whatsnew.txt

绝对经典,老外制作的功能强大的matlab实现PLS_TOOBOX

		of lower / upper_interval from ".../(num_color-2)" to 
		".../(num_color-1)", which is more accurate. However, 
		user will not notice the change, and won't be affected.
	3.	Fixed a bug in checking bad behavior data.

Version 4.0601061  January 6, 2006
	1.	Fixed a bug when read some ERP text data.

Version 4.0601041  January 4, 2006
	1.	Correlation Matrix is checked before decomposed. This
		is only for people using PLS to analyse structural 
		data, where number of data points (ROI) can sometimes
		be very small.
	2.	Modified Seed PLS procedure "SeedPLS.txt".

Version 4.0512201  December 20, 2005
	1.	Removed behavior input field from "Session Window", 
		because it is more convenient to input behavior data
		at "modify behavior data" menu under "Deselect" menu
		in "Run Analysis Window".
	2.	In E.R.fMRI and Blocked fMRI, "Merge Data" option is
		now moved to the session window.
	3.	If "Within Each Run" is chosen for merging data, same
		condition name in different runs will be treated as
		different conditions. e.g. Run1Cond1, Run2Cond1, etc.
	4.	All existing session file, datamat file, and result 
		file can still be used. However, in order to obtain
		accurate result, any datamat that was created under
		"Within Each Run" choice should be re-created. In 
		addition, all datamats that are used in an analysis
		should have same number of runs, as well as same
		number (and name) of conditions.
	5.	For "Multiple Voxel Extraction" input, the program
		is now also checking XYZ with head dimension, as
		well as checking XYZ with brain area.

Version 4.0511252  November 25, 2005
	1.	Removed "Change Current Working Directory" menu in 
		the start window, since the current directory is now
		changed according to the session file, datamat file,
		or result file you selected.

Version 4.0511211  November 21, 2005
	1.	Random number generator is now seeded before call.
	2.	Fixed a bug to create MRI single subject datamat with
		any scans skipped.
	3.	Added menu bar to the NIFTI/Analyze embeddable viewer
		"view_nii". So this independent package can also have
		features like "orient", "image information" etc.

Version 4.0511161  November 16, 2005
	1.	"PLSgui in batch", an alternative way to run PLSgui,
		is now available. As is explained by its name, 
		"PLSgui" is a Matlab program with a graphic user 
		interface (GUI) driven by messages from mouse and 
		keyboard. "PLSgui in batch" load messages from a 
		batch file, and automatically send them to the
		program in batch. Now, you can fire batchs at the
		end of a day, and the computer will create all 
		datamats one by one and run all analysis for you.
		When you come back next day, the PLS result file(s)
		is ready for you to display.   ( Notes: You MUST
		read all the contents in the "batch_plsgui_hlp.txt"
		file carefully before using this batch feature.
		Otherwise, you will more likely get either error
		messages or wrong data. )

Version 4.0511071  November 7, 2005
	1.	Images whose cardinal planes are slightly off 
		Cartesian coordinates will also be loaded. However, 
		this approximation is based on the following 
		assumption: In affine matrix, any value (absolute) 
		below a tenth of the third largest value (absolute) 
		can be ignored and replaced with 0. In this case, 
		fields 'old_affine' & 'new_affine' will be added 
		into hdr.hist. If you can not accept the above 
		assumption, simply discard any nii structure with
		fields 'old_affine' & 'new_affine'.

Version 4.0510211  October 21, 2005
	1.	ANT's average data (binary) and EGI's simple-binary
		data can now be directly loaded for ERP module.

Version 4.0510072  October 7, 2005
	1.	Like ASCII files without header or with 1 line text 
		header, NeuroScan average data (binary) can now be 
		directly used as subject files to create datamat for
		ERP module.

Version 4.0509271  September 27, 2005
	1.	Added neighbors' XYZ location to the _rf_plot file.

Version 4.0509261  September 26, 2005
	1.	Output standard deviation and "Number of neighbors" to
		the _rf_plot file.
	2.	Display "Number of neighbors" in the RF window.

Version 4.0509221  September 22, 2005
	1.	Added a new feature in "Voxel Intensity Response Plot"
		(for PET, Blocked fMRI), and "Response Function Plot"
		(for E.R.fMRI). Now, people can use average intensity
		of its neighborhood voxels for intensity of the clicked 
		voxel. Neighborhood size is 0 by default (no neighborhood
		voxel is included). If it is not 0, it represents the 
		number of voxels from the clicked voxel. if neighborhood
		voxel is included, the average intensity will include
		those voxels: A) The clicked voxel; B) The "stabled" 
		voxels that meet the bootstrap threshold criteria, if 
		bootstrap result is available; C) The cluster mask of 
		the current view. (Cluster mask of BrainLV View is 
		different from that of Bootstrap View).
	2.	Above feature also applied to "Multiple Voxel Extraction"
		for "Seed PLS". "Voxel Neighborhood Size" dialog box will
		be prompted, and it is also 0 by default.
	3.	Added warning message for users who would like to change
		the default normalization checkbox status.

