| MVPA Tools |
The ROI-SVM tool has been enhanced substantially. SVM learning and testing now supports multiple classes including creation and visualization of "class-vs-other-classes" weight maps. To support this, the VOM data structure and file format has been extended to handle multiple values per voxel and to create multiple native-resolution VMPs. Furthermore, a permutation test is available in the ROI-SVM "Options" dialog allowing to assess whether an observed above-chance accuracy is significant or not. The permutation procedure trains and tests the classifier with randomly assigned (i.e. wrong) labels resulting in a null-distribution of accuracies. The null distribution is automatically displayed in a box-whisker plot togther with the accuracy obtained when using the correct labels and the accuracy of the test data allowing easy assessment of significance. For further details, see section "Assessing the Significance of SVM Accuracy Values" in the User's Guide. |
| RFX-GCM GUI Plugin |
A RFX version of the Cranger Causality Mapping (GCM) plugin (version 2.0) is available that allows to run GCMs for data sets of multiple subjects. Since this plugin is written as a GUI plugin, VOI, VTCs and time window specification can be conveniently done in the associated "RFX GCM" dialog. The functional data (VTCs) belonging to each subject are identified and used to run individual GCMs, one for each subject; the result of these GCMs are integrated in two multi-subject volume maps with proper naming of subject maps so that they can be directly used for random-effects statistical results using the "CombineVMPs" or "ANCOVA" dialog. The standard plugin (version 1.5, introduced in BVQX version 2.1) can still be used to process single-subject data sets. For more details, see the RFX-GCM help page available from the "Description of Plugins" page that can be invoked in the "Plugins" menu. |
| Preference Maps |
It is now possible to visualize the content of a map that is thresholded by another map. This possibility is an extension of lag / cross-correlation maps that allow to visualize information from one quantity (lag value) that is thresholded by another quantity (correlation value). Since correlation values are in a fixed range of -1 to +1, the two information sources could be expressed in a single quantity (e.g. 3.4 can be decomposed in a lag value "3" and a correlation value "0.4"). In order to allow this feature for general combinations of two quantities, one map can now refer to another map to be used for thresholding the visualized map. This possibility is useful if one wants to show qualitative variables that are thresholded by a quantitative variable. One example are "preference" or "winner" maps that show to which condition a voxel (vertex) responds best. These preferences can be encoded, e.g., by a map with non-thresholded integral numbers indicating different condition indices as a qualitative variable; a second map containing statistical values about the significance of a voxels' preference can then be used to threshold the preference map. BrainVoyager also allows to create such dual maps automatically from a set of standard statistical maps, each containing statistical values for a different condition; to use this tool can be invoked by clicking the "Winner" button in the "CombineVMPs" and "CombineSMPs" dialogs. |
| MVPA, GLM - Empirical Hemodynamic Responses |
For GLM calculations, the 2 gamma impulse function with standard parameters is usually a good model of a generic hemodynamic impulse response function. For some purposes, hemodynamic modeling might benefit from using individ measured responses. This is especially relevant for modeling single trial responses in the context of multi-voxel pattern analysis. The GLM dialog as well as the MVPA dialog now allows to specify a "empirical hemodynamic response" (EHR) file. This file must contain measured responses that will be used to fit a (single trial) GLM. |
| CBA - Vertex Movements |
As part of the new quality assurance tools, it is now possible to inspect the movement of vertices resulting from cortex-based alignment (CBA); vertex movement is visualized as color-coded surface maps; this tool is useful to inspect CBA results for individual cortex hemispheres; the tool also allows to quantify mean vertex movement of all hemispheres of included subjects in order to reveal which regions in the brain have moved more or less than other regions. The tool is available in the "Vertex Movement" dialog that can be invoked from the "Options" tab of the "Cortex-Based Alignment" dialog. Furthermore, the "mesh-to-mesh morphing" tool has been improved in this version and is now located in the same dialog as the vertex movement visualization tool and a calculated 3D morphing can now also stored as a MPEG4 movie. |
| EMEG Suite - Import Wizard |
The EMEG module has been extended now containing a EEG/MEG data import wizard that allows importing EEG and MEG data sets from most raw data files generated, e.g. from CTF, NeuroMag, Neuroscan, EGI, BESA and Brain Vision devices/software. The raw data is converted in the EEG/MEG file format of BrainVoyager QX together with auxiiary files for distributed source modeling if the necessary additional information is contained in the input files. The new wizard can be invoked by clicking on "Import EEG/MEG data" in the "EEG-MEG" menu. For details, consult the "EEG / MEG Raw Data Import" topic in the "EMEG Suite" chapter of the User's Guide. |
| EMEG Suite - Filter Dialog |
The EMEG module now allows filtering EEG and MEG data sets and eventually update channel and configuration and protocol data before entering the EEG/MEG distributed source modeling module. The digital filters in BrainVoyager QX can be used to suppress unwanted low and high frequency noise or to enhance a periodic pattern around the frequency of interest. The filter dialog can be invoked by clicking on "Filter EEG/MEG data" in the "EEG-MEG" menu. For details, consult the "EEG / MEG Data Filtering" topic in the "EMEG Suite" chapter of the User's Guide. |
| Plugins Update |
