displayed image into another
		directory.

Version 3.0411051  November 5, 2004
	1.	Fixed a bug in Blocked fMRI BootStrapdisplay.

Version 3.0411041  November 4, 2004
	1.	Modified "Contrast" edit window and "Non-Rotated Task
		PLS" routine for all modules. So, it can take different
		contrast for different groups now. That means, if you
		have 2 groups and 3 conditions, you need to put 6 rows
		in the contrast data. First 3 rows belong to Group 1, 
		and next 3 rows belong to Group 2.

Version 3.0410292  Octobor 29, 2004
	1.	Added a new feature to allow user 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.

Version 3.0410201  Octobor 20, 2004
	1.	Removed (uV) sign from the legend axis for ERP Electrode
		Salience window.

Version 3.0410151  Octobor 15, 2004
	1.	Modified the save of session file and datamat file. It
		now prevents users from saving to a filename other than
		_PETsession.mat, _BfMRIsession.mat, _BfMRIdatamat.mat,
		_PETdatamat.mat, _fMRIsession.mat, _fMRIdatamat.mat,
		_ERPsession.mat, _ERPdatamat.mat.
	2.	Since we only read .mat from the current directory,
		which can be changed through "Change Current Working
		Directory" item under "Tools" menu in the first PLS 
		window, there is no need for another "PLS Working 
		Directory" in the session window. Now, this field has
		been removed from all modules, and the path is 
		automatically set to the current directory.

Version 3.0410061  Octobor 6, 2004
	1.	Fixed data path bug.

Version 3.0409301  September 30, 2004
	1.	Added following features for session windows. However,
		please keep in mind that you are NOT required to modify
		paths session files after you moved data from one
		location to the other, unless you would like to modify
		the contents of the session file. This is because that
		"Run Analysis" and "Show results" only read file from
		the current directory.
	2.	Added a feature in the Session windows to let users
		change old data (image, EEG etc.) path to new data
		path, as well as the change of new session path for 
		*session.mat file. When users click "Change Data Paths"
		under "Edit" menu, the "Change Path" window will pop
		up, and users can change both session path and data
		path. Please see the detail and the restrictions in
		FAQ.txt file.
	3.	The program will also do a preliminary scan for the
		first run (or subject for PET & ERP) sub-folder. If 
		the path is invalid, it will diplay a message at the 
		bottom of the session window, and prompt users to go 
		to "Edit" and "Change Data Paths" menu.
	4.	"Change PLS Path" button in the first PLS window is
		removed, because this program will only look current
		directory for "*datamat.mat", and "*result.mat" when 
		users run analysis and show Results.
	5.	Default value of "Number of charactors for subject 
		initial" in "Edit Subject" window for ERP and PET is 
		set to -1. This way, the consistency of subject file
		name convention will not be checked in the Subject
		Detail window (when clicking Add or Edit). If this
		number is not -1, please check Help and the FAQ.txt
		for details regarding to the consistency. In addition,
		this value is now saved to the session profile, so
		it will be remembered when the session profile is
		loaded next time.
	6.	Fixed several bugs.

Version 3.0409152  September 15, 2004
	1.	Added "Save Datamat As" feature in ERP "Modify Datamat"
		window. So datamat can be saved into a different name
		with (or even without) any modification. The datamat
		with new name will still point to the same data file.
		We did this because the data file is usually much larger
		than datamat file. This way, several different datamat
		files can point to the same data file (reservoir).
	2.	Added Bootstrap display for ERP correlation window. The
		"BootStrap options" item is also added into its "Tool"
		menu.
	3.	Substituted "Plot Canonical Scores" with "Plot Canonical
		Correlations" for ERP behavior PLS result.
	4.	Disabled false warning message in result file that does
		not store the timestamp information.
	5.	Removed redundant file pet_bootprocrust.m.
	6.	Fixed a bug in detail window of ERP correlation.
	7.	Fixed a bug that used wrong data path.

Version 3.0408201  August 20, 2004
	1.	In ERP result window, "Spatiotemporal Correlations" is
		added under "View" menu.
	2.	In ERP result window, wave selection box like "All Cond",
		"All Subj" etc is added in "Display Options" window of
		"Subject Amplitude" view, "Average Amplitude" view, and 
		"Spatiotemporal Correlations" view.
	3.	"Deselect" option is added in ERP "Run PLS Analysis"
		window.
	4.	In "Edit Behavior Data" window, "remove selected behavior
		name" option, and "Save current behavior data" option has
		been added.
	5.	Timestamp information is imbeded inside the result files.
		The program will automatically check for the timestamp 
		integrity for datamat file (and also session file if MRI),
		and will prompt with a pop-up window if necessary.
	6.	Fixed several bugs.

Version 3.0407291  July 29, 2004
	1.	Fixed an axes limit problem for behavPLS in correlation
		overview window.

Version 3.0407283  July 28, 2004
	1.	Also check the valication of the contrast file after
		click "Run" in the "Run PLS Analysis" window.

Version 3.0407271  July 27, 2004
	1.	For "Non-Rotated Task PLS", non-linear contrasts and
		non-orthogonal contrasts will be accepted, but a 
		warning message will be prompted.
	2.	For "Non-Rotated Task PLS", display all LVs when plot
		singular value or crossblock covarience.

