Version 6.15 July 06, 2015 1. New: When split-half resampling was enabled, the incorrect permutation test was called for the overall assessment of significance. This has been fixed. This bug does not affect permutation tests done without split-half resampling. Version 6.14 December 9, 2014 1. New: Fixed bug in using the wrong mean-centering approach for confidence interval estimate for non-rotated PLS scores. Version 6.1311050 November 5, 2013 1. New: computation change for "Single Condition Task PLS". Therefore, please run such analysis again with this latest version of PLS applications. 2. Fix: crash when you have more numbers of bootstrap than what is limited by numbers of subject. Version 6.1306040 June 4, 2013 1. New: add "Use segment data" checkbox under Structural PLS analysis window. By default, it is selected (i.e. assuming that you are using segment data). If you are not using segment data, you should deselect it. 2. New: change label by replace ucorr_prob & vcorr_prob with p_braincorr & p_designcorr. Version 6.1305080 May 8, 2013 1. New: plscmd_cluster_report.m is provided to get cluster information for command line PLS application (i.e. pls_analysis.m under plscmd folder). The result is not viewable by GUI application. If you have PLS result file from GUI application (i.e. *result.mat), you should use GUI, or create_cluster_report.m to create cluster report, which can be viewed under GUI, or view_cluster_report.m. Version 6.1305010 May 1, 2013 1. Fix: missing menus are added for multiblock PLS. Version 6.1304190 April 19, 2013 1. New: ucorr_prob and vcorr_probs from splithalf test are displayed in "Design LV and Design scores Plot". 2. New: bootstrap type feature is temporarily disabled. 3. Fix: bug crashs single subject result. 4. New: User Guide for PLS Applications is modified. http://research.baycrest.org/pls/UserGuide.htm Version 6.1304020 April 2, 2013 1. Fix: bug in single condition Mean-Centering PLS. Version 6.1303150 March 15, 2013 1. Fix: bug in 'session2sessiondata' when run it from different folder. Version 6.1303010 March 1, 2013 1. New: An upgrade of PLS applications has been done on 29-OCT-2012. For certain reasons, we did not release that new version until now. Therefore, I would like to repeat some of the whatsnew contents that have been listed under Version 6.1210291 below. 2. New: Since PLS user interface will use Command-Line PLS to run all PLS analysis, folder plsgui and plscmd must be kept under the same parent folder, and their folder names (i.e. plsgui and plscmd) can not be changed. 3. New: session.mat / datamat.mat files are now combined to a single sessiondata.mat file. To provide seamless upgrade, a new program "session2sessiondata.m" is included. You can run this program to convert old session / datamat files to new sessiondata file, either for a single session or for entire folder. For more information, please type: help session2sessiondata 4. New: Command-Line PLS will take optional argument for other parameters like num_permutation etc. For more detail, please type: help pls_analysis Version 6.1302280 February 28, 2013 1. New: When some conditions of behavior measures are not available in behavior block of Multiblock PLS, the brain data of those unavailable conditions will be included in permutation loop. 2. New: "nonstrat" boot type is purely experimental, do not select it unless you have good reason. Version 6.1302200 February 20, 2013 1. New: Brain data, not behavior data, is resampled for splithalf permutation. 2. New: Non-Rotated PLS is changed back to old way (i.e. to use un-normalized salience) for conventional bootstrap in order to avoid bootstrap ratio scaling problem. Version 6.1301160 January 16, 2013 1. Fix: Result window for correlation plot crash problem for certain skewed data. Version 6.1301040 January 4, 2013 1. New: The electrode channel layout of MEG CTF-150 is modified. Version 6.1212310 December 31, 2012 1. New: "non-rotated bootstrap" and "splithalf permutation" is linked, and "non-rotated bootstrap" selection is removed. Version 6.1212060 December 6, 2012 1. New: If Number of Permutation Split is greater than 0, ucorr_prob_LV & vcorr_prob_LV will be displayed in Permuted Singlar Values window. 2. Fix: A bug in new code (never published) to generate bootstrap sample for method 3 & 5. Version 6.1211270 November 27, 2012 1. Fix: Possible inverse zoom problem after Matlab 7.4. Version 6.1211200 November 20, 2012 1. New: Removed unused fields compare_v, v_se, and zero_v_se from boot_result. Version 6.1211140 November 14, 2012 1. Fix: Within "parfor-loop", the figure command does not work properly. So I have to use command window display, rather than progress bar figure, to show the steps of splithalf permutation. Version 6.1211130 November 13, 2012 1. Fix: Checked and made sure location inputs for text() command are in double; otherwise MATLAB may crash. Version 6.1211120 November 12, 2012 1. New: If there are session / datamat files in current folder, but there is no sessiondata file, it indicates that this is probably an old PLS user, who is not aware that the session / datamat files need to be combined to sessiondata file. New plsgui & batch_plsgui will show prompt message, if this user is trying to run analysis or edit session profile. 2. New: After PLS detects the availability of parallel setting, now it will further detects whether matlabpool is open. Only when matlabpool is open (i.e. the size of pool is greater than 0), the "parfor-loop" will be selected in splithalf permutation block. Otherwise, regular "for-loop" will always be selected. Version 6.1211010 November 1, 2012 1. New: Program "session2sessiondata.m" can be applied on both old session filename or session folder. For example: session2sessiondata('.') will convert all the old session / datamat files in the current folder to new sessiondata files. Note: old session / datamat files will NOT be removed or modified. 2. Fix: Bug in splithalf_perm_par function. Version 6.1210290 October 29, 2012 1. New: Since PLSgui will use Command-Line PLS to run all PLS analysis computations, folder plsgui and folder plscmd must be kept under the same parent folder. 2. New: session.mat / datamat.mat files are now combined to a single sessiondata.mat file. To provide seamless upgrade, a new program "session2sessiondata.m" is included in PLSgui. You can run this program to convert old session / datamat to new sessiondata. For more information, please type help session2sessiondata 3. New: Command-Line PLS will take optional argument for other parameters like num_permutation etc. Please type help pls_analysis for more detail. 