The "nifitconverter" plugin (v1.0.8) is now a GUI plugin presenting a dialog to control import and export of nifti files and it now also includes useful image transformations. A new "Temporal ICA" GUI plugin has been added to aid in artefact detection as an add-on to the EMEG Suite. It is possible to extract the temporal ICA components of EEG and MEG continous time-course data sets and to select components for data reconstruction. In order to visualize ICA components (as well as signal distributions across channels for time points of event-related data), the EMEG Suite now allows to show 2D "topo plots". For details, consult the "EEG / MEG Temporal Independent Component Analysis" topic in the "EMEG Suite" chapter of the User's Guide. For developers, the plugins API has been further improved: The plugins constructor, the "initPlugin()" function and the destructor are now called consistently for both pure computational plugins as well as for GUI plugins; this allows to properly manage memory allocation and release; it can be used also to cancel further execution of a plugin by returning "false" in the "initPlugin()" function in case that checked requirements are not met. |
| Scripting from Matlab |
BrainVoyager's in-built scripting environment is useful for writing and running cross-platform scripts. It might be, however, desirable to launch BrainVoyager and to run scripts from outside the program. On Windows, this is made possible by the COM (Component Object Model) binaray interface. On Windows, BrainVoyager is running as a COM server allowing all programs and scripts supporting the COM interface to remotely access BrainVoyager's functionality. Since Matlab supports the COM interface, it can be used to script BrainVoyager (as in pre- 2.0 versions). This might be particularly useful for power users who want to mix custom analysis routines written in Matlab with the processing and visualization capabilities of BranVoyager QX. For details, see the "Scripting BrainVoyager QX from Matlab" guide. Other "COM aware" evironments can also be used to automate BrainVoyager, including external script programs written in Visual Basic or JScript. |
| Scripting Commands |
When running scripts from within BrainVoyager, the set of available commands did not allow to read or write data to custom files. This possibility has been added, for details consult chapter 4 "Reading and writing files" in the "Scripting User's Guide" and the script "UsingCustomFiles.js" that is located in the "BVQXExtensions/Scripts" folder after installation. There are now also new commands allowing to run preprocessing of VTC files; the names of the new commands are identical to the ones used for FMR preprocessing and the correct routines are called based on the calling document type (FMR-STC or VMR-VTC); for details, look at the script "PreprocessVTC.js" and "Preprocessing.js". It is now also possible to create MTC files from VTC files using the "CreateMTCFromVTC" command.
|
| Map to VOI(s) |
The function to convert a map into VOIs has been improved. After clicking the "Convert Map Clusters to VOI(s)" item in the "Options" menu, a new "Convert Map to VOIs" dialog is shown that allows to decide whether each cluster of the current overlaid map should result in a separate VOI or whether the whole map should be converted into a single (large) VOI; the latter possibility is, for example, useful when one intends to analyze all voxels of a statistical map. |
| Speed Improvements |
This version of BrainVoyager QX further speeds up compute-intense routines by integrating optimized basic linear algebra routines from the Intel MKL library exploiting MMX, SME and multiple cores. Due to this library the ICA plugin is now significantly faster and can be used for large data sets consisting of several giga bytes. The optimized MKL routines are also used internally for Fourier-based 3D operations. |
| Submission of Bug or Suggestion |
Using the new "Submit Bug / Suggestion" item in the "Help" menu, it is now easy to submit a bug or suggestion directly from the running program. This function calls the default email client, creates an email addressed to our support and fills it with detailed information about the computer platform used (Windows, Mac, Linux), the BrainVoyager version and license info. Your bug description or wish/suggestion can then be added and the finished email can then be submitted. Using the generated information in your emails will help our support team to answer your requests as quickly and effectively as possible. |
| Mac GUI Improvements |
The user interface of the 64-bit Mac (Cocoa) version has been enhanced to increase productivity and usability. Mac sheets are now used for message boxes and open/save widgets instead of detached modal dialogs. An important option for file open dialogs is the possibility to remove unwanted files from display. While this is not Mac-like (usually files matching a current filter are shown as well as those not matching the filter, the latter are, however, greyed-out and not selectable), hiding files that do not pass a specified search filter (as on other operating systems) seems to be preferred by many users and is very helpful in case that folders contain many files, e.g. imaging (raw) data. The described settings are optional and can be turned on or off in the "Global Preferences" dialog in the "Behavior of File Open dialogs and message boxes (Mac OS X)" field of the "GUI" tab. Another enhancement concerns navigation in the surface window when using two-button mice; in previous versions right mouse button clicks intended for translation movements often invoked instead the context menu; now the latter is only triggered if one holds down the right mouse button for about a second without moving the mouse. Another improvement is that the Finder now shows icons for standard BrainVoyager project files (VMR, FMR, DMR, SRF); as with other file types, clicking an icon will launch BrainVoyager (if not running) and the selected file will be opened.
|
| Movie Studio |
In previous versions, movie studio exported rendered frames as a series of bitmaps that one needed to integrate into movies using external platform-dependent tools. In this version, MPEG4 movies can now be created that are stored as standard .MOV (Mac) or .AVI (Windows) movie files. Movie export can be turned on in the "Render Movie" tab of the "Movie Studio" window. |
| Setting Doc Path |
When multiple documents are open in the workspace, and one switches from document to document, the default path is now reset to the "core" document path allowing more efficient handling of multiple documents; in previous version the default folder shown when calling a Open File dialog was often not related to the currently selected project but showed a path that was used when another document was the active.document. |