Version 3.0407261  July 26, 2004
	1.	Added "Non-Rotated Task PLS" option to run non-rotated
		version of Task PLS Analysis.
	2.	"Using Helmert Matrix" PLS Option has been completely
		removed from the "Run PLS Analysis" window. Instead, it
		is added under the "File" menu of contrast window.
	3.	When running Bootstrap Analysis, the bootstrap result is
		now checked and replace meaningless data with 0. Thus,
		reduced the display crash when rendering the bootstrap
		result.
	4.	Related Documents are modified to represent this new
		release.

Version 2.407141  July 14, 2004
	1.	Modified program so it now only requires matlab toolbox.

Version 2.407131  July 13, 2004
	1.	In plsgui start window, when the "Show PLS Result"
		or the "Run PLS Analysis" button is clicked, the
		program will assume that all the related matlab 
		files (*.mat) are sitting in the current directory,
		thus, avoid trouble when those matlab files are
		copied between systems. In other words, people do not
		need to use the "Change PLS Path" button any more
		when copy those matlab files between systems. If the
		related matlab files are not sitting in the current
		directory, people can use the "Change Current Working
		Directory" submenu under "Tools" menu in this start 
		window to change the directory containing those matlab
		files as current directory.
	2.	"Save display setting" for result window dialog box 
		will not be prompted out every time when people change
		the display setting and close the result window. Instead,
		program will now read status from "Save display setting"
		submenu under "Tools" menu in the start window to decide
		whether save the display setting for users. In addition,
		when people open start window, program will not prompt
		"Create PLS Profile" message, and by default, status in
		"Save GUI position" submenu under "Tools" menu will be
		set to "Off" at beginning.
	3.	In ERP "Edit Channel Order" window, added number beside
		"Channels:" label and "Selected Channels: " label, and
		implemented multiple remove in "Selected Channels" panel.

Version 2.406181  June 18, 2004
	1.	Fixed a bug in Blocked fMRI RF Plot when prefix of
		datamat is different from that of session file.
	2.	Added a warning window after the datamat saved into
		a different prefix, and the "datamat prefix" in
		session file is updated.

Version 2.406111  June 11, 2004
	1.	When the "Cluster Mask" item under "Report" menu is
		checked, both "Save display" and "save result" under
		"File" menu will save the current masked image. When
		"Cluster Mask" is unchecked, they will save the 
		unmasked image.

Version 2.405101  May 10, 2004
	1.	Add a "Create Figure" sub-menu under 'Window' menu
		in "3 Cardinal Plane View" window.

Version 2.404132  April 13, 2004
	1.	Used standard normal distribution to calculate p-value
		in Cluster Report.
	2.	If any column of behavior data contains the same data
		for each group, program will stop proceed, and prompt
		error message.

Version 2.404081  April 8, 2004
	1.	Added merge conditions option in creating datamat
		window for both PET and ERP modules. (E.R.fMRI and
		Blocked fMRI modules already have the option).
	2.	Prompted file name after save or export a file in
		Cluster Report window.

Version 2.403301  March 30, 2004
	1.	Fixed a cond. labelling bug in PET brain scores plot.

Version 2.403181  March 18, 2004
	1.	Added feature to export canonical scores for ERP
		results.

Version 2.403081  March 8, 2004
	1.	Modified fMRI response function, and make average
		plots have own Y scales.

Version 2.403031  March 3, 2004
	1.	Worked around to make program not crash in extreme
		situation when max_blv(bsr) = thresh = 0 or 
		min_blv(bsr) = thresh = 0.

Version 2.403023  March 2, 2004
	1.	Fixed a bug that was introduced in on Jan. 9, which
		can cause PLS result display frozen on some PC.
	2.	In '3 Cardinal Plane view', XYZ & Value are updated
		with the 3 sliders now.

Version 2.402271  February 27, 2004
	1.	Added a feature to display all three cardinal planes
		for the PLS result data. To view all three cardinal 
		planes, click '3 Cardinal Plane View' submenu under
		'Windows' menu.

Version 2.402181  February 18, 2004
	1.	Modified 'fmri_plot_hrf', so it can read session file
		with empty onset data in one or more conditions for a
		single run.

Version 2.402131  February 13, 2004
	1.	Modified 'fmri_plot_hrf', so it can read both old and
		new fMRI session file.

Version 2.402121  February 12, 2004
	1.	Saving result to an IMG file now has two different ways.
		When saving 'BLV (or BSR) result to IMG' file, it only
		saved the BLV data (or BSR) data to an IMG file, and
		does not include colormap or background image. When
		saving 'Current Display to IMG file', it will include
		colormap and background image.

Version 2.402111  February 11, 2004
	1.	Modify Edit Runs, so the MRI session file is consistant
		no matter using text file to input onset data or enter
		onset data manually.

Version 2.402101  February 10, 2004
	1.	Reversed 2 changes made in Version 2.402051 (1 & 2).
		So we still export the whole time series, instead of
		only export the active time lag.
	2.	Cluster Report can be saved in tab-delimited .txt file,
		as well as in matlab .mat file.
	3.	Made XYZ(mm) field editable.

Version 2.402051  February 5, 2004
	1.	Changed the XYZ text box to edit box, so the current
		location can be set from this text box, rather than
		go to 'Set cluster report options' menu. For Event
		Related fMRI, [Lag X Y Z] is used, and for others,
		[X Y Z] is used.
	2.	The data export in response function and Multiple