4. New: Natasa's features are included, which includes: splithalf permutation, nonstrat bootstrap, non-rotated bootstrap, non-rotated multiblock PLS, parallel option, mean-centering type, correlation mode. 5. New: Command-Line cluster report programs are available to create and view cluster report for both old and new version of PLSgui result file. Version 5.1209101 September 10, 2012 1. New: Will check percentage of brain region in image volume before creating Structural datamat. If the mask is larger than 25% of the volume, the program will ask user whether to proceed or to stop and check brain mask file. Version 5.1206281 June 28, 2012 1. Fix: Disabled false alarm about 64-bit single precision between MATLAB version 7.10 and 7.39. Version 5.1110251 October 25, 2011 1. Fix: Structural label feature is now available even there is no bootstrap test in result file. Version 5.1110202 October 20, 2011 1. New: If the dimension of raw imaging data is 41x48x35, "View 41x48x35 Structural Label" menu is added under "View" menu for fMRI result window; otherwise, if the dimension of raw imaging data is not 41x48x35, you won't see this menu. When this menu is checked, the label of structural map will be displayed on top of BLV or BSR area. Version 5.1109191 September 19, 2011 1. New: Duration lenth can be entered for "Use HRF" feature under "Blocked fMRI" session window. By default, it is set to 0, which is for event-related response. For epoch-related response, you need to set the duration. 2. New: In Generate Datamat window, now we have HRF1 and HRF2. In HRF1, TR will be further divided into smaller bin when calculating design matrix, and the default HRF is SPM HRF. In HRF2, TR is always the smallest unit when calculating design matrix, and the default HRF is GAMMA function from AFNI's HRF. 3. New: "Degree of Legendre Polynomials for regressors" field is added. By default, it is 0, which provides a single column of all ones. This is also a feature from AFNI's HRF. 4. PLS User Guide is also updated: http://www.rotman-baycrest.on.ca/pls/UserGuide.htm Version 5.1105181 May 18, 2011 1. Fix: Write permission will be checked before starting PLS analysis. Version 5.1105121 May 12, 2011 1. Add in FAQ: When "Use HRF" is selected, the order of slice must be sequential and ascending if you are trying to use decimal number in "onsets" field. 2. Add in FAQ: Get some value from "*result.mat" in MATLAB command window. Version 5.1105052 May 5, 2011 1. Fix: "Run Info" window crash. 2. Fix: "HRF over run" window cannot bring to the front. 3. Fix: "HRF over run" window display error for skipped scan. 4. Fix: Message of "out of bound" scans for HRF fMRI. Version 5.1105021 May 2, 2011 1. "Use HRF" selection box is available in Blocked fMRI session profile window. This feature is actually designed for Event Related fMRI. Since most of the user interfaces are compatible with Blocked fMRI, I have to build it on Blocked fMRI platform. 2. By default, SPM's HRF model is used. However, you can also design your own HRF model by clicking "Customize HRF" button. You can either type 1-D vector in the "Data:" field, or write your 1-D vector (all numbers) in a text file and then load this text file. You can also plot the convolved HRF by clicking "Plot Regressors" button. 3. When you use HRF feature, there is no more necessary to do "Normalize data with ref. scans", since the low frequency drift is removed by SPM High Pass filter. There is a selection box called "Use SPM ReML" in "Create Datamat" window. If this box is selected (by default), the voxel outlier over the run will also be removed. 4. While developing the "Use HRF" feature, I noticed some buggy functions, and they have been taken cared in the following manner: "Number of scans to be skipped" field is moved to the "Edit Runs" window. "Run to be included" field is removed. If you want to exclude the run, simply open "Edit Runs" window, go to the run that you need to delete, and click Edit->Delete. "Slice to be ignored" field is also removed. We can pre-process the raw image to remove those slices. Version 5.1102241 February 24, 2011 1. Use 'round' instead of 'floor' to round the decimal in fMRI onset time. Version 5.1102041 February 4, 2011 1. Fixed a bug when loading a quaternion form NIfTI data. Version 5.1102011 February 1, 2011 1. Fixed bugs in "Task PLS Brain Scores with CI" window for Multiblock PLS. The analysis will need to be re-run in order to see the fix. 2. Added a function (dset2img.m) to create a simulated 4D NIfTI image and a corresponding brain region mask from a SUMA's 1D.dset file in order to run PLS. 3. Added a function (plsgui2dset.m) to extract BrainLV / BSRatio from PLS result to SUMA's 1D.dset files in order to visualize the BrainLV result and BSRatio result from SUMA. 4. Added a function (fmri2dset.m) to extract fMRI datamat to a SUMA's 1D.dset file for special SUMA processing. 5. Added a function (dset2fmri.m) to update fMRI datamat with the SUMA processed 1D.dset file. Version 5.1007191 July 19, 2010 1. Added "Load from Batch" button in PLS analysis window. Version 5.1004262 April 26, 2010 1. Added "Subject Amplitude for Given Timepoints" item under "View" menu of ERP salience plot. This item will bring a "Plot Detail" like window, which allows you to plot the response of datamat value, and extract multiple time points of the datamat value. Version 5.1003291 March 29, 2010 1. Reversed the feature of checking timestamp in the result file. Because it brings too many troubles, the program will no longer warn you if you forget to re-run the PLS after modifying the datamat. It will be users' responsibility to re-run the PLS whenever a datamat is changed. Version 5.1003081 March 8, 2010 1. Added options for normalizing volume mean when using batch file to create datamat. Version 5.1002191 February 19, 2010 1. Fixed a bug of false alarm for duplicated bootstrap order. Version 5.0912111 December 11, 2009 1. Fixed a bug when reading a volume from 4D Analyze data. Version 5.0912081 December 8, 2009 1. Add data check when using batch to create datamat. Version 5.0912072 December 7, 2009 1. Since MATLAB allows less amount of data to be saved by using '-append' switch than without using '-append' switch, '-append' switch has been take away when saving result files. However, the saving time will be a longer. So, the "Save GUI Position" & "Save Display Setting" under "Tools" menu of the first window is also taken away. 2. Fixed a scroll bar bug. Version 5.0912011 December 1, 2009 1. Fixed a bug for Brain Score Plot crash when some subjects are deselected in Structural PLS. Version 5.0910261 October 26, 2009 1. Thanks to the feedback from Yunjo, and the recursion limits is set to 100 for cluster report creating. On telesto computer that I tested today, RecursionLimit is set to 100 by default for all MATLAB versions lower than MATLAB 7.6 (R2008a), and it is set to 500 by default for MATLAB 7.6 & 7.8. However, with higher recursion limits, 2 or more different clusters are combined together unnecessary. This problem is solved when RecursionLimit is set to 100 just for PLS. Version 5.0910111 October 11, 2009 1. Fixed a bug in MRI behavior & multiblock PLS. Version 5.0910022 October 2, 2009 1. Value of confidence level that is input by users for bootstrap test is now saved in result file under boot_result.Clim. 2. Fixed several bugs that cause crash when displaying result file. Version 5.0909171 September 17, 2009 1. Single subject analysis with different number of onsets among conditions can also be analyzed. Version 5.0908261 August 26, 2009 1. Added "Task PLS Brain Scores with CI" feature for Multiblock PLS analysis and its result window. Like the one in Mean-Centering & Non-Rotate PLS, you must run bootstrap test in order to get this feature. Version 5.0908231 August 23, 2009 1. Fixed a progress bar bug, which cause crash. Version 5.0908141 August 14, 2009 1. Fixed a bug in using "RandStream" function, which cause crash. Version 5.0908041 August 4, 2009 1. Fixed a bug in selecting Cluster Report Options, which does not allow any selection in some cases. Version 5.0907231 July 23, 2009 1. Using "RandStream" instead of "rand('state')" to control the state of MATLAB random functions in MATLAB 7.8 (R2009a) and above. Version 5.0907221 July 22, 2009 1. Voxel with NAN value will be marked as non-brain area. Version 5.0907171 July 17, 2009 1. Fixed ERP plot detail window crash problem for new version of MATLAB. Version 5.0907162 July 16, 2009 1. Added file format field in ERP session window, so some data like ANT, NeuroScan, can be properly extracted. Version 5.0907141 July 14, 2009 1. Fixed a bug to select a file name in subject select window. Version 5.0907131 July 13, 2009 1. If you are using MATLAB 7.4 (R2007a) and above, the warning message for MATLAB Bug Report ID 268001 regarding to the single precision computation on 64-bit Intel based system is now removed. Version 5.0906092 June 9, 2009 1. Program "flip_plsgui.m" is created and only served as a remedy for those who missed orientation check during datamat creation. Before a datamat is created, please always remember to use the existing "Check Image Orientation" button in "Create Datamat" window of "plsgui" program to do the flipping. If you are using "batch_plsgui" program, you can flip raw images using "flip_lr.m" program. This program is in the same folder as "batch_plsgui" and "plsgui" program. By the way, "flip_lr.m" will save image in NIfTI format. Version 5.0905112 May 11, 2009 1. Added a new feature under "Tool" menu of ERP display window to export the plotted wave data and the time information inside the window that is clicked. 2. Fixed a bug in displaying Condition Average and Condition Difference for ERP module. Version 5.0904241 April 24, 2009 1. For Task PLS bootstrap test, variable 'b_scores2' (or 'brainscores2') is saved under 'boot_result' structure. This Brain Score 2 here is created with mean-centered datamat, which is used in the "Task PLS Brain (or Scalp) Scores with CI" feature. 2. Command line program "batch_alter_fmri_onset.m" is created to alter the onset values in type one batch script for creating fMRI session/datamat files. Version 5.0903041 March 4, 2009 1. When you display result file, missing datamat or session file will now be prompted. Version 5.0902131 February 13, 2009 1. Data exported from Voxel Intensity Plot window now contains 'data_mean' variable, which stands for the the mean values numbers that are displayed in the Voxel Intensity Plot window. Version 5.0901211 January 21, 2009 1. Fixed a bug in "Datamat Correlations Plot" window to display result without bootstrap. Version 5.0901071 January 7, 2009 1. Add "Multiple Corrs Extraction" in PET Behavior result window to extract multiple correlation values. Version 5.0811121 November 12, 2008 1. Fixed the problem of "Datamat Correlations Plot" crash on new version of MATLAB. 2. Fixed "Datamat Correlations Response" data export error for PET & Structural modules when 2 groups of datamat have different masks. Version 5.0810231 October 23, 2008 1. Fixed problem to list a single file in old MATLAB. Version 5.0809051 September 5, 2008 1. Keyword "intel_system" can be added into PLS analysis batch text file. By default, it is set to 1. If you are sure that you are using 64-bit non-Intel system with Matlab 7 and above, you can set it to 0 to allow single precision math computation. Version 5.0808261 August 26, 2008 1. Fixed a bug when condition(s) are removed from MRI session file. Those modified session file will make PLS analysis crash. In that case, you can apply a patch to those session file before re-run analysis. Here is an example of how to apply the patch: mri_session_patch('a_BfMRIsession.mat'); or mri_session_patch('b_fMRIsession.mat'); 2. Absolute value is used for elements inside function of square root to prevent complex number. 3. When clicking "Save Current Display" in File menu of the result display window, the colormap is now saved to a MATLAB file that is ended with "_cmap.mat". 4. "reslice_nii.m" is provided to preprocess the NIfTI format image file that containing non-orthogonal or oblique affine transform. Version 5.0807231 July 23, 2008 1. Changed "Reference Scan Onset" label under MRI "Edit Condition" window to "Relative Ref. Scan Onset" to prevent users from using absolute scan onset. 2. Updated PLS User Guide with the changes. Version 5.0807161 July 16, 2008 1. Added "Single reference scan" feature in creating MRI datamat window. 2. Added "Peak threshold" feature in Cluster report options window. Version 5.0807091 July 9, 2008 1. Modified both computation and display routine of the "Brain (or Scalp) Scores Plot for Task PLS" feature, and renamed it to "Task PLS Brain (or Scalp) Scores with CI". The menu item only available for Mean- Centering PLS and Non-Rotated Task PLS with more than one bootstrap tests. 2. Since the computation is changed, you will be prompted to re-run PLS with this modified program. Version 5.0806111 June 11, 2008 1. Fixed a bug in non-rotated PLS. Version 5.0806031 June 3, 2008 1. Added Non-Rotated Behav PLS analysis feature for all the modules of PLSgui and PLScmd. 2. Added "Brain (or Scalp) Scores Plot for Task PLS" for all the modules of PLSgui. If there are Bootstrap test loops, the distribution of usc (Brain or Scalp Scores) are also computed for both PLSgui and PLScmd. 3. Like other modules in PLSgui, now ERP module also splits its Threshold field in BootStrap Option wildow into two field - Pos.Thresh and Neg.Thresh. 4. Removed "Using Helmert Matrix" menu selection from the contrast window. 5. Created last good files folder that can be accessed from: http://www.rotman-baycrest.on.ca/pls/source/lastgood or /b/jimmy/plsgui/lastgood & /b/jimmy/plscmd/lastgood on Rotman cluster servers. Version 5.0804282 April 28, 2008 1. More changes in generating cluster report. First, undo the change I did on April 25, 2008. Actually, there is no skipped clusters. According to the comments of the original author of this cluster report program, when a cluster found later can be joined to the cluster found earlier, they should be combined together. According to the comments, the reason that the program can not find all active voxels in the earlier cluster at once is due to the recursion limit of MATLAB. Second, there is a bug in the original cluster report program, which lost some found active voxels in the clusters (because of the combination). Now this problem has been fixed. I still have to let you know that due to the recursion limit, you may not be able to find all active voxels in a cluster, or one cluster is divided to several clusters, etc. I have updated PLS User's Guide and FAQ, which will provide you more details. Version 5.0804251 April 25, 2008 1. Fixed a bug in generating cluster report, which skipped some clusters. Version 5.0803181 March 18, 2008 1. Cluster with minimum cluster size in "Set Cluster Report Options" window is included. i.e. If "Minimum cluster size" is equal to 5, a cluster with 5 voxels is now counted. Version 5.0802271 February 27, 2008 1. Fixed a bug that causes crash when changing to other view from Axial view in fMRI Bootstrap Ratio window. Version 5.0802221 February 22, 2008 1. Implemented the workaround for "persistent" variable that is provided by Matlab Tech Support, which can prevent from using global variable as a replacement for MATLAB 7.2. Version 5.0802011 February 1, 2008 1. Instead of throwing an error for a very oblique image, now only a warning message will be displayed. Version 5.0801211 January 21, 2008 1. When the "Filter" of simplified UIGETFILE/UIPUTFILE is not using wildcard (* or ?), its "File Name" field is now filled. Version 5.0801031 January 3, 2008 1. Added "EGI128_v2" electrode system for ERP module. Version 5.0712061 December 6, 2007 1. Last change for creating MRI datamat with onset marked -1 still having problem with certain data. It is now fixed. Version 5.0711221 November 22, 2007 1. Modified simplified version of UIGETFILE/UIPUTFILE so it will now take directory name from the input filter pattern and the File Name field. Version 5.0711211 November 21, 2007 1. Filter in simplified version of UIGETFILE/UIPUTFILE is now working on new version of MATLAB. Version 5.0711203 November 20, 2007 1. Fixed a problem to load datamat file for analysis in the simplified version of UIGETFILE/UIPUTFILE window. 2. Made simplified version of UIGETFILE/UIPUTFILE work on directory and filter. Version 5.0711161 November 16, 2007 1. Modified Threshold field on the Result display window of PET, Structure & MRI module. Now two different thresholds (Pos / Neg Thresh) are set up, and it is only for the situation where the distribution of data is extremely biased. Therefore, it is still suggested to use symmetric threshold, and it is not recommended to modify the threshold arbitrarily, unless you know what you are doing. Version 5.0711132 November 13, 2007 1. Fixed a bug when displaying Structural PLS data in a different path. Version 5.0711121 November 12, 2007 1. Fixed the bug when creating MRI datamat with certain onset marked -1. For those existing (already created) datamats, a patch needs to be applied before re-run analysis. Here is an example of how to apply patch: mri_datamat_patch('a_BfMRIdatamat.mat'); or mri_datamat_patch('b_fMRIdatamat.mat'); To create a new MRI datamat, you don't need patch. Version 5.0711061 November 6, 2007 1. Fixed a bug in task PLS analysis with single subject data. Version 5.0711051 November 5, 2007 1. MATLAB changed their UIGETFILE & UIPUTFILE, which causes some of the old scripts no longer to be able to run on some platform with new version of MATLAB (version 7 and above). Therefore, I have to built a simplified vesion to workaround this issue. Version 5.0710161 October 16, 2007 1. Fixed a bug when using Matlab Version 7.4.0 to build Structural module session file. Version 5.0710091 October 9, 2007 1. Bootstrap input dialog box in plscmd is replaced by input text string as requested. Version 5.0709121 September 12, 2007 1. Fixed a bug to create datamat for single slice Structural MRI data. Version 5.0705021 May 8, 2007 1. Command-line PLS help information is included in the Appendix of PLS User's Guide. Version 5.0705021 May 2, 2007 1. Modified "load_ant.m" based on the changed .avr file information provided by ANT staff. So now PLS can load ANT's average binary data format again. Please see detail in: http://www.rotman-baycrest.on.ca/pls/FAQ.txt Version 5.0704241 April 24, 2007 1. A rounding issue in the code caused multiple voxel extraction routine to fail in some situations. This problem is fixed now. Version 5.0704231 April 23, 2007 1. Stop supporting ANT average binary data format. 2. Start supporting users' own scalp electrode system. 3. Updated http://www.rotman-baycrest.on.ca/pls/FAQ.txt and http://www.rotman-baycrest.on.ca/pls/UserGuide.htm Version 5.0704201 April 20, 2007 1. Fixed the display of CTF150 location for ERP module. 2. Jordan Poppenk found that the voxel value can be negative, if a brain mask is used. So the previous restriction is remvoed from FAQ file. 3. "load_nii" will automatically load SPM affine matrix M in .mat file, if it detects that the file name is the same as the Analyze file. Version 5.0704091 April 9, 2007 1. Modified normalize.m and add load_acq.m. Version 5.0703272 March 27, 2007 1. Fixed a bug for the wrong scaling dispay in the Subject and Average Amplitude window in the ERP module, which was introduced from on March 9 from version 5.0703091. Version 5.0703221 March 22, 2007 1. Fixed a bug in saving data to a text file. Version 5.0703191 March 19, 2007 1. Fixed a bug in exporting cluster report all location. Version 5.0703151 March 15, 2007 1. Fixed a bug in bootstrap test for Multiblock PLS. Version 5.0703091 March 9, 2007 1. The display of "Design LV and Design Scores" window in other module follows the way that is already in place for E.R.fMRI. i.e. all the groups will display together in the same window. 2. The subject name in all MRI module is now using the datamat prefix name defined in its session file. 3. "Scale by Singular Value" button is added in all result display window. It is the same button called "Rescale" previously only for PET and Structural. 4. The "Voxel Intensity Response" window will get the same axis for all the groups. However, if you first click a new group that exceeds the min/max of currnet value, the axis will still adjust to the new min/max. If you click back, the axis will stay unchanged. 5. Added a "Create Batch File" button in the "Run PLS Analysis" window. So people can using this created plain text file (batch file) to feed "batch_plsgui" program. We may also do some test with an external program that is compiled in C language, and it will also use the same batch text file to read MATLAB files (Session / Datamat file) and write a MATLAB file (Result file). but it is not available yet. 6. Updated PLS User's Guide. Version 5.0703011 March 1, 2007 1. Prompt user to delete some subjects in Structural session information window when there is too much data to process. Version 5.0702261 February 26, 2007 1. Mofified User's Guide. 2. Fixed false warning when there is no match subject files. Version 5.0702221 February 22, 2007 1. Used different way to check low variability of behavior data for bootstrap test. Version 5.0702212 February 21, 2007 1. "num_LowVariability_behav_boots" field is added to the "boot_result" struct for the bootstrap test containing behavior data. In the case that behavior data does not have enough variance the following warning message will also be displayed in the command window: "For at least one behavior measure, the minimum unique values of resampled behavdata doesnot exceed 50% of its total". 2. Fixed display problem for the plot with special character in subject name or condition name. The program now can accept special character (e.g. underscore "_"). 3. Removed "Merge Conditions" button for Structural PLS. Version 5.0702161 February 16, 2007 1. Fixed a bug in bootstrap test in handling bad behavior data. 2. MATLAB 7 has a little difference in handling "uiputfile" in that it will include the wildcard string PLS program provided. This problem has been solved. 3. Made a workaround for single condition Mean-Centering PLS. 4. Structural MRI module is implemented. Version 5.0702061 February 6, 2007 1. Fixed a bug in permutation test of Non-Rotated PLS for MRI modules. 2. Fixed a dialog box error message asking about default button. 3. In datamat correlation window for behavior PLS result, the "Save ... to IMG file" will now apply the bootstrap mask that filters out the unreliable voxels. Version 5.0701151 January 15, 2007 1. Fixed a bug in detecting group contrast rank deficiency. Version 5.0701101 January 10, 2007 1. When exporting all locations of cluster report, values (BrainLV or BSRatio) for the corresponding voxels are also exported into "*_MODULEcluster_num.txt". The first column of this file is still Cluster ID#; the second column of this file is now the corresponding BrainLV or BSRatio value; the last 3 columns are still XYZ locations. Version 5.0701032 January 3, 2007 1. Integrated single precision math operation feature of MATLAB 7 (R14) above into the PET & MRI modules of the program. If MATLAB is running on 64-bit system, a dialog box will be popped out to ask user for the system's processor. If the answer is "Don't know" or "Intel processor", double precision will be used according to MATLAB Bug Report ID 268001. (If you are using RRI Linux cluster, "telesto" is the only 64-bit system that has non-Intel processor, which supports single precision math operation). 2. Removed unnecessary rounding (ceil) for the bootstrap test of behavior PLS analysis, which caused inaccuracy when number of bootstrap is small. "zero_brain_se" is also added in "boot_result", which represents the index of those brain_se with zero standard error. Version 5.0612081 December 8, 2006 1. Neuroscan version 4.3 also has 32-bit acquisition for its continuous data files. By default, it collects 16-bit integer data with the original SynAmp (SynAmp1). With SynAmp2, it will collect 32-bit integer data. According to Neuroscan tech support, "this file format must be determined prior to reading the file, i.e. there is no flag within the file itself to identify a file as 32-bit". In order to read 32-bit data format, optional input "fileformat" of "load_neuroscan.m" function must be specified to 'cnt32'. For example, you can load data using: ns = load_neuroscan('myfile.cnt', 'cnt32'); Type "help load_neuroscan" for the usage of "fileformat". Because now the continuous data file can be very large, you can specify cnt_start_time and cnt_end_time. Their units are "second". For example, if you only want to extract data from 0 second to 1.998 second, you can type: ns = load_neuroscan('myfile.cnt', 'cnt', '', 0, 1.998); The actual rounded start_time and end_time will be displayed in ns.start_time and ns.end_time. Version 5.0612051 December 5, 2006 1. Added "behavior_name" field for the "analysis batch file" processing program. Demo "analysis batch file" are: batch_pet_analysis.txt, batch_erp_analysis.txt, batch_bfm_analysis.txt, and batch_fmri_analysis.txt. Version 5.0611021 November 2, 2006 1. Fixed a bug when brain mask only contains 1 slice. Version 5.0609251 September 25, 2006 1. Both EGI 128-Channel and EGI 256-Channel are provided along with BESA and CTF-150. 2. Script "erp_single_folder" is included in PLS for a special reason, and we do not recommand normal user to use this script. 3. Added "mat_into_hdr.m" script to convert SPM ANALYZE Reoriented image file into NIfTI format and integrate its matlab file into its header file. Version 5.0609151 September 15, 2006 1. We decided to use XYZmm, voxel location with unit in millimeter, for the entries of Multiple Voxel Extraction" voxel location text file. In earlier version, we were using XYZ, absolute voxel location, for the entries of voxel location file. In order to convert your absolute voxel location file to voxel location with unit in millimeter, we provided a handy script called "xyz2xyzmm.m". 2. Both "Peak Locations" and "All Locations" that are exported from "File" menu in "Cluster Report" window are also changed to voxel location with unit in millimeter. This way, people perform "Seed PLS" do not have to to any extra conversion. 3. "Posthoc Data" button in "PLS Analysis" window is now removed. 4. Since new BESA file can have more than 1 header lines, ERP code is modified to accommodate this change. That means, ERP module can load BESA file with no header, or with any amount of headerlines, as well as binary files like NeuroScan, ANT, or EGI. Version 4.0609071 September 7, 2006 1. A bug was introduced during last change (Version 4.0608291), in which the neighborhood voxels were not exported without averaging together. Since last change only applied on MRI "Multiple Voxel Extraction", only MRI module was affected. It is now fixed. 2. In Matlab 2006a, the bootstrap test sometimes giving you a feeling of "frozen". This is caused by the bootstrap progress bar sometimes conflict with the permutation progress bar. I have also fixed this. Version 4.0608291 August 29, 2006 1. Modified "Multiple Voxel Extraction" part of the program for MRI module, so it will consume less memory. The result remains the same as the earlier version. Version 4.0608111 August 11, 2006 1. The message of "Duplicate bootstrap order" was not popped out, and it is now fixed. Version 4.0608091 August 9, 2006 1. When exporting all locations of cluster report, a new file that is named "*_MODULEcluster_num.txt" will be created at the same time as "*_MODULEcluster_all.txt" file. In this new file, a column with cluster # is added in front of XYZ locations to indicate which cluster each exported voxel belongs to. Version 4.0608021 August 2, 2006 1. Provided a workaround for "persistent" variable issue in Matlab R2006a (a Matlab bug). Version 4.0607111 July 11, 2006 1. Fixed a bug when moving existing session file while the sub-folders also needs to be changed. Version 4.0606231 June 23, 2006 1. "expand_nii_scan.m" is modified so the expanded image volume scan files will be appended with a 4-digit number starting from 0000. Version 4.0606201 June 20, 2006 1. The original display routine assumed the result data have both positive and negative values, and it crashed otherwise. Now the problem is fixed, and it can display all positive (or all negative) data. Version 4.0606091 June 9, 2006 1. Cluster sizes were over counted during combination. It is fixed now. Version 4.0606061 June 6, 2006 1. Program "m2hdr.m" is created to integrate affine matrix generated from old SPM into NIfTI *.hdr file. 2. There was a bug in converting some permuted images to RAS orientation. It has been fixed now. Version 4.0606011 June 1, 2006 1. There is a bug (crash) in fMRI non-rotate, if just doing bootstrap test. It is fixed. Version 4.0605261 May 26, 2006 1. Modified cluster report "Export All Location" menu, and now the voxel is in the order of clusters. If you have two clusters, one with 30 voxels, and the other one with 20 voxels, the first 30 lines correspond to cluster one and the second one correspond to cluster two. If you have saved "*cluster.mat" from previous version, you have to re-generate it before exporting all locations. Version 4.0605111 May 11, 2006 1. When clicking "Save Current Display to IMG file", or "Save BLV/BSR result to IMG file" under "File" menu, those img/hdr files can be saved in a directory that is different from result file directory. Version 4.0604261 April 26, 2006 1. When editing existing fMRI session file, existing conditions were protected to prevent being modified. Now, the protection is removed. Version 4.0604201 April 20, 2006 1. Size of some image data is incorrectly larger than what specified in "hdr.dime.dim" field. So it caused problem to load image data. Image data is now always loaded according to the size that is specified in its header. 2. When editing existing fMRI session file, the "DELETE" buttons in "Edit Condition" window is now enabled. Version 4.0603211 March 21, 2006 1. Tools for NIFTI image now supports both COMPLEX64 and COMPLEX128 data type. Version 4.0603192 March 19, 2006 1. "UserGuide.htm" file is included in the package to replace the old out-of-dated "*_hlp.txt" files. The entire PLS User's Guide is still under processing. Version 4.0603062 March 6, 2006 1. Modified "Export Data" for fMRI "Response Function Plot" and "Temporal Brain Scores Plot". The "st_evt_list" in the exported file is always sorted as condition-within- subjects, so as the "data" variable. 2. Added "data_mean" variable to the above exported MATLAB data file. Rows of "data_mean" stand for conditions, and subjects for each condition are averaged together. Version 4.0602241 February 24, 2006 1. When loading some NIFTI data, there is an ordering problem in "hdr.dime.pixdim" and "hdr.hist.originator" fields. It is now fixed. Version 4.0602231 February 23, 2006 1. Modified NIFTI package to tell if the loaded NIFTI data is converted to RAS system. (see detail in FAQ.txt) Version 4.0602072 February 7, 2006 1. Removed unused "Group Analysis" check box from E.R.fMRI and Blocked fMRI analysis window. 2. Made fields in PET and ERP session window look even, because behavior data fields were removed from session window on version 4.0512201. 3. Moved "Load Behavior Data" to a button in PLS option frame, which looks better. Version 4.0601271 January 27, 2006 1. "Load Onsets from a text file for this run" and "Save Onsets to a text file for this run" submenu is added under "Edit" menu in both E.R fMRI & Blocked fMRI "Run Information" window. 2. When "DONE" button in above window is clicked, "Data Directory", and "Data Files" for all the runs will be checked, to make sure they are all filled. 3. Check session information further before creating MRI datamat. 4. When adding more subjects for PET and ERP module, the program will not always start from the working directory. Instead, it will remember parent directory of the first subject, and start to look for more subject directories from there. Version 4.0601251 January 25, 2006 1. Change "Save Background Image" label in result window to "Save brain region to IMG file". 2. When display activation map, changed inaccurate display 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 PLS, 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. PLS 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 PLS 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: 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 October 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 October 20, 2004 1. Removed (uV) sign from the legend axis for ERP Electrode Salience window. Version 3.0410151 October 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 October 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 PLS 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 Voxel Extraction will now only export the data in the corresponding lag number. 3. SeedPLS document modified because of above change. Version 2.402021 February 2, 2004 1. Updated MRI datamat creation help file. 2. Program can now set current location based on value in 'Current location (/ Current lag)' field(s) under 'Set cluster report options' submenu under 'Report' menu. The result is the same as clicking the specific location. Version 2.401281 January 28, 2004 1. When saving cluster report, if the suffix is not entered, program will now automatically add one. 2. When loading cluster report, it looks for proper suffix now. 3. Changed the representation of cluster mask. Instead of putting a marker on voxel, now it only displays the clustered voxels. 4. All parameters in the create datamat window are now stored in a structure named 'create_datamat_info'. Version 2.401191 January 19, 2004 1. Added HRF Plots in MRI Run information window. 2. Created help file for this plot. 3. Added 'Save Figure' in File menu for several windows. Version 2.401131 January 13, 2004 1. fMRI canonical brain scores can be exported out. Version 2.401091 January 9, 2004 1. In result window, 'Cluster Mask' submenu has been added under the Report menu. 2. Added instruction into help files. Version 2.401051 January 5, 2004 1. In Cluster Report window, 'Export All Locations' item has been added under the File menu. Version 2.312231 December 23, 2003 1. For fMRI Response Functions Plot and Canonical Scores Plot, the Average plots is now scaled independently. 2. In addition to the HRF correlations, as for task PLS, HRF Response Function is now also plotted for Behav PLS. 3. Modified Seed PLS document 'SeedPLS.txt', and allow user to use 2 different way to input extracted behav data. Version 2.312222 December 22, 2003 1. Change Pointer to 'Watch' while waiting for data exporting from 'Multiple Voxels Extraction'. 2. Modified Seed PLS document 'SeedPLS.txt'. Version 2.312191 December 19, 2003 1. Allow ERP Behavior PLS Scores Plot display more than 48 subjects. 2. Added option to threshold the correlations based on bootstrap ratio. 3. Added a submenu under Datamat menu in session window to input Seed PLS Behavior data and modify Datamat. 4. For Multiple Voxels Extraction submenu under Windows menu, it now extracts the behavior data with the same amount of rows as 'datamat' variable in datamat file. Version 2.312162 December 16, 2003 1. Added color selection for Crosshair. Version 2.312151 December 15, 2003 1. Added a Point-to-Text button for ERP plotting subject amplitude detail. The selected point will be appended into a text file entry after click this button. The file name of the text file will use the same prefix and ended with '_ERPdetail.txt'. Version 2.312081 December 8, 2003 1. Modified MRI datamat generation function, so it will not use large memory to hold an onset of data. Version 2.312041 December 4, 2003 1. Fixed a cond. labelling bug in PET brain scores plot. Version 2.312011 December 1, 2003 1. Added Crosshair for brain image plot. Version 2.311252 November 25, 2003 1. Fixed a bug for voxel selection, so the voxel location is correct now. Version 2.311211 November 21, 2003 1. Re-Scale HRF & Canonical Plots to make them the same across all conditions & groups. 2. Add stable display for HRF, if it is a bootstrap analysis. Version 2.311201 November 20, 2003 1. In MRI session window, Merge Condition can now take conditions with different numbers of onsets Version 2.311191 November 19, 2003 1. Added a new electrode system for ERP/EGI Version 2.311113 November 11, 2003 1. Make Onset Timing Plot a Gaussian Curve, from Onset to Onset plus 16 seconds. 2. Add (TR) after 'Event Onset' and 'Block Onset'. Version 2.311111 November 11, 2003 1. Added an Onset Timing Plot menu in MRI Edit Runs window to display onset timing for all conditions. 2. In ERP Create/Modify Datamat window, Analysis Start/End Time now accept numbers that can not be evenly divided by Digital Interval and then round to the closest number that can be divided by Digital Interval. 3. Move Zoom menu of ERP Plot window to the right of Edit menu. Version 2.310301 October 30, 2003 1. Allow user to apply STD on their MRI data, and hopefully this could remove some spikes noise from the brain region. To do this, the MRI datamat must be created first, and then choose 'Apply STD to Datamat' from 'Datamat' menu in Session Profile window. Version 2.310261 October 26, 2003 1. Integrated the MRI convert_task into PLS. So instead of prompting re-run MRI task analysis, it will prompt and ask for the new result file name. 2. removed the convert_task M file. Version 2.310242 October 24, 2003 1. Instead of re-run MRI task analysis, you can now type: convert_task(oldfile, newfile); to convert your old fMRI/BfMRI task analysis result file to the readable new result file. Version 2.310241 October 24, 2003 1. Session Profile list file can not be save and load in MRI Select Session Profiles window. 2. Corrected MRI Brain Scores Plot. However, all the Task fMRI/BfMRI analysis must be re-run to include the correct Brain Scores row index information. 3. Fixed bug that not saving st_datamat. Version 2.310231 October 23, 2003 1. Added new feature to display the subject ID by click the marks for MRI brainscores x designscores plot. Version 2.310153 October 15, 2003 1. Added export for Correlation RF. 2. For Datamat Correlation Plot, now it can load / save background image, and save Datamat Correlation image. Version 2.310142 October 14, 2003 1. Fixed a bug in fMRI Canonical Brain Correlations plot. 2. Asking PLS result filename before analysis begin. Version 2.310101 October 10, 2003 1. Save fields value after display the result file. 2. XYZ(mm) in the window will be updated after changing Origin in 'Set Cluster Report Option'. Version 2.310081 October 8, 2003 1. Plot Canonical Brain Correlations for Behavioral fMRI PLS result. Version 2.310011 October 1, 2003 1. Fixed bug in reading ERP header. Version 2.309301 September 30, 2003 1. Fixed color of minimum value for BLV / BSR display. Version 2.309291 September 29, 2003 1. Save background image while saving BLV or BSR to IMG. 2. Save MaxValue/MinValue of IMG into glmax/glmin field for image header with float type. Version 2.309231 September 23, 2003 1. Changed ERP header reading function to let it be able to read different headers. 2. Modified Change Path function to fix bugs that occurred during reading PC data on Linux machine, and vice versa. 3. Added new feature to view Sagittal and Coronal view, as well as Axial view for PET and MRI. Version 2.309171 September 17, 2003 1. Modified legend item in Sigular Values Plot Window, so that only meaningful components are displayed as legend item now. The meaningful components are defined such that its Percent Crossblock Covarience is no less than 1%. Version 2.309161 September 16, 2003 1. Added new feature for ERP to be able to read subject data both with header or without header. Version 2.309081 September 8, 2003 1. Added 'Subject Amplitude' in 'View' menu to view group subject amplitude. 2. Added 'Zoom' menu in 'Plot Detail' window, and displayed XY value when click anywhere inside any plot. Version 2.309021 September 2, 2003 1. Fixed a bug in creating new ERP session file. Version 2.308271 August 27, 2003 1. Fixed a bug that cause crash when modify behavior data during analysis but there is no behavior data in the datamat file. Version 2.308251 August 25, 2003 1. Added Canonical scores plot for ERP data. Version 2.308181 August 18, 2003 1. Added a new check box when creating E.R.fMRI or Blocked fMRI datamat, so user can have option to uncheck 'Normalize data with baseline signal'. 2. Added electrode system choosing option in Edit Channel Order window in ERP session profile, so user can use ERP module to analyze other electrode system, like MEG etc. Version 2.308122 August 12, 2003 1. Fixed bug in plotting old result file. Version 2.308011 August 1, 2003 1. Fixed a bug to write PET Brain LV to img. 2. Add new feature to let user deselect some conditions and modify (or load new) behavior data right before running the analysis. 3. Added new feature to PET to read mask from another image file, and select whether or not to normalize the datamat. Version 2.307142 July 14, 2003 1. Fixed a bug for group fMRI bootstrap test, which stops in the middle. 2. After datamat created, now the fMRI session profile window still leave open. Version 2.307103 July 11, 2003 1. Fixed a bug when save for fMRIdatamat, which sometimes cause frozen. 2. Added a warning message about not manually changing file names. Version 2.307091 July 9, 2003 1. Fixed a bug in fMRI/Block fMRI bootstrap, which sometimes cause frozen. Version 2.307021 July 2, 2003 1. Modified Edit Run for fMRI and Blocked fMRI module, so the command after @ entered in the Edit Onset field will be case sensitive. Version 2.306301 June 30, 2003 1. Modified Multiple Voxel Extraction for fMRI module. Now it includes all the time series, instead of average. Version 2.306271 June 27, 2003 1. Fixed Datamat Correlation Plot Current Value update problem. Version 2.306261 June 26, 2003 1. Separate Datamat Correlation Plot for different behavior measures. 2. Fixed color bar divided by 0 problem. 3. Stop running observation test for bootstrap if bootstrap can not run. Version 2.306252 June 25, 2003 1. When subjects are no more than 8, we get bootstrap order randomly from a pool that contains only the legitimate bootstrap orders. 2. Modified Plot Detail window for ERP plot, and it now has a 10% margin for bootstrap ratio plot. Version 2.306231 June 23, 2003 1. Fixed a bug in Plot Detail window for ERP plot, and now the Plot Detail window represents the correct grand average for ERP plot. Version 2.306201 June 20, 2003 1. Modified fMRI 'Export Peak Location' for cluster report window, and keep the duplicated voxel in the exported text file. Version 2.306161 June 16, 2003 1. Modified PET result display: A. added color bar; B. took away the default background image, and saved it into 'pet_template.img (.hdr)'. So, you need to click File menu and choose 'Load Background Image', if you still need to display this background image. Version 2.306121 June 12, 2003 1. Fixed "Change PLS Path" for "Select more files". 2. Added "Export Peak Location" choice for Cluster Report window. This choice will export the peak location XYZ to a text file. 3. Added "Multiple Voxels Extraction" menu. This choice will ask for a location text file, e.g. the one you exported from Cluster Report window, and will generate text files contain all the voxels listed in the location text file. Version 2.306111 June 11, 2003 1. Modified Average ERP Amplitude Plot, and display average conditions for each groups. 2. Fixed crash problem when trying to remove an averaged condition from "Display Condition Average" in Average ERP Amplitude Plot 3. Fixed "Change PLS Path" for *ERPdatamat. Version 2.306101 June 10, 2003 1. Modified Display Option in ERP Amplitude Plot. So users can now select "All subject in condition X" and "All condition in subject X". Version 2.305282 May 28, 2003 1. Modified Change PLS Path module. So users can search old path by clicking 'Search' button. 2. Added "Change Current Working Directory" under "Tools" menu of the very first window. Version 2.305273 May 27, 2003 1. Fixed voxel intensity display problem. 2. Modified Change PLS Path module. So users can enter any 'Old Path' they ever used, and change that old path to the corresponded 'New Path'. Version 2.305261 May 26, 2003 1. Updated FAQ.txt file. 2. Added 'Export data for behav analysis' for PET and fMRI. So the exported text file can be directly read into the program as behavior measure during Seed PLS. Version 2.305233 May 23, 2003 1. Added "What's new" into "Help" menu. It updates log history. 2. Modified voxel intensity for PET and Blocked fMRI. So they are now exporting extracted voxel data. 3. Fixed a bug in ERP module, which caused "Plot Scalp Scores" display crash when deselect any behavior measure. 4. Added "Save Background Image" for PET and fMRI. 5. Added "Voxel Intensity Display" for Blocked fMRI. 6. Added "Correlation Overview" for all module to display all groups. 7. Fixed a bug in fMRI module, which caused "Design Scores" display crash when results were from group analysis. Version 2 May 21, 2003 * First beta-release is officially announced. :)