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 Octobor 29, 2004 1. Added a new feature to allow user to use Analyze images in any orientation for PET, E.R.fMRI and Blocked fMRI. In "Create Datamat" window, a new button named "Check image orientation" is added beside the "Create" button. Once you click this button, the 3-View of one of the subject images will be displayed in the "Change Image Orientation" window, and you can re-orient it by click the "Re-orient" button. Once you click the "Re-orient" button, it will ask you to input the orientation of the CURRENT DISPLAYED image. If you did not get the correct orientation, you can do as many times as you want to make it standard Analyze orientation, i.e. from Left to Right in X orientation, from Back to Front in Y, and from Bottom to Top in Z. If you closed the "Change Image Orientation" window, you can re-open it by click the "Check image orientation" button in "Create Datamat" window again. For people that already generated the result file in wrong orientation but did not correct it during creating datamat, we provided axial view of "Convert Orientation" (under "Image Rotation" menu in the result window) only for PET and Blocked fMRI. However, we do not recommend people to use this limited patch. Instead, we recommend people to use the feature in "Create Datamat" window to correct the orientation during creating datamat. Version 3.0410201 Octobor 20, 2004 1. Removed (uV) sign from the legend axis for ERP Electrode Salience window. Version 3.0410151 Octobor 15, 2004 1. Modified the save of session file and datamat file. It now prevents users from saving to a filename other than _PETsession.mat, _BfMRIsession.mat, _BfMRIdatamat.mat, _PETdatamat.mat, _fMRIsession.mat, _fMRIdatamat.mat, _ERPsession.mat, _ERPdatamat.mat. 2. Since we only read .mat from the current directory, which can be changed through "Change Current Working Directory" item under "Tools" menu in the first PLS window, there is no need for another "PLS Working Directory" in the session window. Now, this field has been removed from all modules, and the path is automatically set to the current directory. Version 3.0410061 Octobor 6, 2004 1. Fixed data path bug. Version 3.0409301 September 30, 2004 1. Added following features for session windows. However, please keep in mind that you are NOT required to modify paths session files after you moved data from one location to the other, unless you would like to modify the contents of the session file. This is because that "Run Analysis" and "Show results" only read file from the current directory. 2. Added a feature in the Session windows to let users change old data (image, EEG etc.) path to new data path, as well as the change of new session path for *session.mat file. When users click "Change Data Paths" under "Edit" menu, the "Change Path" window will pop up, and users can change both session path and data path. Please see the detail and the restrictions in FAQ.txt file. 3. The program will also do a preliminary scan for the first run (or subject for PET & ERP) sub-folder. If the path is invalid, it will diplay a message at the bottom of the session window, and prompt users to go to "Edit" and "Change Data Paths" menu. 4. "Change PLS Path" button in the first PLS window is removed, because this program will only look current directory for "*datamat.mat", and "*result.mat" when users run analysis and show Results. 5. Default value of "Number of charactors for subject initial" in "Edit Subject" window for ERP and PET is set to -1. This way, the consistency of subject file name convention will not be checked in the Subject Detail window (when clicking Add or Edit). If this number is not -1, please check Help and the FAQ.txt for details regarding to the consistency. In addition, this value is now saved to the session profile, so it will be remembered when the session profile is loaded next time. 6. Fixed several bugs. Version 3.0409152 September 15, 2004 1. Added "Save Datamat As" feature in ERP "Modify Datamat" window. So datamat can be saved into a different name with (or even without) any modification. The datamat with new name will still point to the same data file. We did this because the data file is usually much larger than datamat file. This way, several different datamat files can point to the same data file (reservoir). 2. Added Bootstrap display for ERP correlation window. The "BootStrap options" item is also added into its "Tool" menu. 3. Substituted "Plot Canonical Scores" with "Plot Canonical Correlations" for ERP behavior PLS result. 4. Disabled false warning message in result file that does not store the timestamp information. 5. Removed redundant file pet_bootprocrust.m. 6. Fixed a bug in detail window of ERP correlation. 7. Fixed a bug that used wrong data path. Version 3.0408201 August 20, 2004 1. In ERP result window, "Spatiotemporal Correlations" is added under "View" menu. 2. In ERP result window, wave selection box like "All Cond", "All Subj" etc is added in "Display Options" window of "Subject Amplitude" view, "Average Amplitude" view, and "Spatiotemporal Correlations" view. 3. "Deselect" option is added in ERP "Run PLS Analysis" window. 4. In "Edit Behavior Data" window, "remove selected behavior name" option, and "Save current behavior data" option has been added. 5. Timestamp information is imbeded inside the result files. The program will automatically check for the timestamp integrity for datamat file (and also session file if MRI), and will prompt with a pop-up window if necessary. 6. Fixed several bugs. Version 3.0407291 July 29, 2004 1. Fixed an axes limit problem for behavPLS in correlation overview window. Version 3.0407283 July 28, 2004 1. Also check the valication of the contrast file after click "Run" in the "Run PLS Analysis" window. Version 3.0407271 July 27, 2004 1. For "Non-Rotated Task PLS", non-linear contrasts and non-orthogonal contrasts will be accepted, but a warning message will be prompted. 2. For "Non-Rotated Task PLS", display all LVs when plot singular value or crossblock covarience. Version 3.0407261 July 26, 2004 1. Added "Non-Rotated Task PLS" option to run non-rotated version of Task PLS Analysis. 2. "Using Helmert Matrix" PLS Option has been completely removed from the "Run PLS Analysis" window. Instead, it is added under the "File" menu of contrast window. 3. When running Bootstrap Analysis, the bootstrap result is now checked and replace meaningless data with 0. Thus, reduced the display crash when rendering the bootstrap result. 4. Related Documents are modified to represent this new release. Version 2.407141 July 14, 2004 1. Modified program so it now only requires matlab toolbox. Version 2.407131 July 13, 2004 1. In plsgui start window, when the "Show PLS Result" or the "Run PLS Analysis" button is clicked, the program will assume that all the related matlab files (*.mat) are sitting in the current directory, thus, avoid trouble when those matlab files are copied between systems. In other words, people do not need to use the "Change PLS Path" button any more when copy those matlab files between systems. If the related matlab files are not sitting in the current directory, people can use the "Change Current Working Directory" submenu under "Tools" menu in this start window to change the directory containing those matlab files as current directory. 2. "Save display setting" for result window dialog box will not be prompted out every time when people change the display setting and close the result window. Instead, program will now read status from "Save display setting" submenu under "Tools" menu in the start window to decide whether save the display setting for users. In addition, when people open start window, program will not prompt "Create PLS Profile" message, and by default, status in "Save GUI position" submenu under "Tools" menu will be set to "Off" at beginning. 3. In ERP "Edit Channel Order" window, added number beside "Channels:" label and "Selected Channels: " label, and implemented multiple remove in "Selected Channels" panel. Version 2.406181 June 18, 2004 1. Fixed a bug in Blocked fMRI RF Plot when prefix of datamat is different from that of session file. 2. Added a warning window after the datamat saved into a different prefix, and the "datamat prefix" in session file is updated. Version 2.406111 June 11, 2004 1. When the "Cluster Mask" item under "Report" menu is checked, both "Save display" and "save result" under "File" menu will save the current masked image. When "Cluster Mask" is unchecked, they will save the unmasked image. Version 2.405101 May 10, 2004 1. Add a "Create Figure" sub-menu under 'Window' menu in "3 Cardinal Plane View" window. Version 2.404132 April 13, 2004 1. Used standard normal distribution to calculate p-value in Cluster Report. 2. If any column of behavior data contains the same data for each group, program will stop proceed, and prompt error message. Version 2.404081 April 8, 2004 1. Added merge conditions option in creating datamat window for both PET and ERP modules. (E.R.fMRI and Blocked fMRI modules already have the option). 2. Prompted file name after save or export a file in Cluster Report window. Version 2.403301 March 30, 2004 1. Fixed a cond. labelling bug in PET brain scores plot. Version 2.403181 March 18, 2004 1. Added feature to export canonical scores for ERP results. Version 2.403081 March 8, 2004 1. Modified fMRI response function, and make average plots have own Y scales. Version 2.403031 March 3, 2004 1. Worked around to make program not crash in extreme situation when max_blv(bsr) = thresh = 0 or min_blv(bsr) = thresh = 0. Version 2.403023 March 2, 2004 1. Fixed a bug that was introduced in on Jan. 9, which can cause PLS result display frozen on some PC. 2. In '3 Cardinal Plane view', XYZ & Value are updated with the 3 sliders now. Version 2.402271 February 27, 2004 1. Added a feature to display all three cardinal planes for the PLS result data. To view all three cardinal planes, click '3 Cardinal Plane View' submenu under 'Windows' menu. Version 2.402181 February 18, 2004 1. Modified 'fmri_plot_hrf', so it can read session file with empty onset data in one or more conditions for a single run. Version 2.402131 February 13, 2004 1. Modified 'fmri_plot_hrf', so it can read both old and new fMRI session file. Version 2.402121 February 12, 2004 1. Saving result to an IMG file now has two different ways. When saving 'BLV (or BSR) result to IMG' file, it only saved the BLV data (or BSR) data to an IMG file, and does not include colormap or background image. When saving 'Current Display to IMG file', it will include colormap and background image. Version 2.402111 February 11, 2004 1. Modify Edit Runs, so the MRI session file is consistant no matter using text file to input onset data or enter onset data manually. Version 2.402101 February 10, 2004 1. Reversed 2 changes made in Version 2.402051 (1 & 2). So we still export the whole time series, instead of only export the active time lag. 2. Cluster Report can be saved in tab-delimited .txt file, as well as in matlab .mat file. 3. Made XYZ(mm) field editable. Version 2.402051 February 5, 2004 1. Changed the XYZ text box to edit box, so the current location can be set from this text box, rather than go to 'Set cluster report options' menu. For Event Related fMRI, [Lag X Y Z] is used, and for others, [X Y Z] is used. 2. The data export in response function and Multiple 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 PLSgui. 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. :)