Version 4.0509151  September 15, 2005
	1.	PLSgui is now support NIFTI data format. This includes
		file extension support for both single file (.nii) and
		dual file (.img/.hdr); temporal dimension support (4th
		dimension in the data); and data value scaling support
		(Y = scl_slope * X + scl_inter). It also support some
		of the sform or qform affine transform. This includes
		any scaling (to get voxel_size), any translation (to get
		originator), any flipping, and a few Rotation (only N*90
		degrees, where N must be integer).

Version 3.0509131  September 13, 2005
	1.	Fixed bugs for the bootstrap of Multiblock PLS.

Version 3.0509121  September 12, 2005
	1.	Add messages to behavior data dismatch dialog box in
		"modify behavior data menu" in "Run PLS" window.

Version 3.0509091  September 9, 2005
	1.	Fixed bootstrap computation for multi-groups.

Version 3.0509081  September 8, 2005
	1.	Fixed display problem for single LV result.
	2.	Fixed correlation computation for multiblock PLS.

Version 3.0508051  August 5, 2005
	1.	Modified "create datamat" routine and single precision
		is used in most steps except calculation.

Version 3.0508021  August 2, 2005
	1.	Modified timestamp check for "run MRI analysis"
		window. Now, user can click "Ignore all" to 
		disregard the fact that "one or more datamat files
		are older than their session files", or click
		"Stop" to re-generate datamat.
	2.	Modified timestamp check for "plot result" window
		for all modules. Now, user can click "Proceed all"
		to disregard the fact that "one or more datamat files
		are newer than their timestamp stored in the result 
		file", and update all timestamp information in result
		file. User can still click "Stop" to re-generate
		result file.
	3.	Fixed a bug in creating ERP datamat, which was
		introduced in on July 28, 2005.

Version 3.0507281  July 28, 2005
	1.	For Multiblock PLS analysis, the conditions for 
		behavior block can now be deselected. It is under
		the "Deselect" menu of the PLS Analysis window,
		and in a dialog box of command-line PLS.
	2.	Fixed the display of Datamat Correlations Plot
		for Event Related fMRI.

Version 3.0507111  July 11, 2005
	1.	Added "Single Subject" option when creating MRI 
		datamat. When this option is selected, each onset
		will be treated as an entry of the datamat. So, the
		numbers of onset must be the same across conditions.

Version 3.0507053  July 5, 2005
	1.	Modified call to Matlab command "uigetfile/uiputfile"
		to make the code competible with Matlab version 7 as
		well as Matlab version 5 & 6. This is because Matlab
		version 7 will automatically append filter suffix to
		the file name even we only need a prefix.
	2.	Removed locations for "uigetfile/uiputfile" dialog
		box. This is because Matlab version 7 changed the
		style dramatically, and it is not competible with 
		earlier version any more. This only affect program
		running on Unix or Linux computers, and the dialog
		box on Unix or Linux computer is always located at
		top left cornor now.
	3.	Fixed a bug for MRI task analysis when people using 
		session file with behavior data.
	4.	If "Save Datamats" is checked when run MRI analysis,
		the st_datamat variable is now saved in group cell.

Version 3.0507042  July 4, 2005
	1.	Changed file name for multiple voxel extraction.
		Since the stacked voxel data file now use the same
		prefix as you entered, it won't get overwritten.
	2.	Updated "SeedPLS.txt" file.

Version 3.0506301  June 30, 2005
	1.	Added Multiblock PLS analysis feature for all the
		modules of PLSgui and PLScmd.
	2.	Reverse Version 3.0504055, so for Blocked fMRI, 
		"Normalize data with ref. scans" is now set back
		to be selected by default. This is because if we
		unselect this option, the brain scores can not 
		be distinguished between conditions.

Version 3.0506161  June 16, 2005
	1.	Removed old submenu "Export data for behav analysis"
		in the brain score and response window. To perform
		SeedPLS, please always extract data from "Multiple
		voxel extraction" submenu, and follow "SeedPLS.txt"
		document.

Version 3.0506141  June 14, 2005
	1.	Modified progress bar, so it potentially could be
		canceled in the middle. (not applied here).
	2.	Modified load_avw, so it speeded up.

Version 3.0506131  June 13, 2005
	1.	Added tooktip for P-Value and Threshold in result
		window.

Version 3.0505191  May 19, 2005
	1.	Fixed a bug in creating cluster report for Sagittal
		View Plot and Coronal View Plot.

Version 3.0505161  May 16, 2005
	1.	Fixed a bug in ERP condition merge.

Version 3.0505041  May 4, 2005
	1.	Fixed a bug in reading certain EEG/ERP file.

Version 3.0504281  April 28, 2005
	1.	Progress bar can now be minimized.

Version 3.0504241  April 24, 2005
	1.	Reversed the previous change back, and disabled the 
		display of Talairach unit. This is because that 
		whether or not to display Talairach unit really 
		depends on how the brain image itself was registered.
		If the brain image was registered in Talairach space,
		the voxel is called Talairach voxel. If the image
		was registered in MNI space, the voxel is called
		volume voxel. Only in the situation when the image
		is registered in one space, and wants to be displayed 
		under a different space, the conversion is required.
		Both tal2mni and mni2tal functions are still included
		in PLSgui package, so people can use them whenever
		there is such needs.
	2.	Modified "Edit Condition" window. Now, if there is a
		valid condition name entered in the condition name
		field, it will be accepted when you click the "Done"
		button, even if the "Add" button was forgot to click.
		In addition, the heading blanks and the tailing
		blanks will be removed from the condition name when
		adding conditions.
	3.	Change label name from "Stim. #1" to "Subj. #1" in
		the response function window for fMRI and ERP.
	4.	By default, "Normalize data with volume mean" will
		not be selected for MRI create datamat window.

Version 3.0504221  April 22, 2005
	1.	When display PET and MRI results, Talairach unit
		can now be displayed and selected besides MNI unit.

Version 3.0504211  April 21, 2005
	1.	Updated FAQ and help file for the multiple-run MRI
		study that do not have all the conditions for every
		runs.

Version 3.0504153  April 15, 2005
	1.	Axis will not be shown when the click of response
		function is anywhere outside the brain.
	2.	Changed EEG read file name.
	3.	Updated 3V files.

Version 3.0504141  April 14, 2005
	1.	Fixed a display bug for response function when the
		first click is anywhere outside the brain.

Version 3.0504132  April 13, 2005
	1.	Fixed a bug for MRI response function when datamats
		have different coords.

Version 3.0504121  April 12, 2005
	1.	Fixed a bug for 3D background image.

Version 3.0504081  April 8, 2005
	1.	Reduced a loop in ERP display routine to improve the
		display speed.

Version 3.0504055  April 5, 2005
	1.	Change label name from "Normalize data with baseline"
		to "Normalize data with ref. scans" for fMRI datamat
		creating window.
	2.	For Blocked fMRI, "Normalize data with ref. scans" is
		now set to "unselect" by default.

Version 3.0504041  April 4, 2005
	1.	Changed AVW file name and updated 3V files.

Version 3.0503301  March 30, 2005
	1.	Changed label name from "Canonical" to "Temporal".

Version 3.0503291  March 29, 2005
	1.	Modified file menu function, so any window can call it
		easily by providing the window's handle. New features
		like copy to clipboard, print preview etc are also
		included.

Version 3.0503171  March 17, 2005
	1.	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' is included to covert the .mat files
		generated from Matlab 7 to be loaded on earlier versions
		of Matlab that are above Matlab 5.

Version 3.0503161  March 16, 2005
	1.	For MRI 'Generate Datamat' window, if behavior data is
		modified, user will be prompted to save data. User can
		choose to save the behavior data or not.

Version 3.0503141  March 14, 2005
	1.	Fixed a bug in MRI result saving, when the result path
		contains empty space.

Version 3.0503092  March 9, 2005
	1.	Fixed a bug to display the skewed result data.
	2.	BrainLV threshold for all modules are now initially set
		to: (abs(max_blv) + abs(min_blv)) / 6.
	3.	Modified cardinal plane view, because most people seems
		like the scroll bar in this new positions.

Version 3.0502181  February 18, 2005
	1.	Fixed a bug in the code that is caused by the precision
		of Matlab, and modified other related files.
	2.	Prestim_baseline in ERP session window will follow the
		digitization interval (if available), and make itself
		evenly dividable by digitization interval.

Version 3.0502011  February 1, 2005
	1.	The "percentage of minimum different subject number" 
		dialog box is moved before permutation loop starts.

Version 3.0501311  January 31, 2005
	1.	Fixed a frozen bug in boot_order function.

Version 3.0501181  January 18, 2005
	1.	Original un-resampled order (sequential index of stacked
		datamat) should never be included in perm_order, because
		we only compare permutation result other than the original
		pattern.
	2.	For boot_order, because all analysis have already been 
		included in the accumulation, except "mean-centering",
		the Original un-resampled order (sequential index of 
		stacked datamat) should not be included in the boot_order
		except for "mean-centering".
	3.	Add one more input parameter for "rri_boot_order", so now: