Home > BrainVoyager > Installation & Licensing > BrainVoyager Release Notes

BrainVoyager Release Notes

BrainVoyager 23.2 Release Notes

BrainVoyager 23.2
This minor release focuses on important improvements and bug fixes.

New Features

Reading 4D Normalized Func NIfTI Files

If 4D functional NIfTI files are in 'Scanner' space, they are imported as FMR/STC documents without applying the spatial transformation. Normalized 4D NIfTI files were only accepted in some cases in previous versions when the spatial transformation (sform code) did not contain rotations and only integral scales. This excluded import of many 4D nifti files that were preprocessed with pipelines such as fmriprep, which often contain non-integral and/or non-iso scales. The new functions in this release read all 4D func nifti files by applying the full transform saving the result as a VTC file with the first functional volume as the visible ('hosting') VMR file. Since nearest neighbor interpolation is used for files with no rotations and only integral scales, the final VTC contains a unmodified copy of the original nifti data in normalized space (placed in a standard bounding box) while in case of rotations or non-integral non-iso scales, the data is interpolated using CPU-parallelized interpolation. The interpolation method (default Lanczos) can be chosen in the 'Reading normalized space 4D NIfTI as VTC' field in the 'NIfTI' tab of the 'Settings' dialog. In all cases, scales are analyzed and used to set the 'func-to-anat' integral scale value (1, 2 or 3) for the transformation; for non-integral scales the nearest (over-sampled) integer value is used, e.g., for a scale of '2.5', a 'func-to-anat' scale of '2' would be used, which can be inspected also after reading the NifTI file in the 'VTC Properties' dialog. Details of how a 4D nifti is processed are written to the 'Log' tab. For more details, consult the 'Functional 4D NIfTI Files' topic in the 'NIfTI Files' chapter of the updated User's Guide.

Cluster-Thresholding GUI Plugin

The cluster-thresholding plugin is available for many years and provides an important additional means to test statistical results for significance by finding an appropriate cluster threshold given an uncorrected single-voxel threshold of p = 0.001 (or smaller). The plugin has, however, not a proper user interface, and its use with a sequence of dialogs asking questions is somewhat inconvenient. While the 'classical' plugin remains available, the new Cluster-Thresholding GUI plugin provides a dialog that allows entering and checking all important information in a single place before committing to the compute-intensive calculation to find a cluster-level statistical threshold. The new GUI version can not only be called from the 'Plugins' menu but is integrated directly in the 'Volume Maps' dialog with a new 'Correct' button in the 'Cluster threshold' field of the 'Statistics' tab. Furthermore, the GUI version can also be called from the 'Analysis' menu. An important improvement of both the 'classical' and GUI cluster-thresholding plugin is that it can be applied more generally since its application is no longer restricted to hosting VMRs with dimensions of 256 voxels.

Enhancements

Writing Normalized NIfTI Files	The writing of 4D normalized VTCs and VMPs as NIfTI files has been improved using default MNI / TAL bounding box ranges for consistency across data from multiple runs and subjects. Furthermore, when saving a normalized VTC as a NIfTI file, a linked protocol is now exported as a TSV file in the same way as when writing FMR / STC documents as NIftI files in 'Scanner' space.
Open (Pure) VTC Functions	The usual way to load a VTC (4D functional time series) file requires first loading a 'hosting' VMR file from which the VTC file is then linked. This has the advantage that one can select different VMRs (from a participant or a template brain) for visualization of VTC derived data such as calculated statistical maps. If one is interested in opening a VTC quickly, one can now use the new 'Open VTC' function in the 'File' menu. Instead of a chosen VMR, this function will display the first functional volume of the VTC as the 'hosting' VMR. A related function, 'Ope Pure VTC' is also provided in the 'Files' menu. The difference is that the 'Open VTC' function places the visualized VTC volume in the position of the respective normalized space (e.g. MNI) in the hosting VMR (usually with dimensions of 256 voxels) using the VTC's bounding box definition (in the same way as when linking the VTC), while the 'Open Pure VTC' version ignores the location in a normalized space and shows the VTC 'as is'. In most cases, the 'Open VTC' variant is appropriate but the 'Open Pure VTC' function might be useful in some cases when inspection of the 'pure' VTC data is sufficient.
VMR View Tooltip With V16 Intensity	The VMR View Tooltip overlay shows the intensity of the underlying VMR when hovering over the orthographic (SAG, TRA, COR) slices. In case that a (16 bit intensities) V16 volume is attached to the (8 bit intensities) VMR, it might be useful to inspect the V16 intensity values next to the 8 bit intensity values. The tooltip now shows the V16 intensity of the voxel below the mouse cursor on the right side of the VMR intensity value. To quickly load the V16 with the same name of the VMR, one can, for example, call the 'Contrast / Brightness' dialog.
Adjusting Intensities To Match Default WM / GM	The 'Contrast / Brightness' dialog contains the 'Set to standard GM WM' button that aims to adjust the VMR/V16 intensities in a way that the mean values of white and grey matter match defaul intensity values, usually GM (grey matter) = 100, WM (white matter) = 150. This function has been substantially improved in this release. It is intended to be used after brain extraction and spatial intensity inhomogeneity correction, i.e. after running the standard IIHC functionality using the '16 Bit 3D Tools' dialog. Setting the WM and GM values using this function prepares the dataset optimally for subsequent segmentation functions, including segmentation for boundary-based registration (BBR) or when using the 'Advanced Segmentation' dialog. The default parameters for GM and WM can be adjusted temporarily in the Contrast / Brightness dialog. If one wants to make permanent changes, one can change the default values in the 'Analysis' tab of the 'Settings' dialog. It is not advised to change the default value of GM (100) since this value is expected by several functions, but changing the WM value to a different value (e.g. 170 or 180) might be useful if one wants to visualize white matter in more white instead of grey color.
Center Cross Function In VMR View Menu	To make it possible to quickly access the 'Center cross' function that can be called using the 'Center' button in the 'Coregister' tab of the '3D Volume Tools' dialog, this functino has been added to the VMR View context menu that can be invoked by right-clicking inside the VMR window.
Show First VTC Volume Function In VMR View Menu	To make it possible to quickly access the 'Show First VTC Volume' function that can be called using the 'Show VTC Vol' button in the 'Spatial Transf' tab of the '3D Volume Tools' dialog, this functino has been added to the VMR View context menu that can be invoked by right-clicking inside the VMR window.
JS Script Commands	For GUI scripts and GUI plugins, new functions have been added to the 'bv' ('BrainVoyager') script object that allow to set the minimum and maximum size of a GUI dialog: 'SetMinimumSizeOfPluginWindow(int widht, int height)', 'SetMaximumSizeOfPluginWindow(int widht, int height)', 'SetMinimumSizeOfGUIScriptWindow(int width, int height)' and 'SetMaximumSizeOfGUIScriptWindow(int width, int height)'. While it is usually not necessary to restrict the maximum size of a dialog window, it is useful to set a minimum size to prevent that a window can be made so small that user interface elements are hidden from view. It is advised to call these functions in the 'Component.onCompleted' function of the dialog (see provided examples in the 'Scripts' and 'Plugins' folders for detail). Furthermore, the 'MessageBox()' function obtained an optional second parameter for a 'detailed message' string (next to the main message string provided in the first parameter). Also the possibility to provide a 'Yes / No' dialog has been added with the new 'YesNoMessageBox()' function, which accepts the same parameters as the message box and shows a 'Yes' and a 'No' button. If the user presses the 'Yes' button, the function returns 'true', otherwise 'false'. The 'document' object obtained the new commands 'ShowVOIsDialog()' and 'HideVOIsDialog()' as well as the 'GetBetaTValueOfROIGLM()' and 'GetBetaPValueOfROIGLM()' functions accepting the index of a fitted beta value as input (these functiosn are defined for the Pyhton interface but were missing for JS scripts).

Bug Fixes

Iso-Voxelation on macOS	Iso-voxelation using Metal shaders on devices with Apple Silicon and Intel chips did not work in the previous release (had been fixed for Apple Silicon in patch release 23.0.9). This issue has been fixed.
Average VTC Volumes	The option 'Average VTC Over Time And Convert To VMR' in the 'Options' menu can be used to average all volumes of a VTC to create a VMR (and V16) file. This function resulted in empty files in version 22.4 and 23.0.8. This issue has been fixed.
Create VTC On Apple Using 'Metal' Compute	Sometimes a crash happened when running the 'create_vtc' Python or 'CreateVTC' JS script function (but also when using the user interface) for large datasets. This has been solved by optimising Metal compute shader code, which now reuses once allocated Metal volume buffers for each volume of a sequence. The improvement has been also applied to FMR motion correction to ensure fast and robust performance.
VOI RFX GLM	When running RFX GLMs for volume regions of interest (VOIs) with (dummy-coded) runs containing predictors with only 0 values in the design matrix, the program crashed. This issue has been fixed.
Automatic Cortex Segmentation For BBR	When running the 'Automatic Cortex Segmentation for BBR' function via script or the user interface, the function sometimes returned without running the cortex (WM) segmentation and cortex mesh reconstruction. This issue was caused by a sub-optimal contrast / brightness setting. This issue is now solved by internally calling the 'Set to standard GM/WM' function described above under 'Enhancements'.
Coregistration Using BBR Script Function	When calling the Python script function 'coregister_fmr_to_vmr_using_bbr' (or the equivalent JS function), the .VOI with the GM boundary before and after the alignment was not created and saved as in the GUI version. This issue has been fixed.
Automatic Creation of Project Folders	In some cases the automatic creation of a 'rawdata' folder did not work correctly (there could be a nested chain of 'rawdata' and 'sourcedata' folders). This issue has been fixed.
LoadVOIFile Script Function	The 'LoadVOIFile()' JS script function did not work in previous 23.x versions. This issue has been fixed.
Windows - No Fibers Visualized in Line Mode	When visualizing fiber tracts and tensor lines, nothing was shown on Windows in previous 23.x veresions. Only if 'tube' rendering mode was used, fiber tracts could be visualized. This issue with visualizing lines on Windows has been fixed in this release.
Interactive Fiber Tracking	Interactive fiber tracking did not work in previous versions. In the current version 'CTRL-click' on a brain slice does still not work but it is now possible via the context menu of the VMR View. After invoking the context menu (usually via right-clicking) at a voxel of a VMR slice, one can select the "Track fibers from cross position" option to launch fiber tracking from the selected voxel. One can then switch to the associated 'Brain Viewer' window to se the tracked slices. It is recommended to 'tile' the VMR and Brain Viewer window next to each other to see both the slice(s) and the tract fibers.
Open Pure VTC - TR Value	When using the 'Open Pure VTC' function from the 'File' menu, invoked time course plots die not show a linked protocol correctly since the VTC TR value was not provided correctly to the 'Time Course Plot' window. This issue has been fixed.
Saving FMR Files	When saving FMR files, a small change had been introduced in 23.0, namely to use the strings 'NrOfColumns' and 'NrOfRows' instead of 'ResolutionX' and 'ResolutionY'. This led, however, to issues in some programs that read FMR files, and this change has been reverted. It is planned to introduce the renaming with the next version update of FMR files.

New Features

Reading 4D Normalized Func NIfTI Files

Cluster-Thresholding GUI Plugin

Enhancements

Writing Normalized NIfTI Files	The writing of 4D normalized VTCs and VMPs as NIfTI files has been improved using default MNI / TAL bounding box ranges for consistency across data from multiple runs and subjects. Furthermore, when saving a normalized VTC as a NIfTI file, a linked protocol is now exported as a TSV file in the same way as when writing FMR / STC documents as NIftI files in 'Scanner' space.
Open (Pure) VTC Functions	The usual way to load a VTC (4D functional time series) file requires first loading a 'hosting' VMR file from which the VTC file is then linked. This has the advantage that one can select different VMRs (from a participant or a template brain) for visualization of VTC derived data such as calculated statistical maps. If one is interested in opening a VTC quickly, one can now use the new 'Open VTC' function in the 'File' menu. Instead of a chosen VMR, this function will display the first functional volume of the VTC as the 'hosting' VMR. A related function, 'Ope Pure VTC' is also provided in the 'Files' menu. The difference is that the 'Open VTC' function places the visualized VTC volume in the position of the respective normalized space (e.g. MNI) in the hosting VMR (usually with dimensions of 256 voxels) using the VTC's bounding box definition (in the same way as when linking the VTC), while the 'Open Pure VTC' version ignores the location in a normalized space and shows the VTC 'as is'. In most cases, the 'Open VTC' variant is appropriate but the 'Open Pure VTC' function might be useful in some cases when inspection of the 'pure' VTC data is sufficient.
VMR View Tooltip With V16 Intensity	The VMR View Tooltip overlay shows the intensity of the underlying VMR when hovering over the orthographic (SAG, TRA, COR) slices. In case that a (16 bit intensities) V16 volume is attached to the (8 bit intensities) VMR, it might be useful to inspect the V16 intensity values next to the 8 bit intensity values. The tooltip now shows the V16 intensity of the voxel below the mouse cursor on the right side of the VMR intensity value. To quickly load the V16 with the same name of the VMR, one can, for example, call the 'Contrast / Brightness' dialog.
Adjusting Intensities To Match Default WM / GM	The 'Contrast / Brightness' dialog contains the 'Set to standard GM WM' button that aims to adjust the VMR/V16 intensities in a way that the mean values of white and grey matter match defaul intensity values, usually GM (grey matter) = 100, WM (white matter) = 150. This function has been substantially improved in this release. It is intended to be used after brain extraction and spatial intensity inhomogeneity correction, i.e. after running the standard IIHC functionality using the '16 Bit 3D Tools' dialog. Setting the WM and GM values using this function prepares the dataset optimally for subsequent segmentation functions, including segmentation for boundary-based registration (BBR) or when using the 'Advanced Segmentation' dialog. The default parameters for GM and WM can be adjusted temporarily in the Contrast / Brightness dialog. If one wants to make permanent changes, one can change the default values in the 'Analysis' tab of the 'Settings' dialog. It is not advised to change the default value of GM (100) since this value is expected by several functions, but changing the WM value to a different value (e.g. 170 or 180) might be useful if one wants to visualize white matter in more white instead of grey color.
Center Cross Function In VMR View Menu	To make it possible to quickly access the 'Center cross' function that can be called using the 'Center' button in the 'Coregister' tab of the '3D Volume Tools' dialog, this functino has been added to the VMR View context menu that can be invoked by right-clicking inside the VMR window.
Show First VTC Volume Function In VMR View Menu	To make it possible to quickly access the 'Show First VTC Volume' function that can be called using the 'Show VTC Vol' button in the 'Spatial Transf' tab of the '3D Volume Tools' dialog, this functino has been added to the VMR View context menu that can be invoked by right-clicking inside the VMR window.
JS Script Commands	For GUI scripts and GUI plugins, new functions have been added to the 'bv' ('BrainVoyager') script object that allow to set the minimum and maximum size of a GUI dialog: 'SetMinimumSizeOfPluginWindow(int widht, int height)', 'SetMaximumSizeOfPluginWindow(int widht, int height)', 'SetMinimumSizeOfGUIScriptWindow(int width, int height)' and 'SetMaximumSizeOfGUIScriptWindow(int width, int height)'. While it is usually not necessary to restrict the maximum size of a dialog window, it is useful to set a minimum size to prevent that a window can be made so small that user interface elements are hidden from view. It is advised to call these functions in the 'Component.onCompleted' function of the dialog (see provided examples in the 'Scripts' and 'Plugins' folders for detail). Furthermore, the 'MessageBox()' function obtained an optional second parameter for a 'detailed message' string (next to the main message string provided in the first parameter). Also the possibility to provide a 'Yes / No' dialog has been added with the new 'YesNoMessageBox()' function, which accepts the same parameters as the message box and shows a 'Yes' and a 'No' button. If the user presses the 'Yes' button, the function returns 'true', otherwise 'false'. The 'document' object obtained the new commands 'ShowVOIsDialog()' and 'HideVOIsDialog()' as well as the 'GetBetaTValueOfROIGLM()' and 'GetBetaPValueOfROIGLM()' functions accepting the index of a fitted beta value as input (these functiosn are defined for the Pyhton interface but were missing for JS scripts).

Bug Fixes

Iso-Voxelation on macOS	Iso-voxelation using Metal shaders on devices with Apple Silicon and Intel chips did not work in the previous release (had been fixed for Apple Silicon in patch release 23.0.9). This issue has been fixed.
Average VTC Volumes	The option 'Average VTC Over Time And Convert To VMR' in the 'Options' menu can be used to average all volumes of a VTC to create a VMR (and V16) file. This function resulted in empty files in version 22.4 and 23.0.8. This issue has been fixed.
Create VTC On Apple Using 'Metal' Compute	Sometimes a crash happened when running the 'create_vtc' Python or 'CreateVTC' JS script function (but also when using the user interface) for large datasets. This has been solved by optimising Metal compute shader code, which now reuses once allocated Metal volume buffers for each volume of a sequence. The improvement has been also applied to FMR motion correction to ensure fast and robust performance.
VOI RFX GLM	When running RFX GLMs for volume regions of interest (VOIs) with (dummy-coded) runs containing predictors with only 0 values in the design matrix, the program crashed. This issue has been fixed.
Automatic Cortex Segmentation For BBR	When running the 'Automatic Cortex Segmentation for BBR' function via script or the user interface, the function sometimes returned without running the cortex (WM) segmentation and cortex mesh reconstruction. This issue was caused by a sub-optimal contrast / brightness setting. This issue is now solved by internally calling the 'Set to standard GM/WM' function described above under 'Enhancements'.
Coregistration Using BBR Script Function	When calling the Python script function 'coregister_fmr_to_vmr_using_bbr' (or the equivalent JS function), the .VOI with the GM boundary before and after the alignment was not created and saved as in the GUI version. This issue has been fixed.
Automatic Creation of Project Folders	In some cases the automatic creation of a 'rawdata' folder did not work correctly (there could be a nested chain of 'rawdata' and 'sourcedata' folders). This issue has been fixed.
LoadVOIFile Script Function	The 'LoadVOIFile()' JS script function did not work in previous 23.x versions. This issue has been fixed.
Windows - No Fibers Visualized in Line Mode	When visualizing fiber tracts and tensor lines, nothing was shown on Windows in previous 23.x veresions. Only if 'tube' rendering mode was used, fiber tracts could be visualized. This issue with visualizing lines on Windows has been fixed in this release.
Interactive Fiber Tracking	Interactive fiber tracking did not work in previous versions. In the current version 'CTRL-click' on a brain slice does still not work but it is now possible via the context menu of the VMR View. After invoking the context menu (usually via right-clicking) at a voxel of a VMR slice, one can select the "Track fibers from cross position" option to launch fiber tracking from the selected voxel. One can then switch to the associated 'Brain Viewer' window to se the tracked slices. It is recommended to 'tile' the VMR and Brain Viewer window next to each other to see both the slice(s) and the tract fibers.
Open Pure VTC - TR Value	When using the 'Open Pure VTC' function from the 'File' menu, invoked time course plots die not show a linked protocol correctly since the VTC TR value was not provided correctly to the 'Time Course Plot' window. This issue has been fixed.
Saving FMR Files	When saving FMR files, a small change had been introduced in 23.0, namely to use the strings 'NrOfColumns' and 'NrOfRows' instead of 'ResolutionX' and 'ResolutionY'. This led, however, to issues in some programs that read FMR files, and this change has been reverted. It is planned to introduce the renaming with the next version update of FMR files.

BrainVoyager 23.0 Release Notes

New Features High-Quality Volume Renderer A new volume renderer has been implem... more

BrainVoyager 22.4 Release Notes

New Features

BV Scene File Format

A new BV Scene file format with the extension '.bvscn' has been introduced that makes it easier to store and reload a set of heterogenous files. Most importantly, the scene file stores also the datasets that are attached to a VMR or Mesh instance, including VOIs, VMPs and VTCs for VMR's and POIs, SMPs, MTCs and fiber tract (FBR) files for meshes. BV Scene files can be loaded and saved using the 'Open Scene' and 'Save Scene' entries in the 'File' menu or by clicking the corresponding 'Open' and 'Save' icons in the main toolbar. For more details, see topic 'Scene Files' in the 'Getting Started' chapter of the User's Guide.

Enhancements

Enhanced Multi-Frame DICOM Files	Classical DICOM files allowed to store only one image in a single file, which often results in a large amount of files per document, especially in case of functional datasets. Manufacturers circumvented this issue either by using custom formats such as PAR/REC for Philips scanners. Siemens platforms circumvented the issue by using the 'mosaic' format that packs multiple slices in a single (large) image. The enhanced DICOM standard provides an official solution to store a series of 'frames' (images) in a single DICOM file. While already around for some time, this approach was only slowly adopted by manufacturers, especially Siemens. With their new 'XA' software platform (that seems to come also to older scanners running the "VB" or "VE" platforms), Siemens now also suports the enhanced DICOM format. In this release, BrainVoyager is adding support for multi-frame DICOM files. Next to extracting multiple images (slices), the enhanced Dicom reader extracts important per-frame data (if available) to create correct position information as well as slice timing tables for functional data (as done for many years for Siemens mosaic files). Note that not only functional and diffusion data is stored in enhanced DICOM format but also anatomical data, i.e. all slices of a T1-weighted scan can be stored in a single multi-frame DICOM file. For more details, see topic 'Supported DICOM Files' in the 'Getting Started' chapter of the User's Guide.
DICOM Files Across Sub-Folders	DICOM files may be exported across several sub-folders. In a variant of SIEMENS export, the files are spread across sub-folders that are limited each to have a maximum of 500 files; this is different from exported folders without a file limit where each folder contains one full series. In the 500 files limit case, the files of a single series may be spread over multiple 500 files sub-folders. Both cases are now transparently handled when using the 'Create Document Wizard' by the new 'Integrate data in sibling folders' option that appears in the 'Select Data Location' tab and is turned on as default. When selecting a DICOM file in a folder, the program then checks whether there are also DICOM files in any sibling folder, which will be integrated in the presented series selection overview table. In case one wants to only use data in a single folder, the 'Integrate data in sibling folders' option can be turned off before browsing to the data. Furthermore, a 'rename DICOM files' process is started in all sub-folders in case a file is selected that has not yet been renamed. The separate 'Rename DICOM Files' and 'Anonymize DICOM Files' dialogs now also have an option to specify whether files should be renamed in the selected folder or in all sub-folders of the selected folder.
Diffusion NIfTI / BIDS Files	The 'Create Document Wizard' now supports creating NIfTI files from diffusion DICOM files. When specified, the NIfTI diffusion files are placed in the appropriate folder of a BIDS project including generation of a JSON sidecar file (see also next point). If available from the header (or provided by a BV gradient file), gradient data will be extracted, converted from scanner to image space and saved as 'bvec' and 'bval' files. Diffusion-related data is extracted both from Siemens mosaic and enhanced DICOM files. Furthermore, when opening (native space) diffusion NIfTI files, BV DMR documents will be created. The new functionality can be used from Python by calling the added commands 'create_dmr_dicom()' and 'create_dmr_dicom_nifti_bids()'.
Overview of DICOM Series	When selecting a folder for DICOM files in the 'Create Document Wizard', a more useful display of all available DICOM series is now provided after selecting a DICOM file. The presented overview table now also has a new column containing the contents of the 'series description' DICOM tag that is helpful in case of multiple series to find a desired scan. The displayed overview shows also DICOM series that refer to data not (currently) supported (such as Spectroscopy and some non-original (derived) DICOM data). When selecting such unsopported datasets, an appropriate message will be displayed.
Data Analysis Manager	The new Data Analysis Manager has been improved in this release. Next to bug fixes (see below), basic support for diffusion-weighted documents has been added. DWI documents can be created in batch mode using the 'Convert DICOM to NIfTI' tool of the Data Analysis Manager that now also has a section for specifying a list of DWI documents to be converted from the provided DICOM files to corresponding NIfTI files that will be stored at the specified sub-folder of the project. The conversion tool calls the new command of the Python interface 'create_dmr_dicom_nifti_bids()' that is also available for Python coding (as well as the new 'create_dmr_dicom()' command). In the same way As with functional and anatomical documents, DWI nifti files will be displayed in the 'Data' tab of the Data Analysis Manager; double-clicking a DWI NIfTI file will open it in BrainVoyager's main document window.
Support for Python 3.8 and 3.10	Python 3.6 is no longer supported in this release. Python 3.8 is now the default and recommended Python version. Support for Python 3.10 has been tested but support is considered experimental (issues with importing e.g. numpy module on macOS).
FMR-VMR Coregistration	The coregistration of FMR and VMR files using the default NGF approach has been improved. This includes also alignment of NIfTI documents that were converted from DICOM files by other software (e.g. dcm2niix that may flip original DICOM files along an axis). Also a potential VMR 'To-SAG' adjustment step (90-degree rotations and axis flip) is performed correctly for NIfTI-derived files.
To-SAG and Iso-Voxel TRF Files	In case the program performed (automatic) To-SAG or Iso-Voxel transformations, the respective transformations are now stored to disk in the same folder as the VMR document to which the transformation is applied. The saved transformation files can then be applied to other anatomical documents that are in the same space then the source VMR.
MNI Space VTC Creation	When the VMR used for FMR-VMR alignment did not have 1mm voxel size (e.g. when using sub-millimeter high-res anatomical data), creation of VTCs in MNI space was not possible since MNI transformation (currently) requires a 1 mm VMR as input. It is now possible to use a 1 mm (scaled) version of the high-res anatomical as the hosting VMR when creating a MNI VTC. The program will now ensure that the data is rescaled to the resolution of the hosting VMR (e.g. 1 mm) before applying the MNI transformation. Note that the FMR-VMR alignment step will be performed using the original VMR voxel size using the resolution value stored in the IA TRF file instead of the resolution of the hosting VMR.
Open VTC Files	Usually VTC files are linked to a 'hosting' VMR so that they are placed at the right location and relative resoluton inside the anatomical document. For some applications it might be useful to visualize VTC data using the actual VTC dimensions (for example when working with high-resolution functional data). The new 'Open VTC' item in the 'File' menu now allows to open VTC files directly without the need to load a hosting VMR. For visualization purposes, a hosting VMR with the same dimensions as the VTC is nonetheless created using the first volume of the VTC dataset. Furthermore the bounding box of the VTC is changed to start at voxel 0 for all dimensions and the functional-to-anatomical resolution is set to 1 (if needed). The VTC with such a modified header is referred to as a 'pure' VTC and is automatically saved to disk with the extension '_PURE.vtc'. The saved 'pure' VTC file can later be opened directly instead of the original VTC. The visualization of the created hosting VMR can be adjusted by using the standard 'Contrast / Brightness' dialog available in the 'Options' menu.
ROI Function: A minus B	It is sometimes desirable to get a ROI without the part that is overlapping with another ROI. Such functionality has been added to the 'Volumes-Of-Interest' and 'Patches-Of-Interest' dialogs. When launching the function using the 'A - B' button, an auxiliary dialog will appear to specify, which of two selected ROIs is serving as 'A' or 'B'.
ROI Functions: Sort and ROI Numbers	It is sometimes desirable to sort a VOI list alphabetically, for example, to find a VOI / POI more easily for selection. While one can reorder ROIs, the fundamental order might follow other criteria (e.g. sorted by location). It is now possible to quickly switch between the defined (fundamental) order and an alphabetic order by using the new 'Sort' toggle button, which is located below the 'VOIs / POIs List' of the 'Volumes-Of-Interest' and 'Patches-Of-Interest' dialogs. Note that selected ROIs in the alphabetically sorted view will stay selected when switching back to the fundamental order. It is now also possible to show the position of VOIs in the fundamental order by using the 'Show No.' toggle button next to the 'Sort' toggle button.
Bulk ROI Movements	It is often desired to rearrange the order of ROIs in the 'Volumes-Of-Interest' and 'Patches-Of-Interest' dialog. In previous versions, it was only possible to move a single selected ROI 'up' or 'down'. This release adds the possibility to move a selected set of VOIs or POIs 'up' and 'down' by clicking the respective 'Move Up' and 'Move Down' buttons. The selected ROIs need not to form a contiguous range.
Event-Related Averaging Plots	The plot of ideal HRF event-related condition curves that was introduced in the previous version has been improved. To remove clutter, there are no longer as many ideal curves shown as conditions but usually only one. In case that there are averaged curves with different event durations, one ideal curve per event duration will be shown. Furthermore the setting (on or off) of the 'Ideal' option in the 'Event-related averaging' field of the 'ROI Signal Time Course' dialog is now permanently saved. If the option is turned off, for example, it will not be turned on in a newly opened dialog in the same or future session until the state of the option is actively changed.
Recent Files	The 'Recent Files' pane has been improved. A category to access recently opened 'BVSCN' files (see above) has been added. Furthermore, a conventional 'Recently opened files' category has been added that keeps a list of recently opened files independent of the file type. This generic recent files category is always available (opened) in the 'Recent Files' pane.
Non-Square Slices	When creating functional and diffusion-weighted documents from scanner data, slices with unequal dimensions were automatically padded with zero values along the smaller dimension to get images with equal dimensions. This 'squaring' function has been turned off as default to get the original (DICOM) slice dimensions. The old functionality can, however, be turned on by using the 'Reframe to square images' option in the 'Non-square images during document creation' filed of the 'Data' tab of the 'Settings' dialog.
VTC in FMR Space	When converting FMR (DMR) data into identical VTC (VDW) data, the resulting VTC dimensions did not always match exactly the ones of the FMR/DMR document. This occured when the data had (padded) zero fringes since the VTC bounding box was determined by skipping 'empty' space around non-zero data values. In order to keep the same dimensions in the resulting VTC, the program now produces a bounding box with the same dimensions as in the source FMR/DMR document.
Dimensions in FMR/DMR/VTC Properties	The 'FMR/DMR Properties' dialogs now show the entries 'Rows' and 'Columns' in the 'General information' field. The 'VTC Properties' dialog now shows the X, Y and Z dimensiions in the 'Dim' row of the 'Bounding box and dims' field. Note that the displayed dimensions are reported in VMR voxels, which corresponds to the VTC voxels directly when using a functional-to-anatomical voxel resolution of '1x1x1'. If the functional-to-anatomical resolution is '2x2x2' or '3x3x3', the displayed dimension values need to be divided by '2' or '3' respectively to get the dimensions of the VTC/VDW data.
BIDS Folder Browsing	When selecting a folder in a dialog that looks for a functional data file, the program has often opened the "anat" folder since the location of the hosting VMR is set as theh default directory path. In the present version, the program switches to the neighboring "func" folder in this case (in case this folder is available), which is in most use cases the more appropriate location.

Bug Fixes

BIDS 'rawdata' Folder Name	In the previous release, the folder containing the original BIDS files under the directory with the project name was called 'sourcedata'. Since this was not in line with BIDS, the name has been changed to 'rawdata' as expected. In order to be consistent with datasets stored using the 'sourcedata' name, both names will be supported for some time but note that the wrong 'sourcedata' name is deprecated and support will be removed in the future.
Location of Converted NIfTI Files	When opening a NIfTI file using the 'Open NIfTI' toolbar or menu item, the corresponding BV file (e.g. VMR, FMR-STC) was saved in a sub-folder inside a (created) 'derivatives' folder at the same level as the raw data (subject, session, type) level. In BV 22.2 the (created) 'derivatives' folder was assumed to be at the same level as the 'rawdata' folder (or 'sourcedata' folder, see above) containing the original NIfTI files. A 'rawdata' (last version 'sourcedata') folder is automatically created by the 'Data Analysis Manager' inside a project folder. In case a BIDS subject-tree is not placed in a 'rawdata' ()'sourcedata') folder (e.g. 'project-name - sub-01' instead of 'project-name - rawdata - sub-01'), the 'derivatives' folder would be created one level too high, i.e. outside the project folder. To avoid this, the program now checks whether the folder name on top of the subject tree is named 'rawdata' (or 'sourcedata') - if this is the case, the 'derivatives' folder will be placed next to this folder, otherwise it will be placed next to the 'sub-01' folders (as was done in veresions prior to BV 22.2 where no 'rawdata' folder was created).
Data Analysis Manager: Changing Projects Path	In the previous version (22.2), the new Data Analysis Manager provided the possibility to change the location where projects are stored to support storing and using multiple locations on the same or additional (network) disk drives. Switching to another location could be done by using the 'Browse' button next to the 'Default projects path' field, which has been renamed to 'Current projects path'. The selected projects path was, however, not used when creating a new project. This issue has been fixed in this release. When changing the projects path (either in the manager window or via the Python API), the 'Projects' pane now shows the discovered projects in the new location; furthermore, a newly created project will now be placed inside the currently selected projects path.
Data Analysis Manager: Iso-Voxelation	In the previous version (22.2), the new Data Analysis Manager provided the option to specify an iso-voxelation step in the anatomical preprocessing workflow but this setting was not performed when running the workflow. This has been fixed in this release.
Data Analysis Manager: Skip Results	When turning on the 'Skip existing results' option in the new 'Data Analysis Manager' window it did not have any effect, i.e. the data of all subjects was re-analyzed. This prevented adding subjects efficiently to a workflow, i.e. without re-running the whole analysis. This issue has been fixed in this release.
Data Analysis Manager: DICOM to NIfTI	When loading a batch DICOM to NIfTI conversion (.D2N) file, one could not change entries (such as paths to DICOM or protocol files) in the 'Convert DICOM To NIfTI' dialog. This issue has been fixed in this release.
NIfTI TRF Matrix From QForm and 'NAN' Values	When opening a 4D NIfTI file, the values in the calculated transformation matrix from qform header values have led to 'nan' values in a special case (when length of quaternion b, c, d vector became slightly larger than 1.0). This issue has been fixed in this release.
Loading 4D NIfTI MNI Files	When opening a 4D NIfTI MNI file, it could happen that the dimensions would not fit in BrainVoyager's (256) bounding box. This release handles this issue by ignoring data outside of the maximum possible bounding box. This should not be an issue since the ignored values are outside the location of the brain in MNI space.
Mesh-Based ANCOVA	When running an AN(C)OVA analysis from a cortex mesh in the 3D Viewer, the program crashed in the previous release. This issue has bveen fixed.
Rectangular Mosaic DICOMs	When reading SIEMENS mosaic files containing non-square slices, the slice extraction procedure did in rare cases not work properly. These rare cases have been addressed in this release by a more robust estimation of the number of rows and columns of mosaic slices.
VMR-VMR Alignment	When performing VMR - VMR alignment, the program sometims refused to run stating that the two VMRs have different voxel resolution even if they would be shown as the same resolution when displayed in the 'VMR Properties' dialog. This release fixes that by allowing very small deviations in voxel resolution between the two datasets when performing VMR - VMR alignment.
SMP Transparency Setting	In previous versions, setting the transparency for surface maps in the 'Blending with SRF and other SMPs' field of the 'Surface Map Options' dialog had no effect. This has been fixed in this release.
Mesh Drawing: POI Visibility	When drawing lines with a series of CTRL-clicks and filling regions using CTRL-SHIFT-clicks, previously created and visualized POIs disappeared, which made it difficult to create a series of neighboring POIs, for example, when drawing and filling a series of POIs for visual area (V1, V2, V3..) on top of e.g. a polar ange map. This issue has been fixed in this release, i.e. POIs remain visible when drawing lines and filling closed regions; Visible POIs also serve as borders when filling a closed contour.
POIs to SMPs	The function to convert POIs into SMPs ('Create' button in 'POIs -> SMPs' field of 'POI Analysis Options' dialog) did not work in previous releases. This issue has been fixed.
POIs to Draw Colors	The function to convert POIs into draw colors ('Create' button in 'POIs -> Regions' field of 'POI Analysis Options' dialog) did not work in previous releases. This issue has been fixed.
pRF Plot	When inspecting pRF data by CTRL-clicking on voxels, the displayed values of pRF maps in the 'Image Reporter' were different than the values shown in the voxel tooltip display (and statusbar) in case that pRF volume maps had lower resoluton than the anatomy. The reason was that the pRF plot used the lower resolution voxels while the tooltip used the upsampled anatomical resolution map values. This has been resolved by using also the upsampled values for the values reported in the pRF plot.

BrainVoyager 22.2 Release Notes

New Features

Project and Workflow Programming Interface	This version introduces a powerful Python programming interface for the management of projects, workflows, datasets and reports. With a few lines of code, one can create and manage projects, define and run workflows, inspect notebook reports, and open and use produced (derived) datasets. Since workflows run in the same way across all subjects, the written Python code serves as an executable document for reproducible data analysis. The Python interface uses the BIDS folder structure to discover the structure of projects, data and workflows without the need of a separate database. Additional meta-information about subjects, analysis parameters and data flow connections are stored in human readable JSON files at appropriate locations in the BIDS directory tree. Furthermore, rich editable quality assurance reports are generated as self-contained BrainVoyager notebook files. For further details of the programming interface, see the "Python Developer Guide".
New Data Analysis Manager	The new Python interface (see above) serves also as the basis of BrainVoyager's new Data Analysis Manager. The predictable BIDS folder structure and supporting JSON files no longer require a separate (MySQL) database as used in the old Data Analysis Manager. Building the programming as well as user interface project management tools on a common interface has the advantage that changes in Python are automatically reflected in the "Data Analysis Manager" window allowing to freely mix the two approaches to project management. This approach makes it also possible to use other (BrainVoyager or other software) tools to process datasets without getting out of synch with the informaton stored in a separate database as could happen in previous versions. Note that the old Data Analysis Manager is still available but marked as deprecated and it will be removed in a future release. It is possible to switch between the old and new Data Analysis Manager in the "GUI" tab of the "Settings" ("Preferences" on macOS) dialog. For details, see chapter "Data Analysis Management" in the updated User's Guide.
Inter-Subject Correlation Analysis	This release adds Inter-Subject Correlation (ISC) analysis. While there was a very old ISC tool available based on multiple regression in past releases, it was rather limited in scope. The new implementation adds the possibility to run pairwise correlations of a provided list of 4D time course (VTC) files [as well as a version calculating the correlation of each 4D dataset with the mean of all other datasets serving as the target. Furthermore, ISC can be computed for a set of provided regions-of-interests (VOIs) producing correlation matrices for mean regional volume time courses. The ISC analysis tool is available in the newly added "FuncConn" menu. For more details, see topic "Inter-Subject Correlation (ISC) Analysis" in the "Functional Connectivity Analysis" chapter of the User's Guide.
Interactive GLM Visualizer	The new Interactive GLM Visualizer, developed originally for the BV EDU version, provides a tool to inspect how a time series is fitted by the weighted sum of predictor time courses. The data time course and scaled predictor time courses are shown in vertical time-aligned plots with associated beta values. Individual predictors can be turned off to study their impact on the overall fitted time course. For didactic purposes, beta values can also be changed, which can be used, e.g. as an exercise, to manually fit a time course. The GLM visualizer can be invoked easily from the context menu of a Time Course Plot window, which will automatically create a design matrix from a linked protocol. For options to define and load custom defined design matrices, the tool can also be called via the "GLM Builder and Visualizer" item in the "Analysis" menu.

Enhancements

Improved MNI Normalization	The MNI normalization function has been improved to provide more robust results in cases of source (native space) brains that are rotated away substantially from the AC-PC plane. The improvement uses a new iterative rigid rotation step bringing the brain in a near-ACPC (nACPC) space before the full (12-affine) normalization. A second improvement addresses the issue that some brains were not exactly fitting in the MNI bounding box after template matching. This is now addressed by a step (enabled as default) that uses a global non-linear adjustment by scaling 6 sub-cuboids into the MNI bounding box. Furthermore, a template with more details is now used as default. For more details, see the updated "MNI Normalization" topic in the "Transformation to Normalized Space" chapter of the User's Guide.
VMR-Specific VOIs	In previous versions only a single set of volumes-of-interest (VOIs) could be loaded and displayed. In this release, each VMR document keeps its own set of VOIs, which makes it possible to display different VOIs for different anatomical documents in the multi-document workspace.
More than 254 VOI Labels	While a VOI file could have an unlimited number of VOIs, only the first 254 VOIs could be visually displayed. This limitation has been lifted to 65534 VOI displays (1 entry of 65535 values is reserved for a "no label" tag) by switching internally from a single-byte (8 bit) to a two-bytes (16 bit) data structure. This is also useful when importing atlas data (e.g. stored in NIfTI files) where each label is marked by a different intensity value. In previous versions a maximum of 254 labels could be processed but now also larger label counts are supported. Note that when importing a (int or float) NIfTI atlas file, the labels are stored in the V16 file generated next to the VMR file (8 bit) itself since the VMR document alone can not show all labels if exceeding 254 values. It is, thus, important to convert the V16 data into VOIs by using the "Conert VMR/V16 Label Values to VOIs " function available in the "Volumes" menu to obtain VOIs for all labels stored in the V16 data set.
Support for 4D NIfTI in Normalized Space	NIfTI files containig 4D time courses were supported already in previous versions but only if they were in native (scanner) space; these 4D NIfTI files are converted into FMR-STC files. It is now possible to save normalized (MNI / TAL) VTC documents as 4D NIfTI files from the 'VTC Properties' dialog. Furthermore 4D NIfTI files in normalized space (sform code of 3 (Talairach) or 4 (MNI)) can now be read and will be saved as VMR-VTC documents. At present, only normalized NIfTI files with a transformation matrix that does not contain rotations (and shears) are supported, i.e. the data must have been stored after normalization in the file. If the transformation matrix contains non-integral scales, the data will be scaled to the next better integral VTC resolution (e.g. a voxel size of 2.4 or 2.7 will be rescaled to a resolution of 2.0); in case of integral scales (e.g. 2.0 or 3.0) the data will not be resampled when creating the VTC document.
Python and Notebook Enhancements	Besides the new Project and Workflow API, Python support has been enhanced. The "Select Python On Disk" dialog now supports multiple different Python versions - in this release both Python 3.6 and Python 3.8 are supported. For better support of TensorFlow, it is recommended to use Python 3.8 and TensorFlow version 2.2, for details see the updated "Installing and Enabling Python" topic in the "General Information" chapter of the User's Guide. The BV Notebook window now auto-saves edited notebooks and asks whether one wants to use them (if available) when restarting after a crash. In addition, the auto-generating Python code functionality has been further extended sending now also commands related to mesh creation and morphing to a receiving BV notebook (support for auto-generating CBA code is planned for the next release). For details, see the updated "Auto-Coding GSG Analysis" notebook and updated topic "From User Interface Actions to Python Code" in the "BV Notebooks" chapter of the User's Guide.
Derivative Predictors	It is now possible to add time derivative predictors next to each main predictor of a single-run design matrix by enabling the "Add time derivative" option in the "Single Factor Design" tab of the "Single Study GLM Options" dialog. The effect of the derivatives can be, for example, inspected using the interactive GLM visualizer by modifying the value of derivative predictor's beta value.
Adjusting Exclusion of First Predictor	When defining main predictors using the "Define Pres" button in the "Single Study GLM" dialog (or the corresponding button in the "Options" dialog), the program uses the global setting to exclude or include a predictor for the first condition. Excluding the first condition is useful in case it is a "Rest" or "Baseline" condition. However some protocols might not define an extra predictor for the first condition, which may lead to the exclusion of a condition predictor. This potential issue could go unnoticed by users. This has been improved by now always displaying all defined predictors as default after using the "Define Preds" function. More importantly, the program now guesses from the name of the first condition whether it is a baseline condition and warns the user in case that the "Exclude first condition" setting does not match to the current protocol. Furthermore, the program pops-up a message offering to adjust the setting automatically - if accepted, the setting is changed and the predictors are redefined accordingly.
Ideal Time Courses in Event-Related Averaging Plots	Event-related averaging plots may now show ideal (noise-free) time courses as predicted by the generic HRF function. This may be useful to assess how good empirical event-related averages match in time and extent with ideal predictions. The ideal time courses can be enabled by turning on (default) the new "Ideal" option in "ROI Signal Time Course" plots. The ideal averaging time courses are only available if a ".dat" file with the same base name as a ".avg" file is available. This file is now created automatically when generating "AVG" files in the "Event-Related Averaging Specification" dialog by saving the time courses displayed in the "Expected response plot" section.
Removing Sections from 4D Time Course Datasets	FMR-STC time courses can now be edited to remove problematic sections (e.g. corrupted by motion) from a time course. In case that a protocol is linked to the FMR-STC data, it will be adjusted accordingly. The hemodynamic delay should be considered, however, when editing time course datasets and it is advised to only remove sections within baseline periods if possible.
Integrated Access to Functional Connectivity Tools	a new "FuncConn" menu has been added in the main menu bar to simplify access of available functional and effective connectivity tools in BrainVoyager, including ICA, GCM, ISC and graph-theoretical connectivity analysis..
Matrix Color Displays with Numbers	When presenting data in image-like matrices (e.g. correlation matrices or dissimilarity matrices), the program now shows teh (e.g. correlation) values in cells in case there is enough space for text available.
Custom Cross Settings	When changing settings of the cross displayed in VMR windows, they were reset to defaults in later sessions. The new 'Save As Default' button in the '3D Coords' tab of the '3D Volume Tools' dialog can now be used to store custom settings permanently. If one wants to go back to the system default cross parameters, one can use the 'Reset' button beneath the 'Save As Default' button.
Show VTC Volume	The 'Show VTC Vol' function in the 'Spatial Transf' tab of the '3D Volume Tools' dialog now creates a 16-bit representation instead of 8-bit. This allows to adjust the contrast and brightness of the visualized functional VMR volume. The 'Contrast And Brightness' dialog is automatically invoked in case the new 'Adjust contrast dialog' option is turned on.
Ultra-High Resolution Sphere for CBA	While the high resolution standard spheres for cortex-based alignment (CBA) have a high enough resolution for most cases (# vertices: 163,842, # triangles: 327,680), a "ultra-high" resolution option has been added with more than a million triangles (# vertices: 655,362, # triangles: 1,310,720) that might be useful for meshes created from sub-millimeter anatomical datasets. The new option is available in the "Resolution" section of the "Curvature" tab of the "Cortex-Based Alignment" dialog. Note that the resolution of standard sphere meshes needs to be selected at the begin of CBA, especially before the standard sphere maps the original folded cortex of hemispheres that have been inflated to a sphere. The ultra-high resolution option has been added experimentally in this release and will need currently some custom fine-tuning of morphing parameters despite provided adjustments of default parameters.
Movie Studio	Animations created with Movie Studio can now be exported as lossless WebP animations, which can be further converted to .mp4 (or similar) movie formats externally using custom quality / file size adjustments. Furthermore, mesh visibility is now stored at each state, which is useful to show/hide meshes in multi-mesh scenes. Also the alpha value of a mesh is now stored at each state making it possible to animate mesh transparency.

Bug Fixes

VMP Smoothing	When spatially smoothing VMP maps by using the "Smooth" button in the "Map Options" tab of the "Volume Maps" dialog, the result was shown as expected but the smoothed map was not saved for further use, i.e. it was not available for saving or for sampling from surface meshes. This issue has been fixed.
Granger Causality Mapping	The 'RFX GCM Plugin' did not work for MNI datasets and also did not produce group VMP maps that can be used as input for an RFX analysis. These issues as well as some minor ones in the (RFX) GCM plugins have been fixed in this release. Note that these plugins can now be called from the new 'FuncConn' menu.
Predictor z-Transformation	In rare cases, the z normalization option for predictor time courses in the 'General General Linear Model' dialog did not work because of unprecise rounding of float data. This issue has been fixed by replacing float with double precision values for the calculation.
Contrast Brightness Dialog	The contrast and brighntess dialog now applies to the secondary VMR if selected using the 'Show secondary VMR' option in the 'Spatial Transf' tab of the '3D Volume Tools' dialog. In previous versions it applied always to the primary VMR even if this was not shown.

BrainVoyager 22.0 Release Notes

New Features

DNN Segmentator	This version introduces brain segmentation using a deep neural network (DNN) with an advanced "Tiramisu" architecture. This DNN Segmentator has been developed for high-resolution sub-millimeter data to segment grey matter with very high accuracy so that both inner (white-grey) and outer (pial) boundaries are obtained that can be used with minimal editing to construct corresponding cortex meshes. The high-quality segmentations are especially suited for cortical thickness measurements and mesoscopic (laminar and columnar) fMRI. The tool has been developed in Tensorflow using Python. The tool can be easily launched from the new "DNN Segmentation" dialog that runs the neural network via the embedded Python interface (see below). After the segmentation process has been completed, the "DNN Segmentation Postprocessing" dialog can be used to fine-tune the segmentation, to separate left and right hemispheres and to create standard segmented VMRs and reconstructed cortex meshes. For details see section "Deep Neural Network Segmentation" of the "Brain and Cortex Segmentation" chapter in the updated User's Guide. Also note that using this function requires an installation of Python 3.6 and TensorFlow 2.0, for details see section "Enabling Python" in the "General Information" chapter of the User's Guide.
BrainVoyager Notebooks	This release adds BrainVoyager Notebooks supporting reproducible data analysis by documenting performed analysis steps in the form of executable (auto-generated or self-written) Python code. BV Notebooks not only offer (script) programmers a means to write and document code but they also support reproducible analyses for non-coders by converting essential GUI actions into corresponding code. If, for example, the "GO" button in the "FMR Preprocessing" dialog is clicked, all selected preprocessing operations with (non-default) arguments are converted in BV Python code and added to the current notebook (if enabled). Note that code can be easily enriched with images, animations, rendered Markdown text as well as embedded BrainVoyager viewers so that users can create rich documents. For more details on how to use BrainVoyager Notebooks, see chapter "BV Notebooks" in the updated User's Guide.
Image Annotator	The new Image Annotator provides a streamlined approach to annotate images with text, rectangles, circles and arrows. The annotations are vector based and stored as overlays that can be edited at any time. The annotator can be called from BV Notebooks that store made annotations automatically for later editing. The annotator can also be used to annotate images in BV's "Image Reporter" that may be used as frames in created movie animations (see below). More details can be found in topic "Image Annotator" in the updated User's Guide.
Animation Player and Movie Generation	The new "Animation Player" is available from the "Options" menu and can play simple movies that are either generated and saved automatically (e.g. during motion correction) or manually composed in the enhanced "Image Annotator". Movie animations are stored in Google's efficient "webp" format and can also be embedded in BV Notebooks (and web sites), e.g. to toggle before / after images that highlight (pre-)processing effects. More details can be found in topic "Animation Player" in the updated User's Guide.
Python Plugin	Python support is now enabled via the new "EnablePythonPlugin" plugin that is only loaded when Python is needed. BrainVoyager can now be launched on any system no matter whether (a supported) Python is available or not. Since Python becomes increasingly important for BrainVoyager, it is, however, strongly advised to install a supported standard Python version. Separating Python in a plugin also now allows to switch between multiple Python versions and environments (currently only 3.6 based environments) using the "Select Python On Disk" dialog. For details on how to setup one or more Python environments with support of Tensorflow for the DNN segmentation tool, see topic "Enabling Python" in the "General Information" chapter of the User's Guide.

Enhancements

Starting with NIfTI Files in Data Analysis Manager	In previous releases, the "Data Analysis Manager" only allowed to start with the "Create Document Workflow" that generates NIfTI files from raw DICOM files. It was, however, not possible to start directly from NIfTI files. The new "Import NIfTI Document Workflow" now supports to use NIfTI files as input, which makes it, for example, possible to start with NIfTI data from public repositories; it also works well with NIfTI / BIDS data created with the updated "Create Document Wizard" (see next point). For more details, consult the "Import NIfTI Document Workflow" topic in the "Data Analysis Management" chapter of the User's Guide.
BIDS / NIfTI Support	This release further improves BIDS support. The "Create Document Wizard" now allows not only to save a new dataset as a NIfTI file but to store it in the correct sub-folder of a specified (existing or new) project, for details consult the "Create Functional Documents" and "Create Anatomical Documents" topics in the "Getting Started" chapter of the User's Guide. Also when linking a VTC from a participants VMR file in a BIDS anat folder, the VTC dialog now opens in the corresponding "..fmr/" folder as default instead of the anat folder. Furthermore, import of anatomical NIfTI has been improved by now also reading (2 and 4 byte) integer and floating point values instead of only byte values. These formats are used to create both a VMR and a V16 dataset when importing NIfTI files; if possible, intensity values will not be rescaled which improves compatibility with atlas-related region (label) files.
Movie Creation with Image Reporter	The "Image Reporter" has been substantially improved to serve now as a composer of simple movies (animations) that can be stored in "webp" format and played in the new "Animation Player " (see above) or embedded in notebooks. Images can be easily added to "Image Reporter" by several keyboard shortcuts catching the whole program window, the current dialog or, most importantly, the view of the current document. To create a movie, all accumulated images must have the same size. Frames can also be annotated using the new "Image Annotator" before creating a movie. For more details, see topics "Image Cells", "Image Annotator" and "Animation Cells" in the "BV Notebooks" chapter of the User's Guide.
BV Python API and IDE	Python integration and tools have been substantially enhanced in this release. The BrainVoyager commands have been rewritten, extended and simplified. Names of commands follow now Python style (e.g. correct_motion instead of CorrectMotion). In BV Notebooks, integrated documentation highlights function signatures as tooltips and a more elaborate description of parameters are displayed in the "API Help Output" pane when hovering with the mouse over commands or when typing commands. See the updated "Python Developer Guide" (WIP) for details.
VTC Preprocessing	While the "VTC Preprocessing" dialog offered the possibility to run high-pass temporal filtering, only the FFT option was supported. The updated dialog now also supports the GLM-Fourier (default) and GLM-DCT high-pass filter options in the same way as is available for FMR-STC data. Note that the GLM-based high-pass filter procedures also remove linear trends since the created design matrix not only contains the sine/cosine basis functions but also a linear trend predictor.
VOI VMR Functions	The Volumes-Of-Interest dialog now is initially smaller. If expanded, it offers new VOI VMR tools including creation of intensity histograms and creation of surfaces from selected VOIs. The main dialog part offers a new Max Component operation that is useful to remove small sub-parts from a (segmented) VOI keeping only the largest connected part.
Zoom View	The Zoom View now shows the same voxel information panel when hovering across voxels than the VMR view including intensity, map and VOI details. This allows to inspect e.g. segmentation results and supports editing operations. In the context of the DNN segmentation tool, one can, for example easily study tissue probabilities and intensity values across tissue borders by hovering the mouse.
Calculate FDR in Maps Dialog	When a statistical volume map did not have a FDR table, the FDR approach for thresholding was not available. The only way to get a FDR table was to (re-)run / overlay a GLM. It is now possible to recalculate a FDR table from the map's data using the new "Calculate" button next to the "Use FDR" option in the "Thresholding" field of the "Statistics" tab of the "Volume Maps" dialog. Note that this only works in case that the map represents a supported statistic and has properly defined degrees of freedom.
Continous Curvature LUT	A new curvature LUT has been added that changes continously from near white to dark grey when curvature changes from high convex to high concave. Values in the transition from convex to concave are colored mid-grey. Note that this color LUT does not highlight the transition from concave to convex as the standard curvature color but it provides a useful visualization, especially for pial meshes, where gyri are colored bright and sulci colored dark. Besides loading the new LUT, the "Background and Curvature Colors" dialog now also has an option to use the new LUT.
Import of FreeSurfer Files	It is now possible to read essential FreeSurfer files (meshes, curv, annot and .mgz). Depending on the format, a file is converted into a BV VMR, SRF, SMP, or POI file. To import a anatomical file, the "Import Freesurfer MGH/MGZ File" item in the "Options" menu can be used. To import a mesh file, the "Binary Freesurfer File" in the "Import Mesh" sub-menu of the "Meshes" menu can be used. A mesh-compatible surface map can be imported by selecting the "Freesurfer 'Curv' files" files filter in the "Open SMP File" dialog (invoked by clicking the "Load" button in the "Surface Maps" dialog). A mesh-compatible annotation file can be imported by selecting the "Freesurfer Annot files (*.annot)" files filter in the "Select POI File" dialog (invoked by clicking the "Load" button in the "Patches-Of-Interest Analysis" dialog).
Auto-Scaling Voxel Beta Bar Plots	The voxel beta bar plots showed data in a fixed value range in order to allow comparison of bar height when hovering the mouse across voxels. When however values exceeded the upper y axis range value, bars were clipped. This release updates bar plots by keeping a default or specified upper value as long as all displayed bars have smaller values. If at least one bar exceeds the threshold, the upper range value is automatically reset to a value a bit higher than the maximum value. This allows to interpret relative heights within the plot of a voxel and allows comparisons across voxel for most cases. If for example the maximum percent signal change value is set to 5.0 (default), most voxel's beta values will be smaller than this value.
PSC in Time Course Plots	When selecting regions with the mouse to invoked time course windows, the displayed values are shown as raw signal values instead of more useful percent signal change (PSC) values. If FMR-STC and VMR-VTC data refer to a protocol, the time course plots now show PSC values as default. The program uses non-defined time points and/or time points defined in a baseline condition to determine (time shifted) periods used to calculate the mean signal of the baselines. Note that the correct baseline setting (no baseline condition or 'Use first condition as baseline' or 'Use last condition as baseline') need to be made to get correct results, which is usually done when performing a "single-study GLM" or using the "Settings" dialog.
VOIs as Masks	When running a spatial mask-based (e.g. brain or cortex-based) statistical analysis, a special MSK mask file can be provided. It requires however an extra step to calculate MSK, e.g. when one has defined a VOI file. It is now possible to directly use a VOI file (and a specified VOI inside the file) as a spatial mask when running linear correlation tests and (single study so far) GLMs.

Bug Fixes

POI Labels	when POIs were shown with 3D text labels and then turned off in the POI Options dialog followed by a click on Hide POIs in the POI dialog, BV crashed. This issue has been fixed.
Outline POIs	The function to create outline (border) POIs from more conventional filled POIs did not work in the previous version. This issue has been fixed.
POI GLM and POI ANOVA	The functions to run POI GLM and POI ANOVA analyses could not be launched from the "POI Analysis Options" dialog in previous releases. These functions have been re-enabled in this release.
Probabilistic Maps from VOIs	Creating probabilistic maps, including MPMs, from overlapping VOIs did not work in the previous release. This has been fixed.
Verification of Functional Coverage	The function to check the region of consistent overlap of functional (VTC) data ("Verify Functional Overlap" item in "Options" menu) did not properly work in the last version; there was for example some noisy coloring for the 100% overlap case and individual volume maps could not be visualized (unless the maps were saved and reloaded from disk). This issue has been fixed.

BrainVoyager 21.4 Release Notes

21.4.5 Patch Release

Volume Maps

When loading volume maps with the same native resolution as the hosting 3D anatomical (VMR) file (VMP resolution relative to VMR resolution = 1), the volume maps were not shown on the VMR when selected. This issue has been fixed in this patch release.

21.4.4 Patch Release

FMR-VMR Alignment	When original 3D anatomical data are not recorded as a series of sagittal slices, the program suggests to reorient them to its standard sagittal orientation calculating a "To-SAG" reorientation matrix. When running FMR-VMR alignment to such a VMR that had been originally recorded in a non-sagittal orientation, the header-based initial alignment step includes the "To-SAG" reorientation transformation when aligning FMR to VMR space. In previous 21.x versions this matrix was, however, not saved in the "_IA.trf" transromation file and one needed to manually add a "To-SAG" matrix. This issue has been fixed in this release, i.e. FMR-VMR alignment works fully automatically also for non-sagittally oriented datasets.
Cortical Depth Sampling	Several improvements have been made for both whole-cortex mesh and local regular grid smapling to improve laminar fMRI analysis. For whole-cortex mesh depth sampling a choice between trilinear (default) and nearest neighbor (new) interpolation to sample volume map data has been added; furthermore a bug has been fixed that prevented running sampling in case that the option to save created depth meshes was not turned on. For local regular grid sampling, a warning is now issued in case one samples depth grids with an input VMR dataset that does not contain grey matter (100) and white matter (150) tissue labels, which is recognized by a "_WM_GM" substring in the VMR file name; this warning is useuful since the GM (100) intensity is used to restrict (mask) provided VOIs to grey matter voxels, which leads to few considered voxels when using a VMR with a range of intensity values for grey matter. Furthermore, issues with the visualization in original (folded) cortex space has been fixed by now positioning representations of grids and connecting streamlines (as lines or tubes) precisely aligned with the visualization of reconstructed depth layer meshes that can be used to sample and visualize functional layer data.
Updating Surface Maps Dialog	When loading a new mesh, the surface maps dialog was not properly updated (cleared) in case that it was used with a previous mesh producing error messages when selecting (no longer existing) maps for visualization. This issue has been fixed.
Converting VOIs to ROIs	While one could convert ROIs to VOIs in previous versions, the inverse transformation, i.e. the possibility to transform VOIs into FMR space was not available, which can be, for example, useful to prepare ROIs for real-time fMRI processing with Turbo-BrainVoyager. This functionality has now been added with the new "Create FMR-ROIs from VMR-VOIs" dialog that is available in the "Transformations" tab of the "VOI Analysis Options" dialog.

21.4.2 Patch Release

IIHC and Advanced Segmentation	Running the intensity inhomogeneity correction (IIHC) tool (availble in the "16 Bit 3D Tools" dialog) could result in a VMR with high contrast rendering grey matter voxels very dark; this could have a negative impact on grey matter detection when subsequently running the advanced segmentation pipeline. This issue has been fixed by better ensureing that identified grey matter and white matter peaks are set to an intensity value of 100 and 150 respectively, in case that the "Map GM and WM peaks to standard VMR values" option is turned on (default). V16 grey and white matter intensity peaks can also be mapped to the standard VMR grey and white matter values by using the new "Standard GM WM" button in the "Contrast And Brightness" V16 dialog that can be called using the "Brightness" button in the "16 Bit 3D Tools" dialog.
Subcortical Structures in Advanced Segmentation Tools	When marking subcortical structures in ACPC space using the "Label As WM" button in the "Preparation" tab of the the "Advanced Segmentation Tools" dialog, a Talairach landmark file needs to be provided to ensure correct adjustment of a normalized template file. In previous versions this was not required leading to application of templates that were not properly adjusted to an individuals ACPC space (only voxel resolution was adjusted). This is now no longer possible, i.e. the subcortical labeling function is only applicable if a .TAL file is provided. Furthermore, a new "Mark Subcortical Structures" dialog can be invoked by clicking the "Options" button next to the "Label As WM" button. The dialog allows to specify details about the performed subcortical labeling operations, including setting the maximum intensity value for ventricle region filling, expansion of marked ventricles into white matter, and whether the adjusted subcortical mask should be applied or not.
Holes after Advanced Segmentation	When clicking the "POlish" button in the "GM-CSF Border" tab of the "Advanced Segmentation Tools" dialog, the resulting "_WM_GM.vmr" output file containing grey (intensity: 100) and white (intensity: 150) matter voxels could contain small black holes in some cases. This issue has been fixed.
POI Details and Document Switching	The "POI Details" button in the "POI Functions" tab of the "POI Analysis Options" dialog did not work, i.e. the "POI Details" window did not appear. Also the "POI Map Peak Vertices Table" button did not work. These issues have been fixed. In case that multiple 3D Viewer windows (with different associated VMR documents) were open, switching from one surface window to another one did not update the POI dialog, i.e. the displayed POIs did not update. This issue has been fixed.
Map to VOIs	When converting map clusters to VOIs using the "Convert Map To VOIs" dialog (invoked using the "Convert Map Clusters to VOIs" item in the "Options" menu), the default value for cluster thresholding was set to 300 reflecting anatomical resolution assuming a factor of 3x3x3 multiplying the number of voxels in a map cluster. Since cluster sizes are expressed in map voxels in recent versions, this value was too high. A new default value of 12 map voxels (or the current map cluster size if that is higher) is now set as default.
Mask Maps with VOI	Using the "Mask with VOI" button in the "Advanced" tab of the "Volume Maps" dialog to mask one or more maps with a selected VOI did not work correctly. This issue has been fixed.
VTC Averaging	When attempting to average VTC files using the "Average 3D Data Sets" dialog (invoked using the "Average 3D Data Sets" item in the "Volumes" menu), an error message occured stating that VTC reference spaces would not match even if they did. This issue has been fixed.
Scripting	When applying MTC preprocessing commands, the "FileNameOfPreprocessdMTC" string property always returned an empty string. This issue has been fixed.
Clicking GLM Predictor Names	There are several possibilities to define GLM predictors in the "Single Study General Linear Model" dialog. While the easiest is to use the "Define Preds" button, some cases may require more interactive definition using clicks in the presented time course plot or clicking on condition names in the "Condition List" box; when clicking on a condition name with the left mouse button, the corresponding condition intervals will be set to 0.0, while clicking with the right mouse button sets them to 1.0. In previous versions this would also happen when predictors had been already defined using the "Define Preds" or "HRF" button, which might lead to non-intended predictor changes. In order to avoid these changes, clicks on condition names are no longer affecting predictors if the HRF function has been applied.
For Pluign Developers - API Changes for VMPs	As detailled in the 21.4 release notes (see "Interpolation Preference for Volume Maps" item below), the volume maps data structure has been reorganized internally in order to remove the need for two different data structures, i.e. native and anatomical volume maps. The new map type is functionally nearly identical to the old "native-resolution" map type but it is also able to store map data in anatomical resolution. While this makes code simpler and functionality more robust (no code needed to keep the two map data structures in synch), it affects the volume map plugin API. In order to keep plugins using NR maps running, the API has not been changed in the 21.4 release, but most functionality of NR map commands is no longer available. Plugins using AR maps need thus to be changed exchanging AR calls with corresponding NR map functions e.g. to get and set header information. The only AR map function still needed is "qxGetARVMPOfCurrentVMR", which provides access to pointers of single anatomical-resolution map data. The corresponding NR functions must also be used to load, save, create and delete maps. Note that the API for the two old map types will be deprecated and replaced with a direct access API to the new unified map type in BrainVoyager 22.

New Features

IIHC of Functionl Volumes

Intensity inhomogeneities are not only observed for anatomical data but may also be present in functional data affecting visualization of statistical maps overlaid on functional data. More importantly, inhomogeneities in functional data may reduce the quality of intensity and gradient-driven coregistration of functional and anatomical data (fine-tuning alignment step). This release introduces intensity inhomogeneity correction (IIHC) for functional data volumes operating in the same way as for anatomical data. This operation is performed on the functional volume created during header-based coregistration, i.e. before starting gradient-based or BBR-based fine-tuning alignment. The IIHC corrected functional volume in native anatomical (VMR) space is also projected back into the FMR slice space (inverting header-based alignment) for visualization purposes. For details, see topic "Intensity Inhomogeneity Correction of Functional Volume" in the "Coregistration" chapter of the User's Guide.

VOIs from Numerical Region Labels

When importing anatomical atlas volumes stored in 1-byte NIfTI files, intensity values often correspond to numerical labels identifying segregated (non-overlapping) brain regions (e.g. to store a maximum probability map). Converting such numerical labels one-by-one using the "Define VOI" operation is a tedious process. In this release a new "Convert VMR Values to VOIs" dialog has been introduced that automates this operation. The dialog can be invoked using the new "Convert VMR Values To VOIs" item in the "Volumes" menu. The inverse operation is also available, i.e. to convert VOIs to numerical region labels. For details, see topic "VOIs from Numerical Region Labels" in the "Regions-Of-Interest" chapter of the User's Guide.

Enhancements

BIDS / NIfTI Support	This release further improves BIDS compliance. TSV sidecar files are now properly used to create BrainVoyager protocol (PRT) files; if available, the "TaskName" entry from the JSON sidecar is also used as the protocol experiment name. TSV files are saved according to the specification when exporting functional datasets. If available (from Siemens DICOM data), slice timing tables are now saved in the JSON sidecar file when saving NIfTI functional files from (scanner-space) FMR files (when created from DICOM files). It is now also easily possible to generate VOI files from imported anatomical atlas NIfTI files that contain numerical labels to identify brain regions (see "Creating VOIs from VMR" item above).
Script Support for NIfTI Files	It is now possible to load and save NIfTI files via Python (and JavaScript) scripts. There is no new command - the respective functionality is invoked in case that the file name parameter of the "OpenDocument" command of the global "BrainVoyager" object contains the file extension ".nii" or ".nii.gz". The NIfTI file extension also triggers exporting VMR anatomical and FMR functional documents as NIfTI files when using the "SaveAs" command of a "Document" object. Note that the earlier deprecated opening and creation document command names using "Project" (e.g. "CreateProjectVMR") have now been removed, i.e. scripts need to use the corresponding "Document" commands (e.g. "CreateDocumentVMR").
Denoising MP2Rage	When opening MP2Rage "UNI" files, the background voxels exhibit high intensity values which makes subsequent processing and visualization difficult. In order to remove the high-intensity background noise, the new "MP2Rage Background Denoising" dialog can be used that is available in the "Volumes" menu. The dialog asks for MP2Rage files ("UNI", "INV1" and "INV2") as input and produces a denoised VMR/V16 as output. For details, see topic "Removing MP2Rage Background Noise" in the "Brain and Cortex Segmentation" chapter of the User's Guide.
Improved (f)CBA	Several Cortex-Based Alignment tools have been improved, most notably the handling of anatomical and functional landmarks in the context of fCBA, which now allows to use multiple surface maps (e.g. from multiple POIs) that are treated as separate alignment constraints with their own set of parameters. For details, see the updated topic "Functionally Informed Cortex-Based Alignment" in the "Cortex-Based Alignment" chapter of the User's Guide.
Oblique Mesh Slicing	The "Mesh and Volume Slicing" panel in the "3D Viewer" now allows visualization of an oblique slice in addition to the 3 orthographic slices. When clicking the oblique slice icon in the right upper corner of the panel, additional buttons will appear allowing to rotate the slice around two angles and to move it in a direction orthogonal to the current slice plane orientation. For details, see the updated topic "The 3D Viewer" in the "Getting Started" chapter of the User's Guide.
Zoom View Editing	The voxel editing tools in the "Zoom View " have been improved, including the possibility to use a pen with a size larger than 1 pixel with support for undo/redo; a spin box to set the pen width has been added to the "Editing" toolbar. Furthermore, the "Editing" toolbar can now be dragged to desired positions inside the "Zoom View". It is now also possible to move the contents displayed in the "Zoom View" by moving the mouse while holding down the ALT key - this will be translated in movements of the zoom rectangle in the "VMR View" window. There is also a new icon allowing to turn on drawing mode without the need to press a meta key (Ctrl or Cmd), which is especially useful when using touch screens with pen support on Windows. For details, see the updated topic "Manual Segmentation Tools" in the "Brain and Cortex Segmentation" chapter of the User's Guide.
Transforming FMR-ROIs to MNI Space	It is sometimes useful - especially when using Turbo-BrainVoyager - to convert ROIs defined in FMR slice space to normalized space. While it was possible to transform ROIs to native, ACPC and Talairach space using the options in the FMR "Region of Interest" dialog (see also bug fix below), this version adds the possibility to transform FMR-ROIs also to MNI space.
Mesh to Filled VMR	A variant of the "Mesh to VMR" function called "Mesh to Filled VMR" in the "Mesh Spatial Transformations" dialog that not only projects the contour (based on mesh vertices) into the linked VMR but also fills the interior of the projected boundary (e.g. for head meshes or hemisphere meshes without holes). This function is supported by a new high-density projection from points subsampled inside mesh triangles resulting in closed VMR contours. This function can be, for example, used to create masks for head meshes, which then can be used to make voxels inside the head non-transparent (see next point). This tool is described in the "Projecting a Mesh as Filled Volume" topic in the "Useful Tools" chapter of the User's Guide.
Range / Box Filling with 2nd VMR as Mask	It is now easier to use masked range and box filling operations in the "3D Volume Tools" dialog. When loading a mask as the second VMR, it can be enabled by turning on the new "2nd As Mask" option in the "Segmentation" tab before using the "Range" or "Fill Box" buttons. The masked range function can be used, for example, for improving Mesh-VMR slicing by setting black voxels (0-10) inside a head or brain segmentation to a non-transparent black value (11) while keeping background values outside the mask at value 0 (shown transparent during slicing). It is now also possible to swap the primary with the secondary (and primary with tertiary) VMR, e.g. to apply operations like region growing.
VMR View Voxel Tooltip	When hovering over the "VMR View", relevant information about the voxel under the mouse cursor is now displayed in a tooltip, including information about the voxel coordinates (in the VMR reference space) and VMR intensity value. If volume maps are shown, the corresponding (statistical) values are also shown in the tooltip for each displayed map. Furthermore, the names of visualized VOIs will also be shown under the cursor. The tooltip appears in close proximity to the current mouse position when hovering. The tooltip is not shown when holding down a mouse button. While the tooltip display is enabled as default, it can be toggled using the "Voxel info tooltip" option in the "3D Coords" tab of the "3D Volume Tools" dialog. If turned off, the voxel information is available in the status bar of the main window as in previous versions.
Interpolation Preference for Volume Maps	It is now possible to set an interpolation preference for volume maps at both individual and global level. The global (persistent) level can be specified in the "Data" tab of the "Preferences" dialog where either the option "Nearest neighbor" or "Trilinear interpolation" can be chosen in the "Preference for resampling volume maps to anatomical resolution" field. When a volume maps file is loaded from disk, the global setting specified is used when upsampling the data of all sub-maps to anatomical resolution (if necessary). For visualization purposes, the global setting can be overridden at a sub-map specific level by toggling the "Trilinear interpolation" option in the "Resampling to anatomy" field of the "Volume Maps" dialog. This flexibility is possible by a reorganization of how volume maps are stored internally: while the new volume maps behave like the old "native-resolution" maps, they are able to store the map data at native resolution as well as at anatomical resolution. This makes the existence of two different map types (native and anatomical) obsolete, i.e. there is now only one volume map type in BrainVoyager.
PDF Viewer	A PDF Viewer has been integrated in BrainVoyager to show PDF documents. This is currently mainly used for the new EDU version of BrainVoyager but also for the reports generated by the Data Analysis Manager. To support efficient document navigation, the PDF Viewer supports an outline view (tree of link entries, usually used for jumping to target pages) as well as clickable hyperlinks (for internal pages, not for external websites) inside the PDF document.

Bug Fixes

Cortex-Based RFX GLMs	When running cortex-based RFX GLMs, the program crashed. This issue has been fixed in this release.
Reading MTC Files	MTIC files contain a reference to the VTC file from which they are created for information purpose, which is displayed in the MTC Properties dialog. In the rare case that this file reference was longer than 256 characters, the program would crash when reading the respective MTC file. This issue has been fixed in this release.
Anonymize DICOMs	When anonymizing DICOMs, the resulting files were not readable anymore in case that large (>500kB) files were processed. This issue has been fixed in this release.
Transforming FMR-ROIs to VMR-Space VOIs	When clicking the "Convert To VOIs" button in the FMR "Region of Interest" dialog the requested function to transform FMR-ROIs to native, ACPC or Talairach space VMR-VOIs was not performed in the previous version (no dialog appeared). This issue has been fixed in this release.
VOI to POI Conversion	The possibility to create POIs from VOIs by sampling volume space from (cortex) meshes did not work in the previous version, i.e. nothing happened when clicking the "Create POIs" button in the "VOIs to POIs field" in the "POI Functions" tab of the "POI Analysis Options" dialog. This issue has been fixed in this release
Update of FMR Time Course Plots	When mouse-selecting regions in FMR documents, an already open time course plot was not updated with the data from the newly selected region in the previous version. This issue has been fixed.
Cortex-Based Alignment	The whole CBA pipeline has been verified and improved in this release, including small issues such as that curvature color could not set to grey scale in the first tab of the dialog. Also a crash at the end of CBA has been corrected that occurred when group output files were prepared.
Color Bar for Range-Colors	When a look-up table is chosen for a selected map in the "Statistics" tab of the "Volume Maps" dialog ("Use LUT" option), the corresponding color bar is shown in the VMR view. If, however, the "Use range colors" option is chosen, the color bar has not been updated accordingly in previous version showing the overlay LUT colors instead. This issue has been fixed.
High-Res Cortex Depth Sampling	When calculating 2D depth grids on high-resolution anatomical datasets, the results were not stored in an output .HRG file when using the option to sample around the coordinates of the current voxel ("Sample region around VMR cross" option in the "High-Resolution Cortex Depth Grid Sampling" dialog). This issue has been fixed.
Mesh Export	Export of meshes to standard formats (Wavefront OBJ, Collada DAE, STL) for further processing (e.g. 3D printing) did not work in previous 21.x versions. This issue has been fixed.
V16 in Data Analysis Manager	When creating anatomical documents from DICOM files, V16 datasets were not alwasy generated and preprocessing pipelines did not work as expected. This issue has been fixed. Furthermore, new projects can now only created in BIDS format, i.e. the option to use the deprecated old data organization has been removed.

BrainVoyager 21.2 Release Notes

New Features

Connectivity and Graph Analysis

This version introduces a new tool ("CGAnalysis" plugin) providing brain connectivity analysis using a graph-theoretical approach. The plugin calculates and visualizes connectivity matrices as well as derived connectivity graphs. The graph analysis tool currently focuses on functional connectivity expecting volume time course (VTC) and volume-of-interest (VOI) files as input. Connectivity matrices can be calculated between voxels of a VOI (voxel-to-voxel) or between a set of VOIs (seed-to-seed) and visualized in a circular plot. Besides visualization of the calculated connectivity, standard graph-theoretical features (e.g segregation, integration, centrality) are calculated and displayed. Further background information and instructions on how to use the new tool can be directly invoked by clicking the "Help" button in the "Connectivity and Graph Analaysis" dialog. The actively developed tool is provided as a technical preview in this release and updates will be provided frequently on our support web site.

Enhancements

NIfTI Support	This release further integrates import and export of NIfTI files. There is now an "Open NIfTI" icon in the main toolbar to open NIfTI files quickly. More data types are now also supported including unsigned short and double values. There is now also direct support to process NIfTI volume maps (see below) usually containing float or double values and an intent code specifying a statistical distribution. In case that a volume map file is opened via the "Open NIfTI" icon (or the respective item in the “File” menu), a BrainVoyager volume map is created and attached to a pseudo-VMR document that is created from the same data. This is necessary since a volume map in BrainVoyager can only be linked to a VMR file. It is now also possible to save NIfTI files either compressed (.nii.gz, default) or uncompressed (.nii) by selecting the respective option in the "Saving NIfTI files from BV documents" field in the "NIfTI" tab of the "Settings" / "Preferences" dialog.
NIfTI Volume Map Files	It is now possible to directly save and load (statistical) NIfTI volume maps from the "Volume Maps" dialog. When exporting VMP data containing multiple maps, each sub-map is exported as a separate NIfTI file. Saving volume maps in normalised (MNI, ACPC, TAL) space as NIfTI file(s) does not resample the VMP float values, i.e. the map is stored in the current volume space except that the BV orientation is converted into neurological RAS orientation. BrainVoyager saves an identity matrix as the orientation (sform) matrix multiplied by scaling values reflecting the relative resolution of the map with respect to the spatial resolution of the hosting anatomy. For details, see topic "NIfTI Volume Map Files" in chapter "Coordinates and Transformations" of the updated User’s Guide.
Huge GLM Files	It is now possible to create, load and visualize GLM files larger than 4 GB as long as enough working memory is available. Huge GLMs may be obtained when analyzing functional data volumes with large dimensions, as used in high-resolution fMRI, combined with a large number of predictors e.g. when calculating separate subject GLMs with many subjects and study predictors.
Installing Missing Plugins and Scripts	When installing BrainVoyager, plugins and scripts are stored in the "BVExtensions" folder inside the current user’s "Documents" folder. In case that another user logs in, the plugins and scripts will not be available in this user’s "Documents/BVExtensios" folder. This release now detects and informs the user about this situation providing a dialog with instructions to install a copy of the "BVExtensions" folder from our web site in the user’s local "Documents" folder.
Sphere ROI	When defining a sphere ROI from the context menu of a VMR View, a dialog will be shown that allows setting the radius of the created sphere. This avoids adjusting the radius in the "Spherical ROI Definition" section in the "Settings" tab of the "Volume Tools Options" dialog (which also allows to switch between drawing directly into the VMR or (default) drawing a VOI). The adjusted radius will be stored permanently as the new default for subsequent sphere ROI definitions. Since ROIs are generated as VOIs , the name and color of the created ROI can be changed in the "Volume-Of-Interest Analysis" dialog.
Auto-Balancing GLM Contrasts	When defining contrasts in the "Overlay GLM Contrasts" dialog, contrasts are balanced on the fly, i.e. it is no longer necessary to click the "Balance +/-" button to balance the selected positive and negative predictor sets.
Auto-Save MDMs	Multi-study design matrix (MDM) files are now stored automatically when using the "General Linear Model: Multi Study, Multi Subject" dialog in a similar way as is available for single-study (SDM) files when using the "Single Study General Linear Model" dialog. The auto-saved MDM name will keep the same information (e.g. GLM type, time course normalisation setting, AR setting) as the auto-saved GLM name. The auto-saved file name is also suggested as initial file name when using the "Save MDM" in the multi-study GLM dialog.
Generated VTC File Names	When creating VTC files, the automatically suggested resulting file names now include not only the target space (e.g. NATIVE, ACPC, TAL, MNI) but also the target cube dimension, spatial resolution and used interpolation method (nearest neighbour, trilinear, since); the file name "[core-file-name]_512_sinc3_2x0.4_TAL.vtc", for example, indicates that a high-resolution VTC is generated with a target cube dimension of 512, that the data is interpolated using sinc interpolation and a spatial resolution of 0.8. The spatial resolution is expressed with the value of the VTC resolution relative to the hosting VMR resolution (e.g. "2") times the resolution of the VMR itself ("0.4"), hence "2x0.4", i.e. the resulting VTC voxel will have a resolution of 0.8 x 0.8 x 0.8. For standard resolution (1 mm) VMRs, the suggested file name will look similar to "[core-file-name]_256_sinc3_2x1.0_MNI.vtc".

Bug Fixes

Sub-Millimeter TAL VTC Creation	When creating VTC files in Talairach space using a sub-millimeter VMR in combination with GPU sinc interpolation, the resulting VTC file was not scaled correctly to the VMR resolution. Creation of sub-millimetre VMR-VTCs in native space, ACPC space or MNI space were not affected. This issue has been fixed in this release.
FMR Multi-Study GLM	When running a multi-study FMR-STC GLM with 2-byte integer data, the program crashed. This issue did not occur for 4-byte float data (default). This issue has been fixed.
Blurry FMR Maps	Bitmaps representing slice (background EPI) data with overlaid maps were interpolated to a 256 resolution for display. This could lead to a blurring effect in case the EPI/map resolution was not 64x64 or 128x128. In such cases (e.g. 100 x 100), interpolation of bitmaps is no longer performed leading to crisp overlaid FMR maps for all resolutions.
Create Mask from Map	The "Create Mask From Map" menu item in the "Options" menu allows to save a mask file from a volume map, which is useful e.g. for GLM masking. Calling this function has produced a crash in the previous version. This issue has been fixed.
Adding POIs	When using the The "Add POI" button in the "Patches-Of-Interest Analysis" dialog to add Patches-of-Interest (POIs), the POIs in the selected file were not added but replaced the existing POIs in the dialog. This issue has been fixed.
Predictor Scaling	When scaling predictors using the "Scale predictor [0..1]" function in the "Predictor Functions" tab of the "Single Study GLM Options" dialog, the resulting predictors could have been scaled in the range of -1 to +1. This issue has been addressed by correcting the behaviour as well as by adding the new option "Scale predictor [-1..1]" that can be used to scale predictors in the range of -1 and +1. Note that the latter function processes purely negative, purely positive or positive and negative pre-HRF predictor time courses differently. For more information, use the extended "What’s this" help offered in the dialog that can be obtained by right clicking the option.
EMEG Tools	Several EMEG tools were not available in the previous version (21.0). This issue has been fixed in this release.

BrainVoyager 21.0 Release Notes

New Features

BIDS-Compatible Data Analysis Manager	The folder structure and file names created by the data analysis manager are now compatible with the "Brain Imaging Data Structure" (BIDS) standard as default; the previous folder structure is still supported but deprecated. BIDS is quickly becoming a standard in the neuroimaging community to organize raw data and metadata on disk in order to facilitate sharing datasets. The raw (e.g. DICOM) data is converted to the NIfTI format (see below) together with sidecar files containing additoinal metadata in the JSON format as well as protocol information in tab-separated value (TSV) files for functional data. Consult the "BIDS Compatibility" topic in the "Data Analysis Management" chapter in the User's Guide for more details.
DICOM-to-NIfTI Conversion	Besides being used for BIDS compatibility, NIfTI files are further supported by the added possibility to directly save FMR and VMR documents as NIfTI files from the "File" menu using the "Save NIfTI" item. Furthermore, the "Create Document Wizard" now provides the option to save created documents 3D anatomical (VMR) and 4D functional (FMR) data in the NIfTI format offering DICOM-to-NIfTI conversion. NIfTI files are also saved when running the "Create Document" workflow in the updated Data Analysis Manager (see above). In addition to a document’s NIfTI file, an additional JSON file is stored with the same name (but with a “.json” file extension) containing metadata about the scanning parameters as well as information entries that are specific to BrainVoyager and usually stored in the header of conventional document files (e.g. FMR, DMR, VMR). For more details about saving DICOMs and BrainVoyager documents as NIfTI files, see topic "NIfTI with JSON and TSV Sidecars" in the "Getting Started" chapter and the section "Saving NIfTI Files" in topic "Processing NIfTI Files" in the "Coordinates and Transformations" chapter of the User's Guide.
New 3D Viewer	This release introduces a powerful new 3D Viewer with a modern user interface. The new 3D viewer is based on modern OpenGL with vertex and fragment (material) shaders and renders substantially nicer and faster (up to 10 times) than the old OpenGL implementation. It comes also with some advanced shader effects such as 2D and 3D texture sampling and integrated volume rendering using 3D raycasting shaders. The new 3D Viewer provides a flexible user interface with a new Mesh Tool Box and floating panels that allows efficient interactive workflows. The 3D Viewer requires at least OpenGL 3.2 (3.3 recommended) core profile. To check the best version available on a specific platform, BrainVoyager writes the detected OpenGL version at start-up in the Log pane but also in the file "bv_ogl.txt" in the Documents folder of the current user; the latter is useful for diagnostic information in case that the program does not start. Details on how to use the 3D Viewer is described in topic "The 3D Viewer" in the "Getting Started" chapter of the updated User's Guide.
Defacing DICOMs and VMRs	For complete anonymization of MRI data, replacing identity information from (DICOM) files is not enough since the identity of a person can also be recovered from 3D anatomical data. This release adds tools to deface created VMR data sets or directly the slice images stored in a series of DICOM files using the new "Deface VMR" or "Deface DICOM Files" items in the "File" menu. To deface anatomical data, BrainVoyager performs a temporary MNI transformation creating a 12-parameter affine spatial transformation matrix that is applied backwards to a bring a MNI space defacing mask into the data’s original (native) space where it is finally applied. This procedure ensures that no interpolation of the original voxel intensities is introduced, i.e. only the voxels inside the defacing mask are set to 0 while other voxels are untouched. In case of defacing DICOM files, the masked data is saved back - slice by slice - to the original DICOM files. The defacing mask file ("MNI152-DEFACE.vmr") is stored in the standard "MNITemplates" directory inside the "BrainVoyager" folder and can be adjusted if desired. For more details, see topic "Anonymization and Defacing" in the "Getting Started" chapter of the User's Guide.

Enhancements

Session Log Files	BrainVoyager now stores the contents of the "Log " pane to disk and provides a new "Session Log Viewer" to inspect previously logged data. The log viewer can be invoked by using the "Show Session Log Files" item in the "Files" menu. Furthermore, the "Data Analysis Manager" now also saves a "Master Log File" for each experiment that can be invoked by using the new "Master Log" icon. Note that log files are saved incrementally to disk and are also available in case of a program crash allowing to inspect what was processed right before an issue occurred.
Reusing Workflows for New Projects	The "Data Analysis Manager" now supports a one-step setup of all preprocessing workflows (functional, anatomical preprocessing, alignment and normalization) by converting the preprocessing workflows of a project into a set of template wokflows. These template workflows can then be used to create all preprocessing workflows in a new project after setting up the raw (BIDS) data. Since the workflow templates include all parameters in a JSON file, it is also possible to quickly adjust preprocessing parameters (e.g. normalizing to MNI vs Talairach space) easily. An example template workflow file ("pExample_PreprocessingTemplateWorkflows.json") is provided in the "BrainVoyager" folder; to modify this file, move it to a location with read and write access. The template workflows import and export tools are available via the new "Options" button in the "Data Analysis Manager" window. For more details, read topic "Applying Pipelines to New Projects" in the "Data Analysis Management" chapter of the User's Guide.
Porting Projects to New Computers	When moving projects managed by the "Data Analysis Manager" to another computer, the dataset itself as well as the information stored in the BrainVoyager database need to be moved to continue managing the data. This release introduces the possibility to export the database of the respective project, that can then be imported from BrainVoyager at the target computer to synchronize the BrainVoyager database with the actual copied dataset. The project database import and export tools are available via the "Options" button in the "Data Analysis Manager" window. For more details, read topic "Moving Projects to a New Location" in the "Data Analysis Management" chapter of the User's Guide.
Psychophysiological Interaction (PPI)	While a plugin to support psychophysiological interaction analysis was available earlier, an updated PPI plugin is now incorporated in BrainVoyager's installation, i.e. it is available as a standard tool from the "Plugins" menu. The updated plugin (version 2.0) now also supports data in MNI space, which was not possible in previous versions.
Python Support	This release now supports Python version 3.6 instead of Python 2.7. All provided scripts have been adjusted to be compatible with Python 3.x. Besides Windows and macOS, Linux is now also supported for the first time. Check the documentation "xx " to learn how to provide a compatible Python version for the used operating system. The Python editor now provides syntax highlighting of the BrainVoyager scripting API commands and syntax highlighting colors are adjusted to fit both the standard and new dark BrainVoyager theme (see below). The "Tab" key now inserts always 4 spaces (instead of a tab as is usually recommended for Python editors) and a return key press on a text line will automatically insert indent spaces at the next line.
Improved Mesh Sampling of Volume Data	When projecting a mesh surface into a VMR, an optional corrective step along vertex normals towards the inside of a mesh has been introduced in version 20 in order to adjust for the fact that a mesh is not reconstructed along the centers of voxels but along the outside faces of voxels, which are located half a voxel away from the center. This corrective step is now enabled as default when projecting meshes in VMR documents and it is now also used when sampling volume maps (VMPs) and volume time courses (VTCa) to create surface maps (SMPs) and mesh time courses (MTCs), respectively. Furthermore, meshes now store the volume resolution from which they were originally reconstructed and this is used to calculate a correct value for the along-normal correction step even in case that the volume used for projection / sampling has a different resolution than the original one. For more details, see topic "Projecting a Mesh in a VMR" in chapter "Useful Tools".
Grey Matter Masking for SMP / MTC Mesh Sampling	When creating surface maps (SMPs) from volume maps (VMPs) or mesh time courses (MTCs) from volume time courses (VTCs), the default option integrates (averages) several data points along the normal of vertices to obtain a single value that is attached to the respective vertex. While the default range along the vertex normal could be changed, a fixed starting and ending value was used for all vertices, which is suboptimal because the cortex varies in thickness. A new approach has been added in this release that automatically limits the sampling to grey matter voxels in case that a VMR dcoument with explicit grey matter labbelling is used (i.e. GM voxels have been assigned an intensity value of 100). If such a VMR is found (checking that the file name ends in "_WM_GM.vmr"), the GM masked sampling approach is turned on as default. For details see topics "From Volume to Mesh Time Courses" and "Overlaying Surface Maps on Cortex Meshes".
Enhanced Grid Sampling for High-Res Data	When defining grids at multiple cortical depth levels, the created rectangular extend did not always capture the provided region-of-interest (VOI) completely requiring repeated manual usage of the tool until optimal coverage was obtained. This has been simplified in the current release by introducing the possibility to automatically explore multiple (e.g. 100) grid samplings in the "Grid Sampling Region" dialog. The launched grid samplings use different starting values for the direction of the major grid lines and it is also possible to specify "oversampling" the region-of-interest. The created high-res grid (.HRG) files are stored to disk with an attached value measuring the VOI coverage (and a second value measuring the oversampled area) allowing to easily select a good grid sampling result for subsequent functional data processing.
Cross-Platform Dark Theme	A new cross-platform dark theme allows content-focused work with a cool interface that looks very similar across platforms. The dark interface is turned on as default but it can be turned on or off in the "Settings" (Preferences) dialog. Note that to take effect, BrainVoyager needs to be restarted after changing the theme. If the dark theme is turned off, the conventional platform-native theme is used. Since the new 3D Viewer currently only works in dark theme mode, it is recommended to also use the dark theme for the overall program. For details about the look of the dark theme, check the topic "The Graphical User Interface" and "The 3D Viewer" in chapter "Getting Started". Note that also the "Getting Started Guide" has been updated for version 21.0 reflecting the new dark theme as well as containing updated contents.
Command Line Parameters	BrainVoyager now responds to parameters when launched via Console: -h (or --help), -v (or --version) and --resetSettings (see below). On Windows the output of the -h (help) and -v (version) parameter is shown in pop-up dialogs while on macOS and Linux the output is printed in the console window when launched from a Terminal.
Reset GUI	It is now possible to reset the GUI to the initial (installation) state using the "Reset Settings" option in the "GUI" tab of the "Settings" ("Preferences" on macOS) dialog. This setting might be useful if one wants to reset the GUI to a "fresh" state and also for fixing rare GUI glitches, e.g. when dialogs or panels are not reachable. In the latter case, one can also force a GUI reset by using the command line parameter "--resetSettings". While the reset option will force BrainVoyager to use original default values for most settings, it keeps the files in the "Recent Files" pane and the documents that were open in the last session as well as enabled OpenCL settings. Since these settings are not changed, the resetting option can be executed safely without loosing important work-related information.
New Default Map Look-Up Table	This release introduces a new diverging color palette as the default look-up table (LUT) for volume and surface maps. From a perceptual point of view, the new palette is more appropriate to (simultaneously) visualize levels of positive and negative activity than the previously used palette. While the new LUT is enabled when using the new release the first time, one can switch to the old (pre-v21) LUT if desired using the options in the "Default Map Look-Up Table (LUT)" section in the "GUI" tab of the "Settings" dialog. Note that the look-up table can also be changed for individual maps using the "Volume Maps" and "Surface Maps" dialogs as in previous versions and this release provides both the pre-v21 and new v21 LUTs (also in a version with inverse color change) in the "MapLUTs" folder in the intallation directory.
Multiple Time Course Plots	When using multiple "Time Course Plot" dialogs, the time course data of a newly selected region was linked always with the last opened plot. It is now possible to make any open time course plot the "current" one by CTRL-clicking (CMD-clicking on macOS) inside the displayed time course of a dialog. The current dialog will be indicated by a filled colored rectangle in the lower left corner while non-current dialogs exhibit an open (non-filled) rectangle. When CTRL-selecting a new region in the VMR View, the time course of that region will be incorporated in the specified current "Time Course Plot" dialog.
Saving and Loading Scene Views	A new ".SVP" (scene viewpoint) file format has been introduced to store information about the viewpoint of the 3D Viewer replacing the old viewpoint (".VWP") file format. The new file format not only saves the view of the "Stage" itself but also saves the local position and orientation of all meshes in a scene. This new feature allows to create reproducible scene arrangements of multiple meshes that are useful e.g. for figures in publications. For more details, check topic "The 3D Viewer" in the "Getting Started" chapter of the updated User's Guide.

Bug Fixes

NAN Values during VTC Creation	In very rare cases (about 1 in 1 million voxels) NAN values could be generated at voxel time courses when creating VTC files using sinc interpolation on the CPU; this issue did not happen when using GPU sinc interpolation (except eventually for the first volume since the first VTC folume is always computed using the CPU). This issue has been fixed in this release.
GCM in MNI Space	The Granger Causality Plugin did not work in version 20.x in case that VOIs (used as reference regions) were defined in MNI space (VOIs defined in native and TAL space worked fine). When using MNI VOIs, the plugin produced empty .GCM maps. This issue has been fixed in this release, i.e. the GCM plugin works as expected also when VOIs are defined in MNI space for standard 256 framing cube dimensions.
Updating Graphs in Dialogs	In several dialogs, including event-related averaging, displayed graphs were updated only when resizing the dialogs or not at all. This issue has been fixed.

BrainVoyager 20.6 / BVQX 3.6 Release Notes

New Features

Nonparametric Permutation Inference

Conventional parametric statistical testing of fMRI data is an efficient technique to test the significance of hypotheses as long as the assumptions are met. Recent critique on parametric cluster-extent multiple comparison testing (Eklund et al., 2016) suggest to complement parametric fMRI analyses with more robust nonparametric inference methods. This release introduces the "Randomise Plugin" that provides nonparametric permutation inference for multi-subject designs. Permutation testing uses random shuffles of observations to obtain the correct distribution of a test statistic under a null hypothesis providing inference with nominal false positive rates. The Randomise Plugin provides direct support for common multi-subject designs including single-group contrast testing and group comparisions. Other more complex designs can be specified using a flexible graphical user interface. Furthermore, the Randomise Plugin allows to apply the thresold free cluster enhancement (TFCE) method to suppress background noise; while TFCE does not provide statistical inference (p values) when used in isolation, it can be integrated in permutation testing further demonstrating the usefulness of nonparametric statistics. A disadvantage of permutation testing is that it is computationally intensive because thousands of permutations need to be evaluated; the Randomise Plugin uses parallelized code (multi-threading) to achieve reasonable computation times when running on multi-core CPUs. For more details consult the documentation of the plugin and the overview provided in topic "The Multiple Comparisons Problem" in the "Statistical Data Analysis" chapter of the User's Guide.

Open NIfTI Files

While BrainVoyager offers the "NIfTI-1 converter" plugin to import and export NIfTI files since many years, this version introduces a more integrated approach allowing to open and save NIfTI-1 files directly from the File menu. Besides convenience, the new routines also better handle conversion to and from BrainVoyagers internal representations so that manual transformation adjustments should not be necessary in most cases. This version supports direct opening of 3D anatomical (as VMR) and 4D functional (as FMR-STC) files. While 3D files are opened in native and normalized MNI or Talairach space, 4D files are currently only opened if they are in native space (i.e. if NIfTI file contains "Scanner" orientation matrix). For further details how NIfTi files are processed when loaded from the File menu, consult the topic "Processing NIfTI Files" in the "Coordinates and Transformations" chapter of the User's Guide.

Enhancements

Maximum Probability Maps	Improved prob maps with MPM and non-overlapping POI generation. More details coming soon...
Bidirectional MNI Transformation	MNI transformation matrices are generated when running the standard template-based normalization procedure. The resulting matrices contain 12 parameters reflecting not only scales, rotations and translations but also shear operations. These transformations were not supported when applied in opposite direction, e.g. when going backwards from MNI space to native space, e.g. when transforming a segmented volume from MNI space back to native space. Forward and inverted 12-parameter (MNI) matrices are now supported for volumes as well as for meshes and VOIs. Furthermore, several dialogs (including "3D Volume Tools", "Mesh Transformation" and "Transformation Matrix") have been updated to properly reflect (decomposed) shear transformations. Information in the "Log" pane now also describe decomposition of 12-parameter matrices when running spatial transformation operations.
Scripting API	New scripting commands have been added supporting the creation of surface maps from available volume maps (CreateSurfaceMapFromVolumeMap, CreateSurfaceMapFromVolumeMapDepth) with parameters to control how volume map data is sampled from the vertices of the target mesh. Also new commands to smooth surface maps (SmoothMap, SmoothMapLags) allow to control this process with all options also available in the GUI. The Python script "test_create-smp.py" has been provided in the "PythonScripts" folder demonstrating the use of these new scripting commands including a description of all parameters. Furthermore, the "add_motion_regressors.py" Python script can be used to append motion regressors to standard single-run .SDM design matrices.

Bug Fixes

Huge VTC Files

Huge VTC files beyond 8 GB can be created and used for whole-brain statistical analysis without problem. Accessing time courses of such files when linked to a VMR (by clicking on voxels or by using VOIs) leads to corrupted time course displays for voxels stored beyond 8 GB in the VTC file in previous versions. This issue has been fixed by using 64-bit integer values when accessing voxel time courses in VTC files.

Black Protocol Dialog on Mac

The "Protocol" dialog was drawn in black on macOS in BrainVoyager 20.4 making it difficult to use the dialog since text was not readable. This issue has been fixed.

BrainVoyager 20.4 / QX 3.4 Release Notes

New Features

Two-Factor ANOVA	A new ANOVA model with two between-subjects factors has been added to the "ANCOVA" dialog allowing to model more complex designs with each subject grouped in two ways allowing to investigate main effects and interaction effects. The implementation supports unbalanced designs using type III sums of squares, i.e. with unequal number of observations (subjects) for level combinations of the two factors. For further details consult the "Two-Factor ANOVA" topic in the "Statistical Data Analysis - Random Effects Group Analysis" chapter of the updated User's Guide.
Equi-Volume Depth Sampling	For the analysis of local sub-millimeter data, BrainVoyager allows to model regular 2D grids at different cortical depth levels. In past versions these grids were placed using an equidistant approach keeping a specified relative cortical depth level with respect to the cortex boundaries. BrainVoyager 20.4 adds an equi-volume approach adjusting the thickness of layers in cortical segments to preserve their volume compensating for cortical folding, which better corresponds to layers in brain tissue than the equi-distant modeling approach. The equi-volume approach is also available for full cortex depth meshes. For further details consult the "Equi-Volume Depth Modelling" topic in the "Analysis of Sub-Millimeter 7T+ Data" chapter of the updated User's Guide.
Decoding pRF Models	Population receptive field (pRF) modeling is a useful approach to map the location and area of the visual field represented by voxels (or vertices) in the visual cortex serving as the basis to calculate eccentricity and polar angle maps. The obtained cortical visual field maps can also be used "backwards" to plot the activation of voxels in visual areas in a visual field representation. This is supported by new tools in BrainVoyager 20.4. First, clicking on a voxel or vertex in the cortex while a pRF map is loaded will show the corresponding location and size of the corresponding pRF model in a visual field plot in the "Image Reporter". Furthermore, the "Decode" button can be used to project the current cortical activation pattern (evoked e.g. by a visual stimulus or visual imagery) in a visual field image. For details see topic "Decoding pRF Models" in the "Population Receptive Field Analysis" chapter of the updated User's Guide.

Enhancements

High-Resolution Data Volume Rendering	In order to visualize high-resolution data, especially "flattened" cortical depth grids, the "High-Resolution Data Volume Rendering" tool has been introduced in BrainVoyager 20.2. This version adds new possibiliities to this tool allowing e.g. to (temporarily) cut out sub-volumes for visualization purposes and to show/hide the 3D reference grid. For details see topic "Advanced Volume Rendering of High-Resolution Data" in the "Analysis of Sub-Millimeter 7T+ Data" chapter of the updated User's Guide.
Anonymization of DICOM Files	In an extension of the Rename DICOM files tool, it is now possible to specify an anonymized code string for a participant (e.g. "P17") that will replace the patient name element in DICOM files and also used for renaming the files. Like the Rename DICOM function, files are renamed to a standard format "PatientsName-SeriesNumber-VolumeNumber-ImageNumber.dcm" that is optimized for subsequent document creation functions. Note that in this version of BrainVoyager the anonymization routine does not change other fields in DICOM files besides the patient name element (other elements will be made available for anonymization in a later release). Note also that all DICOM files found in the specified folder receive the same new (coded) patient name, i.e. all files in the directory should be from the same participant. The tool can be invoked using the "Anonymize and Rename DICOM Files" in the "File" menu.
Scripting API	New scripting commands for FMR-VMR coregistration (with and without BBR), MNI normalization and VTC creation in MNI space have been added to the (VMR) document object. Furthermore, the anonymization functionality described above has been also made available via scripting ("AnonymizeDicomFilesInDirectory" command). A new "Python Developer Guide" has been made available that can be launched from the "Help" menu and in the "Python Development Window". Also more Python scripts and plugins are made available in the "PythonScripts" and "PythonPlugins" folders. Note that the Python and JavaScript scripting API now expects "BrainVoyager" instead of "BrainVoyagerQX" as the main application object. The same holds true also for the external COM-based access on Windows (e.g. from Matlab). While both names can still be used during the 20.x releases, version 21 of BrainVoyager will only support the "BrainVoyager" application object. Note also that the "CreateProjectFMR/DMR/VMR/AMR" commands have been renamed to "CreateDocumentFMR/DMR/VMR/AMR" to be consistent with the terminology used in the data analysis manager and now generally in BrainVoyager. For the 20.x releases, the "CreateProject.." names can still be used, but they will be removed in version 21.
POI to SMP	The "Create SMP" button in the new "Create SMP from POI" field in the "Advanced" tab of teh "Surface Maps" dialog allows to convert a specified POI into a surface map where the vertices of the POI are set to an "active" value (default: 1.0) while all other vertices are set to value 0.0. This function may be useful in some cases, e.g. when a map is needed from interactively specified vertices (see, for example, description in interactive pRF decoding section in the "Decoding pRF Models" topic in the User's Guide). A similar conversion is available with the standard VOM to VMP conversion in volume space by using the "Create VMP" button in the "Visualize VOMs" dialog; this conversion is now also possible when the VOM contains no map data (only voxel coordinates); in this case the voxels of the VOM will be set to activity value 1.0 while all other voxels of the map will be set to value 0.0 in the resulting volume map (with bounding box dimensions from a previously created/loaded VMP).
Document Context Menus	A useful and quick way to launch often used operations is available via local menus for FMR, DMR, VMR, and SRF documents that can be shown by context-clicking (e.g. right clicking) the title bar of a document tab (or window) or by using the document thumbnail in the "Open Documents" pane. The local menus have been extended with entries for invoking document property dialogs (e.g. "VMR Properties" dialog) as well as entries to show property dialogs of linked data if attached to a document ("VTC Properties", "VDW Properties", "MTC Properties"). The local menu of VMR documents now also contains an entry to call the "Volume-Of-Interest Analysis" dialog and SRF documents contain an entry to call the "Patches-Of-Interest Analysis" dialog.

Bug Fixes

Bridge Removal	When running the bridge removal tool more than once, BrainVoyager 20.2 would crash; this included running the automatic segmentation pipeline from the "Automatic Cortex Segmentation and Reconstruction" dialog with the "Remove bridges LH" and "Remove bridges RH" options enabled. This issue has been fixed.
NIfTI Plugin	On Windows the NIfTI plugin did not work in BrainVoyager 20.2. This issue has been fixed.
Changing Inter-Slice Time Value	When changing the "Inter slice time" value in the "FMR Properties" dialog, the value was set to the default value (TR value divided by the number of slices) when relaoding the saved FMR file from disk, i.e. the displayed "Inter slice time" value did not match the value in the FMR file. This issue has been fixed.
ACPC Space Flag	When running the automatic ACPC-TAL normalization routine by clicking the "Auto-ACPC-TAL" button in the "Talairach" tab of the "3D Volume Tools" dialog, the space of the created ACPC VMR file was incorrectly set to "unknown" instead of "ACPC" space. This has been corrected.
VOIs in MNI Space	If VOIs were defined in MNI space, they were stored to disk as internal BV coordinates, which could lead to subsequent errors, e.g. when adding them to other VOI files. Like TAL space VOIs, the coordinates of VOIs in MNI space are now saved and loaded properly marked as being in MNI space. In order to more easily recognize the space of the currently loaded/created VOIs, a new reference space label has been added to the "Volume-Of-Interest Analysis" dialog.
VDWs in MNI Space	Transforming DMR data into MNI space VDW files did not work properly in previous 20.x versions, i.e. the resulting bounding box could be different for each data set. This has been fixed and VDW files created from DMR data from different runs/subjects are now placed in the standard MNI bounding box.
GLM as Input for ANOVA	When using a GLM as input for the ANOVA (1 between factor) model in the "ANCOVA" dialog, the program would crash; the tool worked, however, well when using properly created VMP/SMP files as input (recommended). The issue with GLM input has been fixed.
LUTs for Volume and Surface Maps	When visualizing volume or surface maps using look-up table (.olt) files, the correct map colors were not always selected for displaying the color bar as well as the map itself; furthermore the map icons in the "Volume Maps" or "Surface Maps" dialogs were often not correctly displayed. This issue has been fixed.
AutoTransform-ToIsoVoxelation	The "AutoTransformToIsoVoxel" scripting command did not work correctly. This issue has been fixed. Furthermore a related new scripting command "TransformToIsoVoxel" has been added allowing to specify explicitly the target resolution and the bounding cube dimension value with additional parameters, which is useful especially for high-resolution VMR data.
Launching GUI Scripts	When launching GUI scripts from the JavaScript Script Editor, the user interface (.ui) file referred in the JavaScript (.js) file could sometimes not be loaded since the path to the .ui file was not determined correctly. This issue has been fixed.
Export DICOM	When using the "Export .DCM" function in the "Spatial Transf" tab of the "3D Volume Tools" dialog, the export could fail in case that the original DICOMS were stored in big endian byte order. This issue has been fixed.
Float DICOM STCs	When creating FMR or DMR projects using non-mosaic DICOM data, the resulting STC/DWI data was always stored in 2-byte integer (short) format even in case that float values were requested (e.g. in the Create Document dialog or via the "Float (4 bytes)" option in the "Data" tab of the "Preferences" dialog). This issue has been fixed.
Motion Correction Clip	When turning on the "Movie" option in the "3D motion correction" field in the "FMR Data Preprocessing" dialog, the respective video clip demonstrating the effect of motion correction was not created correctly and the program could crash. This issue has been fixed.

BrainVoyager 20.2 / QX 3.2 Release Notes

New Features

Boundary-Based Registration (BBR)

Boundary-based registration (BBR) has been added at various processing stages since it provides high-quality coregistration of anatomical and functional data sets (as well as other modalities) of the same subject. BBR uses a reconstructed white matter / grey matter cortex mesh representing the anatomical data that can be automatically created. The mesh is "projected" into a functional (or other) data set and spatially transformed in such a way that the vertices are located at positions where the white / grey matter intensity gradient along the normal direction is maximized. This is the case when the vertices align along the white grey matter boundary. BBR is provided as the default fine-tuning alignment approach when using the FMR - VMR coregistration workflow in the data analysis manager. It is also available for standard FMR - VMR (DMR - VMR) fine-tuning for standard and (sub-millimeter) functional data in FMR-VTC space. Furthermore, BBR can be used to optimize the sampling of functinal data on a cortex mesh. For further details consult the "Boundary-Based Registration" topic of the updated User's Guide.

High-Resolution Data Volume Rendering

While BrainVoyager has a real-time volume renderer, there are some advanced features that are useful for high-resolution (sub-millimeter) data such as showing functional data within transparent grey matter tissue in small cortical regions as analyzed with the cortical depth grid sampling method. To allow advanced visualization optimized for such data, a new high-resolution data volume rendering tool is now available that can be called using the s"High-Res Data Volume Renderings" item in the s"Volumess" menu. The tool can also be used to visualize volumetric grid data (see below). For more details, see topic s"Advanced Volume Rendering of High-Resolution Datas" in the "Volume Rendering" chapter of the updated User's Guide.

Enhancements

Data Analysis Manager	The data analysis manager now supports saving custom choices of preprocessing options in json files allowing consistent data preprocessing across projects. Furthermore, the default parameter setting files can be shared with other BrainVoyager users to ensure consistent preprocessing choices in a team or between colleagues in different labs. For details see topic "Default Preprocessing Choices" in the "Data Analysis Management" chapter of the updated User's Guide.
MNI Segmentation Templates	In the previous version, Talairach segmentation templates were used to remove subcortical structures and the cerebellum when running the standard and advanced segmentation pipelines from T1 weighted VMRs transformed in MNI space. For improved subcortical segmentation results, this version provides new segmentation templates that have been created in MNI-152 space. The segmentation templates are installed in the BrainVoyager folder ("BrainMNIMask.vmr" and "BrainMNIMask_0.5mm.vmr" files) and used when segmenting 3D anatomies in normalized MNI space. This change is reflected in the respective "Automatic Cortex Segmentation and Reconstruction" and "Advanced Segmentation Tools" dialogs showing an MNI space option (next to ACPC and TAL) that is automatically turned on when starting the tools from a MNI space VMR.
Cortical Depth Grids As Volumes	Reconstructed cortical depth grids can now be converted into VMR volumes together with any sampled map data by stacking the sampled grids on top of each other. The created VMR and VMP data provides a useful "flattened" volumetric visualization of sub-millimeter MRI depth data from a folded cortical region. The volumetric representation allows, for example, the analysis and visualization of activity along the cortex in two dimensions and across cortical depth in the third dimension. The tool can be launched using the "Export Grid Volume" button in the "Visualization" tab of the "High-Resolution Cortex Grid Sampling" dialog. The resulting volumes can be visualized with the advanced volume rendering tool described above. For details see topic "Depth Grids As Flattened Volumes" in the "Analysis of Sub-Millimeter 7T+ Data" chapter of the updated User's Guide.
Mesh VMR Projection	Projecting a mesh into a VMR has been improved including automatic creation of a VOI overlay instead of directly drawing into the VMR as in previous versions. The VOI color can also be selected from a set of color buttoons before clicking the "Mesh → VMR" button in the "Mesh Transformations" dialog. The "Adjust Origin To VMR" button aligns the center of the mesh to the VMR, which may be necessary in case that the mesh has been transformed from one space to another space (e.g. when using Un-TAL/inverse ACPC transformation into native space with a different number of dimensions). The projection into the hosting VMR can also be controlled using the "Adjust Vertex Coords" option to displace the drawing along the vertex normal. For details of these new options, see topic "Projecting a Mesh in a VMR" in the "Miscellaneous Tools" chapter of the updated User's Guide.
Secondary/Tertiary VMR	In previous versions it was possible to generate, load and save (only for secondary VMR) VMR data sets that are attached to the primary VMR. In this version both secondary and tertiary VMRs can be loaded, saved and removed using the respective entries in the "File" menu.
Spatial Transformation	When applying a spatial transformation, it is assumed that the target space has the same framing cube dimension as the source space. For some transformations such as when transforming a VMR or mesh (e.g. for BBR) from native space to FMR-VTC space, this assumption may be wrong resulting in VMRs and meshes that are displaced with respect to the FMR-VTC space. In order to ensure correct transformations also in such cases, the "Mesh Transformations" and "Transform Native VMR To FMR-VTC Space" dialogs now allow to specify the framing cube dimension of the target space leading to expected transformation results.
VOI Visualization	When selecting and showing different VOIs in the "Volume-Of-Interest Analysis" dialog, the cross in the current VMR data is adjusted to the center of gravity of the selected VOI. While this is usually helpful, it is sometimes desired to keep the slicing constant when switching VOIs. This scenario is now supported by turning off the new "Adjust VMR cross" option before clicking "Show VOIs".
Reveal document in Explorer/Finder	The context menu that is available by right clicking on a documents tab, title bar or document icon in the Open Documents pane helps to quickly launch document specific functionality. The new "Reveal In Finder" (Mac OS X) or "Reveal in Explorer" (Windows) item in the context menu allows to reveal the file location of the respective document in the systems directory tree, i.e. the file location will be marked within an existing or newly opened window in the standard Finder/Explorer of the operating system. This functionality is also available in the "Data" tab of the data analysis manager since BV 20.0.
Open Template MNI/TAL VMR	As a convenience, the two entries "Open MNI VMR" and "Open TAL VMR" have been added to the "File" menu allowing to quickly load a template VMR file in MNI or Talairach space from the "MNITemplates" folder. These VMRs can be, for example, used to visualize multi-subject GLM or ANCOVA results complementing other underlying VMR visualizations such as using the brain of an individual or the result of averaging brains from all participating subjecgts.

Bug Fixes

Fine-Tuning Adjustment	When running the FMR-VMR coregistration tool, the default (gradient-based) fine-tuning alignment step did not perform well in the previous version. Since the header-based initial alginment works properly, this issue usually resulted only in small deviations when visualizing functional data in subsequently created VTCs with respect to anatomy. This issue has been fixed. To be on the safe side, it is recommended to re-analyze data that has been processed with the default FMR-VMR fine-tuning adjustment tool of the 20.0 version (earlier versions are not affected). We apologise for any inconvenience this may cause.
Non-Mosaic DICOMs	When creating FMR or DMR projects from non-mosaic DICOM files, the program would produce empty data sets or crash. This issue has been fixed.
Mesh Scaling	When applying spatial transformations to meshes (e.g. to apply ACPC .trf files forward or backward) results were as expected in case that no scalings were involved; in case that scalings were included in the transformation they were not compatible with VMR derived .trf matrices and applied inversely. This issue has been fixed in this version.
Verifying Functional Coverage	The "Functional Coverage" dialog is useful to verify how well VTC files overlap in a common normalized space. While one can add individual VTCs for this comparison, it is more convenient to simply add all VTC files that are referenced in a selected multi-run multi-subject design matrix (MDM) file. In previous versions this did only work when called after running a MDM-based GLM analysis. This issue has been fixed.
VTC Creation After mTAL Normalization	The template based normalization introduced in BV 20.0 can also be used to perform template based normalization to an approximate Talairach ("_mTAL.vmr") space. In the previous version only a .trf file had been produced but no .tal file that is required in the "Create VTC" dialog and for the FMR normalization workflow of the data analysis manager. This issue has been fixed, i.e. the Talairach template normalization now produces both a "_mACPC.trf" and "_mACPC.tal" file.

BrainVoyager 20.0 / QX 3.0 Release Notes

New Features

Data Analysis Management	The new data management tools enable a new way of handling and working with (large) data sets: Instead of isolated documents, data is entered and managed in a hierarchical manner. At the top level, projects are created that refer to the data of a whole experiment. Under each specified project, subjects and workflows are added. For each project, workflows can be defined that process input data and create desired output data. Since workflows know about the data belonging to a project, processing can be performed in the same way for the data of all subjects providing a powerful batch processing mechanism without the need to write scripts. Furthermore, workflows create detailed reports in HTML and PDF format as a basis for quality assurance and documentation of performed analysis steps. For details about the new data management tools and supported workflows, consult chapter "Data Analysis Management" in the User's Guide.
MNI Normalization	This version supports MNI space normalization using automatic template-based alignment. MNI space normalization can be selected as an alternative to Talairach space normaliztion for individual dcouments using the "Volumes > Normalize To MNI Template Space" menu, as well as for normalization workflows in the context of the new data management analysis tools. The VTC creation dialog has been updated to allow specifying a 12 parameter MNI transformation file to create MNI space VTC files. For further details, consult the "Brain Normalization > MNI Normalization" section in the "Basic (f)MRI Data Analysis" chapter of the User's Guide.
Representational Similarity Analysis	Representational similarity analysis (RSA) uses activity patterns in fMRI data to analyze the response similarity between conditions in selected regions-of-interest. For each ROI a representational dissimilarity matrix (RDM) is computed and graphically displayed containing distance measures (1-correlation) between pairs of distributed activity patterns. Multi-dimensional scaling (MDS) is performed to visualize the similarity structure in two dimensions. At a second level, the calculated similarity structure between conditions can itself be compared across ROIs. Since data from various sources can be integrated in the analysis, this second-level procdedure allows to compare RDMs across subjects, other measurement modalities as well as between computational models without requiring voxel-level correspondence. For further details, see chapter "Representational Similarity Analysis" in the User's Guide.
VTC-VTC Alignment	Analyzing sub-millimeter fMRI data poses specific challenges for the alignment of the data from multiple runs of an experiment within a scanning session since even small misalignments will strongly reduce the detectability of fine-grained feature or layer-specific activation clusters. The alignment of sub-millimeter fMRI runs is also difficult since such experiments usually acquire only a small portion (slab) of the brain. In order to perform optimal across-run alignment a VTC-VTC Grid Search Alignment tool has been introduced that works at the level of, optionally masked, VTC data. The VTC-VTC alignment tool uses spatial cross-correlation to assess how well the the source VTC's first volume and target VTC's first volume, match each other. For further details, see topic "VTC-VTC Alignment of Multiple Runs" in the "Analysis of Sub-Millimeter 7T⁺Data" chapter of the User's Guide.
Open Documents Panel	The main window provides a new "Open Documents" panel that is always available via a toggle icon in the main toolbar. The panel provides a graphical overview of available (open) documents presented in a "cover flow" layout. The Open Docs panel is especially useful when many documents are available since it allows to select a document using its current visual representation. By moving the mouse to the left and right while holding it down it is also possible to quickly browse through the documents and to select a document. Furthermore, a right (context) click on the central (current) document provides a context menu (like for tabs) that can be used to call relevant document-specific functionality.
Zoom View Panel	The main window provides a new "Zoom View" panel that is always available via a toggle icon in the main toolbar. Using a mouse selection while holding down the ALT key, any rectangular section of the current FMR or VMR document can be selected to be displayed in the Zoom View panel. This is especially useful for inspecting spatial details of the anatomy and overlaid functional maps from high-resolution (sub-millimeter) scans. For VMR documents, the panel also allows to draw inside the volume using the zoomed section as a proxy to the data. For each open VMR document, the program also keeps a full drawing history allowing undo/redo operations for manual segmentation operations. The zomming rectangle can also be moved to new locations by clicking inside while holding down the ALT key follwoed by mouse movenents. For more details, consult the "Manual Segmentation Tools" topic in the "Brain and Cortex Segmentation" chapter of the User's Guide.
Python for Scripting and Plugin Development	Python is an increasingly popular language for scientific programming as well as scripting. In this version, experimental support for Python is provided (for Mac and Windows 64-bit) with the goal to provide an easy and unified alternative to both the current JavaScript scripting as well as C++ plugin development. The core of the new tools forms an embedded Python interpreter (based on PythonQt, [link]). Since the Python interpreter is enriched with access to the Qt API, it is easy to add cross-platform user interfaces for scripts and plugins in Python. The interpreter also has full access to the BrainVoyager API enabling scripting and batch programming in the same way as with the embedded JavaScript environment. Since Python supports powerful modules for scientific computing such as NumPy and SciPy, the same language can also be used to extend BrainVoyager's computational capabilities. Plugin development is also supported by the "bv" Pyton C module that provides access to internal BrainVoyager volume and surface data as numpy arrays. For details, consult section "Additional Documentation - Python Scripting and Development" in the BrainVoyager User's Guide.

Enhancements

Phase Encoding Based EPI Distortion Correction	The COPE (Correction based onOppositePhaseEncoding) plugin was available as an experimental feature with BVQX v2.8.4 and is now released as version 1.0 after substantial testing and additional improvements. The new release contains also embedded information ("Help" tab) explaining the options of the plugin in detail.
Fast FMR Creation for Mosaic Dicoms	Reading and parsing Siemens mosaic DICOM files has been substantially improved. The creation of FMR and DMR documents from such mosaic files will, thus, be much faster than in previous versions.
Overlay GLM: Multiple contrasts and contrast names	The "Overlay GLM" dialog now supports overlaying multiple defined contrasts when selecting the new "Overlay all contrasts" option. A special set of contrasts, where each main predictor gets a 1 contrast weight and all other predictors a 0 weight, can now be created by using the "Add 1 Per Pred" button. The dialog now also creates better default contrast names for resulting maps that are based on the involved betas when selecting the new "Include predictor names in contrast name" option (on as default).
Mesh Depth Sampling of Multiple VMPs	When providing a data VMP file in the "Cortical Depth Sampling" dialog, only the first volume map was used to create surface maps at the specified depth levels. The tool now creates depth-level surface maps for all maps in the provided data VMP file when using the "Create depth surface maps" option is turned on.
12 Parameter Transformation Matrices	The new MNI transformations use matrices with 12-parameters describing shear values in addition to the previously supported translation, rotation, scale values. These matrices are fully supported and also displayed by checking the "Matrix" option in the "Coregistration" tab of the "3D Volume Tools" dialog.
ROI-GLN Beta Bar Plots	When running ROI/VOI GLMs, the estimated beta values are now shown in a bar graph. Also the voxel-beta plot now shows bar plots instead of the previously used line plots; line plots can still be used by changing the default plot style in the "Settings" dialog.
CBA Improvements	Cortex-based alignment can now be used for non-1mm VMR data sets, including segmented brains from sub-millimeter human and monkey MRI.
Curvature calculation of current mesh state	When calculating mesh curvature maps, the curvature of the linked mesh of another folded state was used if established. While this is often useful, it has been cumbersome to calculate curvature for the current state of the mesh, e.g. when smoothing or inflating a mesh; it required unlinking a mesh in the "Mesh Morhphing" dialog first, which then needed to be often re-established. The new Use "linked mesh" option in the "Background and Curvature Colors" dialog can now be used to decide for which mesh state the curvature should be calculated.
FMR 3D ROIs	ROIs of FMR projects are now true 3D ROIs. This increases compatibility with the real-time fMRI Turbo-BrainVoyager software.
Target Space for VMR Transformation	When spatially transform VMR data sets using the "Spatial Transformation of VMR" dialog, one could edit the name for the resulting VMR but the reference space was set to "unknown". The dialog now has an option to set the target space (Unknown, Native, ACPC, MNI), which will also modify the file name accordingly.
New Scrpting Commands	Note that for Python scripting, the "BrainVoyager" object must be used instead of the "BrainVoyagerQX" object for JavaScript scrpting (that will also transition ot "BrainVoyager" in the future). It is now possible to ask for the number of volume and surface maps using the "NrOfVolumeMaps" and "NumberOfSurfaceMaps" functions; Python scripts/plugins can also access the content of maps using the "bv" extension module. Processed fuctional (FMR) data can be saved to disk using the "SaveFMRAndSTCFromMem" command. The "MeshScene" property of a VMR document provides access to an existing surface window; in case that a surface window should be created when not yet existing, the "GetMeshScene" function must be used. When updating the visualization of a mesh object after changing curvature or other maps, the "UpdateAppearance" command can be used (the "UpdateSurfaceWindow" command of the hosting VMR doucment is not sufficent since it does not update surface maps). The "UpdateWindow" command of VMR objects will update also the state of visualized volume maps. Volume and surface maps can be loaded using the "LoadVolumeMaps(filename)" and "LoadSurfaceMaps(filename)" script commands and a specific VMP or SMP sub-map can be displayed using the "ShowVolumeMap(index)" or "ShowSurfaceMap(index)" command for VMR and mesh objects, respectively; furthermore, the names of a specific volume or surface sub-map can be extracted using the "GetNameOfVolumeMap(index)" and "GetNameOfVolumeMap(index)" commands.

Bug Fixes

ACPC-TAL for sub-millimeter VMRs	The ACPC to TAL and Un-TAL functions did not properly work for high-resolution (sub-millimeter) VMRs with large bounding boxes (384, 512 or higher). This issue has been fixed. Large VMRs are now also supported by GPU sinc interpolation.
Brdge removal for sub-millimeter VMRs	The bridge removal tool now supports non-1mm resolution non-256 bounding box VMRs without removing information about bounding box, voxel resolution and other extended-header information.
Consistent cluster colors	When converting volume map clusters into surface clusters, the color of sub-clusters within a map did not all received the correct color (soe got the default blue color). This issue has been fixed.

BrainVoyager QX 2.8 Release Notes

New Features

Population Receptive Field (pRF) Estimation	This version introduces the population receptive field (pRF) estimation method. Using appropriately described stimuli, the model-driven pRF method estimates the location and receptive field size of each voxel or vertex included in the analysis. Since eccentricity and polar angle maps can be derived from estimated pRF parameters, the pRF method is usually used as an alternative to conventional phase-encoded retinotopic mapping but it provides more information such as estimates of the population receptive field size. For more details how to use the method for volume (VMR-VTC) and surface (SRF-MTC) data, consult the "Population Receptive Field Estimation" chapter of the User's Guide.
Multi-Dimensional Similarity Scaling (MDSS)	Multi-dimensional similarity scaling (MDSS) is a statistical tool to visualize the (dis)similarities between pairs of objects in which the objects are represented as points in a low dimensional space and the dissimilarities as distances between these points. The visualization in the low (e.g. 2) dimensional space is performed under the constraint that the distances between points correspond as closely as possible to the dissimilarities between the objects in original (high-dimensional) feature space. With the new MDSS plugin it is now possible to calculate and create such visualizations where the objects correspond to spatially distributed brain activity patterns originating from several fMRI observations in a given anatomical space, e. g. multi-voxel patterns in volume space (volume maps) or multi-vertex patterns in cortical surface space (surface maps). The interactive visual tool provides many new possibilities, e.g. it helps to find outliers and it allows to explore whether maps from different subjects form a single cluster or whether they form separate clusters; in a cognitive experiment, the latter case could potentially indicate that subjects have used different cognitive strategies to perform the "same" task. For further details, consult the documentation provided by the plugin (select the help link in the short description for the MDSS plugin available under "Plugins - Description Of Plugins" menu).
Multiple Linear Regression	… For further details, consult the documentation provided by the plugin (select the help link in the short description for the MLR plugin available under "Plugins - Description Of Plugins" menu).
Adaptive Map Smoothing	… For further details, consult the documentation provided by the plugin (select the help link in the short description for the MLR plugin available under "Plugins - Description Of Plugins" menu).

Enhancements

Automatic Advanced Segmentation	In previous versions of BrainVoyager, two segmentation pipelines were available. The standard automatic segmentation pipeline was used to obtain topologically correct cortex meshes for many purposes, including advanced 3D visualiation and cortex-based alignment. The advanced segmentation pipeline was used to perform cortical thickness analyses. The standard segmentation pipeline operated at 1mm resolution VMRs (in ACPC or Talairach space) while the advanced segmentation operated at sub-millimeter (usually 0.5mm) resolution. These two formerly separate analyses are now integrated, i.e. it is possible to run the automatic segmentation pipeline using the routines previously only available for advanced segmentation. Furthermore, the advanced segmentation dialog now contains a new tab allowing to create cortex segmentations in both sub-millimeter and standard (1mm) VMR resolution. This allows to optionally use the advanced segmentation dialog to fine-tune processing options if needed. Furthermore, the segmentation routines have been further improved (see also next two points), including anatomical preprocessing (e.g. ventricle removal) at any (sub-)millimeter resolution. For further details, consult the User's Guide...
Advanced Mesh Smoothing	When segmented cortical hemispheres are reconstructed, a mesh smoothing step is usually applied in order to remove the "jags" stemming from the voxelated initial surface representations. The standard smoothing has, however, the disadvantage that mesh vertices are displaced inwards, i.e. the depths of gyri and sulci tend to "shrink" and the resulting smoothed mesh no longer represents the originally reconstructed volume segmentation accurrately. The newly introduced advanced mesh smoothing routine avoids this problem, i.e. smoothing is restricted to high-frequencies such as the jags resulting from voxel reconstructions. The new "reco" smoothing has been built into the improved standard and advanced segmentation pipelines and it is also available in the "Meshes - Advanced Mesh Smoothing" menu.
Resolution-Independent Talairach Processing	In previous version Talairach coordinates could be defined only on 1 mm (256 dimensions) VMR data sets (with limited support for 0.5 mm VMRs). It is now possible to define Talairach coordinates and to run Talairach transformations on any high-resolution VMR data sets. It is now also possible to create VTC files in ACPC and Talairach space with transformation and Talairach landmark files defined on sub-millimeter VMRs. Furthermore, Talairach grids are visualized correctly at any resolution and Talairach coordinates are converted to system coordinates and vice versa at any voxel resolution. The new possibility is also built into the "Advanced Segmentation" dialog (see also above), which accepts data sets in ACPC and Talairach space with any (sub-millimeter) resolution. For further details, consult the topic "Creation of High-Resolution VTCs" in the "Tools for High-Resolution Data" chapter of the User's Guide.
Mesh Scripting	The available scripting commands have been substantially extended in this release. The most substantial change is the addition of a "mesh" object that allows to call, among others, mesh morphing, CBA and statistical routines. A number of new example scripts are provided (file names start with the "Mesh" substring) demonstrating how to use the new scripting possibilities. For further details, consult the...
Plugin API	The BVQX Plugin interface API now supports access to GLM data structures. Furthermore the API functions for data plotting have been extended, including the possibility to display provided axis labels. For further details, consult the updated BrainVoyager QX Developer's Guide. In order to use the new functions, the latest API include files need to be downloaded from the plugins web site.
Improved High-Res Grid Sampling Export	The "High-Resolution Cortex Grid Sampling" dialog now supports more convenient export options for sampled surface map data. Futhermore, it is now possible to export grid-sampled time course (VTC) data in addition to volume map (VMP) data. For details, see the updated documentation in the User's Guide.
GPU-Based Sinc Interpolation	The GPU-based sinc interpolation routine introduced in the previous version for anatomical and map transformations is now also available for converting FMR data to VTC data in native, ACPC [todo: and Talairach] space. If enabled in the "Preferences" dialog, the fast routine is automatically used when selecting sinc interpolation in the "Create VTC Options" dialog. Furthermore, spatial transformation of V16 data now also uses GPU-based sinc interpolation if enabled.
Threshold Map Delegation	In the context of "Preference" maps it became possible to visualize the content of a map that is thresholded by another map. This possibility has now been extended from preference maps to any combination of map types, i.e. it enables visualization of information from a selected map that is thresholded by another map (containing e.g. t or correlation values). This threshold map delegation approach is, for example, used in the context of derived pRF retinotopic maps to visualize angle maps that are thresholded by a separate multiple correlation map. The feature can be turned on manually by adding to a map name the string "UseThreshMap: " followed by the name of the thresholding map. It is also possible to create a new version of a map that is filtered by the thresholding of another map; in a filtered map, all values not passing the threshold of the referenced thresholding map are set to 0.0. This filtering option can be applied using the new "Filter UseThreshMaps" button available in the "Combine VMPs" and "Combine SMPs" dialogs. For further details, consult the topic "PRF Estimation in Cortical Surface Space" of the User's Guide.
Angle Maps	In the context of pRF estimation, a new "angle" map type ("a") has been introduced in order to appropriately represent, process (e.g. spatially smooth) and visualize (polar) angle maps. Furthermore, to facilitate the mapping of displayed map colors to the represented angle, a filled circle (disk) is now displayed in volume and surface windows in addition to the standard map bar. For further details, consult the topic "PRF Estimation in Cortical Surface Space" of the User's Guide.
Brain Peeler	The Brain Peeler has been improved providing robust results. The version in the "Main " tab of the "Volume Tools" dialog now allows to run only the first steps of the tool that mainly involve a high-pass filter to reduce intensity inhomogeneities without actually removing tissue. Running the tool with the "Apply only high-pass filter" option is recommended when one wants to reconstruct the skin of a participant's head.
Image Reporter	The Image Reporter tool stores relevant image information when executing various routines, including automatic Talairach transformation and pRF estimation. Besides the previously available possibility to save individual frames as images to disk, Image Reporter now allows exporting all available images as a standard movie file.

Bug Fixes

Reaaply Spatial Transformation	The reapply spatial transformation operation (available in the "VMR Properties" dialog) did not work if started from a VMR in Talairach space, i.e. the resulting VMR contained only empty (0-value) voxels. Furthermore, additional reapplication operations could not be launched sinde the "Reapply" button was disabled after using it once. These issues have been fixed.
To-SAG Transformation	When applying a "To-SAG" transformation, the VMR data is not transformed by a standard transformation-with-interpolation routine but the axes of the VMR are simply changed accordingly; the resulting fast 90 degree rotation transformation has the advantage that the voxel values are not changed. Also the dimensions are only "rotated" but not changed (e.g. to 256). In case of non-isovoxel data sets, the voxel dimension were, however, not reassigned to the new axes in previous versions. This issue has been fixed.
GLM Settings	When running GLMs, some settings such as serial correlation was sometimes turned off when overlaying contrasts (especially beta maps). When re-running the GLM, it looked as if the results have changed but the difference was related to the different GLM settings. This issue has been fixed, i.e GLM settings are not changed by subsequent "Overlay" functions.
Philips REC/PAR on Linux	When creating projects from Philips REC/PAR files on case-sensitive file systems (e.g. Linux and some Mac systems), the .PAR filecorresponding to a selected .REC file can sometimes not be located even if it exists. The reason is that BrainVoyager looked only for lower-case file extensions (e.g. ".par") but not for upper-case (e.g. ".PAR") extensions. This issue has been fixed.
DICOM on Mac OS X	When creating projects from DICOM files on Mac OS X, the program would hang when looking for files in a folder that does not contain any files; this was due to an issue with the reporting dialog that could not be launched. This issue has been fixed.
Adding ArVMPs on Mac	When adding anatomical-resolution VMPs on Mac after loading the first ArVMP from the native resolution dialog, the program produced a crash. This issue has been fixed.
Readability of texts in surface window	When visualizing surface maps, text labels depicting threshold values and statistical information (e.g. t, p values) were not visible when using a white background color. This has been fixed by ensuring that the text color always differs from the chosen background color.
Quality of Snapshot Export	The quality hint in the "Bitmap" tab of the "Preferences" is used when saving snapshots of windows and dialogs to disk in .jpeg and .tiff formats. In case that not the default setting was used, the value selected by the quality slider was not intepreted correctly. This issue has been fixed.

BrainVoyager QX 2.6 Release Notes

New Features

Functionally Informed CBA (fCBA)	This version adds the possibility to use functionally defined regions as additional targets during cortex-based alignment (CBA). Weighting parameters are provided that balance purely anatomical (curvature-driven) and functional alignment forces. In case that homologue ROIs are available for all included subjects, fCBA allows to perfrom a single analysis integrating whole-cortex and ROI-based analysis instead of two separate analyses. See the topic "Functionally Informed CBA" in the "Cortex-Based Alignment" chapter of the User's Guide for further information.
ASL Analysis	It is now possible to analyze aterial spin labelling (ASL) MRI data. The new slice-based and volume-based ASL plugins generate perfusion-weighted time-course data and absolute (quantitative) cerebral blood flow (CBF) maps for single- and multi-subject analyses. Absolute CBF quantification is especially useful for (patient) group studies. For details, consult the documentation provided by the plugins (select help link in short description available under "Plugins - Description Of Plugins" menu).
EMEG: Realistic Head Model	Until this release, the EMEG tools used a spherical head model for distributed source modeling. This version supports a realistic head model potentially increasing the precision of topographic results in source space. Besides relying on standard segmentation tools, the new EEG-MEG forward model routines call the "OpenMEG" library (http://openmeeg.gforge.inria.fr) to fit the head model. For detailed instructions on how to obtain realistic individual head models, consult the users' guide (EEG-MEG chapter).
GPU-Based Sinc Interpolation	While BrainVoyager uses CPU-based parallelization exploiting multiple processor cores to speed up performance since many years, modern graphics cards contain general purpose processing units (GPUs) that provide very powerful possibilities to parallelize calculations. This release is the first that offers the option to run non-graphical compute-intense algorithms directly on the graphics board. More specifically, sinc interpolation and sigma filtering can now be performed on the GPU. Sinc interpolation is especially important since it can be used in many compute-intensive routines, including motion correction and VMR/VMP/VTC spatial transformations. Depending on the graphics hardware, the new GPU implementation achieves results that lead from modest to dramatic reductions in calculation time. GPU-based sinc interpolation and sigma filtering can be enabled and tested using the "Speed" tab of the "Preferences" dialog. For more details, consult the "Exploiting the Power of GP-GPUs" topic of the "Additional Documentation" chapter in the User's Guide.
Sulcal Depth Maps	Sulcal depth volume and surface maps can now be created that provide information about the depth of voxels or vertices within sulci. Besides scientifically interesting macro-anatomical information (e.g. how sulcal depth differs in patient or age groups), the sulcal depth surface maps may also be used for surface visualization of folded, inflated and flattened cortex meshes as an alternative to the standard curvature-based visualizations. For further details, check the "Creating Sulcal Depth Maps" topic in the "Miscellaneous Tools" chapter of the User's Guide.

Enhancements

MVPA - Searchlight	In previous versions the searchlight MVPA tool only provided descriptive information. With this release, BrainVoyager provides SVM-based and MANOVA-based searchlights: At each voxel a SVM classifier or a multivariate t test (Hotellings T) is now computed providing accurracy maps (from SVM version) and F statistics (from MANOVA version). For details, consult the "Multi-Voxel Pattern Analysis" chapter of the User's Guide.
MVPA - ROI-SVM	It is now possible to run analyses in batch mode to reduce GUI interactions. The new batch mode tools allow, e.g. to perform and integrate results of all possible leave-N-out training testing combinations. For details consult the "Multi-Voxel Pattern Analysis" chapter of the User's Guide.
Regular-Grid Cortical Depth Sampling	The visualization of high-resolution grid sampling results have been substantially improved now showing rectangular grids (instead of lines in only one dimension) as well as sampled functional data directly in 3D space. Furthermore display of grids (and meshes) can be constrained to be visible only close to the currently used cut plane; this is a useful option to precisely follow different depth level grids or meshes as they run along the cortex. For further details, consult the updated topic "Regular-Grid Cortical Depth Sampling" in the "Tools for High-Resolution Data" chapter of the User's Guide.
VMP -> SMP, VTC -> MTC	The creation of surface maps (SMPs) from volume maps (VMPs) and mesh time courses (MTCs) from volume time courses (VTCs) has been improved allowing for better control how access of volume data should be performed from the vertices of a mesh. When clicking the "Create SMP" button in the "Surface Maps" dialog, a new "Depth Integration" dialog will appear that allows to specify whether volume data should be sampled at the 3D position of a vertex only (preferred choice for mesh-based cortical depth sampling) or whether functional data should be integrated along the depth of the cortex. The same options are also integrated in the "Create MTC from VTC" tab of the "Mesh Time Courses" dialog. Furthermore, it can be specified whether volume data sampling should use trilinear interpolation (default) or nearest neighbor interpolation. For details, consult the User's Guide.
High-Resolution CBA	Cortex-based alignment (CBA) is now possible also with high-resolution sherical meshes. The new "Resolution" field in the first page of the CBA dialog allows to set one of three resolutions, high, standard and low. Based on the chosen setting, the creation of sphere meshes as well as parameters for morphing and alignment are adjusted in subsequent processing steps. lInstead of standard SPH meshes with 81920 triangles (40962 vertices), the high-resolution meshes use 327680 triangles (163842 vertices). Since CBA calculations are substantially slower with these high-resolution meshes, this option should only be used in cases that target alignment of functional data with (sub)-millimeter resolution. For details, consult the "Cortex-based alignment" chapter of the User's Guide.
GLM and ANOVA	The default time series normalization method has been changed to percent signal change since this is most widely recommended in the literature for (multi-subject) GLM data analysis (see User's Guide for more details of provided normalization schemes). In previous versions, the beta values from the baseline condition was included as a level of a within-subjects factor when starting ANCOVA analysis from a GLM data file. Since the baseline predictor (and its beta and variance estimation) is not comparable to other main predictors, it does no longer appear as a within-factor level (this has been already changed for ROI GLMs in the previous release); without the baseline, the prerequisites for the 2-level mixed effects summary statistics model for balanced designs are met (for details, consult the User's Guide). To help users better judge what model is defined when changing the number of factors and covariates, the specified design is now also described directly in the "Design" tab (and as before in the "Table" tab). For designs with one main condition or one contrast, the single-group t test design is automatically chosen. It is now also possible to run a 1-between factor model (classical single-factor ANOVA) in case that only one main condition is available; in previous versions this could only be done by extracting betas for one level first in a VMP file that was then used as input. For ROI-based ANOVAs, the plotting function of betas has been improved now separating data from different groups with different line colors.
Plugin API - Plots and Documentation	While plugins can be programmed with cross-platform complex GUI components (GUI plugins), it was not possible to provide graphical output to plot calculated values. This version adds the possibility to draw bar graphs, line plots and scatter plots with a few simple commands. The produced plots look identical on Windows, Mac and Linux. For further information, run the "Plot Demo" plugin and inspect its source code; for a description of the new API functions, consult the new Developer Guide that is available under "Help -> Developer Guide".
Plugin API - FMR/MAPs and SRFs	Plugin developers can access pointers to all major data formats except FMR and MAP data. New functions to access that data are now available. The commands for processing mesh (SRF) data have been extended by adding functions for loading and saving meshes and the possibility to remove meshes from scenes in a surface (OpenGL) window. For further information, consult the new Developer's Guide that is available under "Help -> Developer's Guide".
Centroid and Border POIs	For some applications it is useful to calculate the centroid of a patch-of-interest (POI), e.g. to obtain representative mean (Talairach) coordinates of a surface area. This is especially relevant for anatomically defined regions since for functionally defined POIs the vertex with highest activity ("peak vertex") is usuallly used to represent the location of an area. It is also sometimes relevant to extract the border of a POI, e.g. in case that one wants to mark a region without interfering with the content within that region. The creation of centroid and border POIs is now possible by using the "Outline POIs" and "Centroid POIs" buttons in the new "Convert area POIs" field in the "Paths / CBA" tab of the "POI Analysis Options" dialog.
Group-To-Individual POI Projection	It is often useful to visualize the result of alignment for specific POIs. While it was possible to map the location of a POI of one cortex mesh on another individual's cortex mesh it was not easily possible to visualize the location on individual cortex meshes that were defined on the group mesh. Using the new "" button in the "" field of the "" tab of the "" dialog, group-level POIs can now be projected back onto any individual cortex mesh that participated in CBA. For details, see the "Cortex-based alignment" chapter of the User's Guide.
Fibers	Fibers are now stored in binary format to increase reading and writing speed under the same ".fbr" extension. Old .fbr text files can still be loaded but should be saved once to convert them to the binary format. Fiber visualization has been improved to allow dynamic displays, e.g. animation of fibers in group bundles "growing" from start coordinates to end coordinates; the dynamic fiber displays also support slice-restricted fiber visualizations that are used e.g. in the context of high-resolution grid visualizations (see above).
Zooming and Tabbed Mode	When using the "Zoom-In" and "Zoom-Out" icons in the toolbar on the left side, nothing happened when tabbed view mode was used; to zoom document views in or out, one needed first to switch from tabbed view mode to multi-window view mode. This is not longer necessary, i.e. when clicking on a zoom icon, the program automatically switches to multi-window view mode and positions the current sub-window in the left upper corner of the workspace; the latter increases the experience of the zooming effect. Note that this behavior is not implemented for OpenGL windows since they allow flexible content viewing also in tabbed view mode.
Touch-Based Navigation	The viewpoint in surface windows can now also be controlled by using touch-based gestures on Mac and Windows PCs. Panning and pinch gestures allow to rotate and zoom using integrated or external (magic) track pads on Mac and touch-enabled screens on PCs running Windows 7.

Bug Fixes

Mixed ANOVA	When specifying contrasts in a mixed ANOVA design with one between and one within factor, different error variances need to be used depending on the defined contrast. In previous versions, a more conservative error variance was always used if a contrast included cells across groups; if, however the same balanced contrast is defined within groups, a more sensitive error variance can be used (the same as for the within-factor F test). This has been adjusted in the current version leading to more sensitive t maps in this case.
POI-VMR Projection	When projecting POIs into VMRs with sub-millimeter resolution, the location of the created VOIs was not correct. This issue has been fixed.
CBA - Single-Vertex POIs	When applying CBA to transform POIs with only one vertex into aligned group space the resulting POI could be empty. This issue has been fixed.
GCM Plugin	In case that a VTC file did not had a protocol attached, the plugin would not work producing an empty GCM VMP file. This issue has been fixed.
SVM - Optimal C Value	When using the cross-validation option to find the C value with best generalization performance, the value chosen was sometimes not the one with best performance. This issue has been fixed.
VOI Dialog	VOIs were always marked as modified triggering a "Save VOIs" dialog when quitting the program. Furthermore, VTC files could sometimes not be removed from the VTC list. These issues have been fixed; the displayed VOI file name should now also correctly indicate (appended star symbol) whether VOIs have been modified or not. Furthermore the display of VOIs is now consistent with the available VOIs in the VOI dialog when switching between multiple open VMRs; in previous versions, VOIs might be shown from an old VOI file after loading a new VOI file. When VOI files were loaded containing voxel coordinates outside the VMR volume, the program could crash. This issue has been fixed.
Create VTC Dialog	When transformation files were not found for native, ACPC or TAL transformations, the respective "To [space]" auto-fill options were disabled in previous versions. While this is useful behavior for many cases, it may be that the respective files are located in another directory, e.g. when using files from another run. In order to avoid restrictions, the "To [space]" options are now always enabled but they indicate with the string "auto" whether a certain space is "reachable" with the "Auto-Fill" option with files in the local directory or not.
ROIs To VOIs	When converting ROIs defined in FMR slice space to VOIs, the transformation always assumed that the target volume has 256 dimensions leading to wrong VOI definitions in case of native/ACPC space transformation. When not going to Talairach space (where this assumption is still made), the program now asks the user to select the desired native/ACPC space VMR file in order to extract the proper dimension values.
ROI-ANCOVA - Correlation	When running correlation analysis between subject's contrast values and provided covariate values for ROIs in the ANCOVA dialog, the program could crash. This issue has been fixed.
Keyboard Shortcuts	Sometimes keyboard shortcuts did not work properly, i.e. despite pressing the right key(s), the corresponding keyboard function was not invoked (e.g. opening a POI dialog). This issue has been fixed.
Convex/Concave Labels	The labels for convex and concave curvature were flipped in the "Graded curvature colors" field of the "Background And Curvature Colors" dialog. This issue has been fixed.
GUI Plugin Dialogs on Mac	When GUI plugins were invoked on the Mac by launching a GUI plugin, the window would disappear from view when clicking outside the dialog. This issue has been fixed.

BrainVoyager QX 2.4 Release Notes

New Features

Automatic AC-PC and Talairach Transformation	In previous versions, the normalization of 3D anatomical VMR data sets into AC-PC and Talairach space required manual determination of the AC and PC landmarks, the specification of angles to orient the brain with the mid-sagittal plane (MSP) and finally the determination of the borders of the cerebrum. These tasks can now be performed automatically for most VMR data sets. The AC-PC - TAL transformatiol can be executed in in one step ("Auto-ACPC-TAL" button) or in two separate steps from the "Talairach" tab of the "3D Volume Tools" dialog. The automatic normalization not only saves time but also allows users to perform ACPC and Talairach transformation that may not have the neuroanatomical knowledge about the location of relevant landmarks. While other (e.g. template-based) automatic alignment tools will be available in the next release of BrainVoyager QX, the new automatic AC-PC/Talairach transformation tools will remain useful in case that rigid body brain normalization (AC-PC space) is desired, e.g. in the context of (TMS) neuronavigation or when a "true" Talairach procedure is requested. For further details, consult the "Brain Normalization" section in the "Basic (f)MRI Data Analysis" chapter of the User's Guide.
Relative Depth Cortex Mesh and Grid Sampling	Several improvements in this version have the goal to allow optimal processing of high-resolution (sub-millimeter) functional data and associated anatomical data obtained from ultra-high field scanners (7 Tesla and beyond). This version introduces high-resolution sampling of funcional data within grey matter (GM) at arbitrary relative depth levels. Two versions are introduced that both are based on the results of advanced segmentation and cortical thickness calculation, preferentially at 0.5mm resolution. The first approach ("Meshes -> Cortical Depth Sampling" menu) creates a series of meshes at different relative depth levels from a mesh reconstructed at the surface running through the middle of the WM-GM and GM-CSF boundary. These created meshes are then used to sample the functional data at the respective depth values. For even more precise sampling of small folded cortical regions, a high-resolution grid sampling tool is available ("Volumes -> High-Resolution Cortex Grid Sampling" menu) allowing to sample functional data at arbitrary relative cortical depth values on regularly spaced two-dimensional grids providing precise detailed topographic information. For further details, consult the "Tools for High-Resolution Data" chapter of the User's Guide.
EPI Distortion Correction (New Plugin)	This functionality makes it possible to apply EPI distortion correction using the pixelshift algorithm (Jezzard & Balaban, 1995) for images that are geometrically distorted due to the susceptibility artifact. This approach requires fieldmaps (either phase and magnitude or real and imaginary), being acquired before the functional run. Secondly, a difference image of two FMRs can be created to evaluate the undistortion/unwarping result visually. Finally, some calculations can be made as well with this plugin, for example to compute the phase encoding bandwidth or to convert between radians and degrees; also Cartesian (real and imaginary) fieldmaps can be converted to polar coordinates (phase and magnitude). Please consult the manual (PDF) for usage and background information.
GLM/GLS Modeling Tool	This tool offers the possibility to create and edit custom design matrices allowing to implement specific models that are not available in the provided ANCOVA module. It also can be used as a teaching tool to better understand existing models. The tool performs standard (ordinary least squares, OLS) GLM estimation on provided (ROI) time course data and also allows to specify the error covaraince matrix for generalized least squares (GLS) estimation.
Image Reporter	The "Image Reporter" serves as a blackboard to store and visualize images. The stored images may be posted from computational routines to present intermediate and final processing results that allow to better understand ongoing processes and to evaluate the performance of intermediate calculations. The tool is also available for plugin writers as a quick means to visualize bitmaps.

Enhancements

CBA	v2.4.2. If a CBA run has been completed, the program now automatically creates group files that can be used to average aligned curvature maps (.CAL file) and aligned shapes (.SAL file), i.e. without the need to manually select individual files. These files are also directly applied at the end of CBA, i.e. the program shows a folded mesh as the result of group-aligned shape averaging with an overlay of group-aligned curvature maps. The created mesh and curvature information can be directly inspected to judge the quality of cortex-based alignment.
New Scripting Commands	v2.4.1. It is now possible to perform temporal high-pass filtering (drift removal) using the GLM approach using Fourier or discrete cosine transform (DCT) basis functions. In previous versions, only the FFT-based high-pass filtering was available. The new commands are "TemporalHighPassFilterGLMFourier()" and "TemporalHighPassFilterGLMDCT()" with one parameter that specifies the number of cycles (pairs of two basis functions) used to build an appropriate design matrix. The installed script "HighPassFilterUsingGLM.js" shows how to use the new commands. It is now also possible to specify a bounding box for VTC creation in any supported target space using the properties "UseBoundingBoxForVTCCreation" and "TargetVTCBoundingBox[XYZ]Start" and "TargetVTCBoundingBox[XYZ]End"; consult the "CreateVTCfiles.js" script for details. Furthermore the command "SaveVTC()" has been added allowing to save, for example, to save a VTC file after linking a protocol with the "LinkStimulationProtocol()" function. The "SaveVTC" command accepts a string (file name) as input; if the string is empty (""), the name of the current VTC file will be used, i.e. the VTC file will be ovewritten (see the example script "LinkPRTSaveVTC.js"). Other new scripting commands allow to interrogate information about the running BrainVoyager version including the build number and whether the program is running in 32 or 64 bit mode. The installed script "VersionScript.js" shows how these commands can be used
Custom Default Scripts Folder	v2.4.1. Scripts are installed in a standard location within the user's "Documents" folder ("BVQXExtensions/Scripts"). For some scenarios, it would be beneficial if scripts could be accessed from a custom folder as default, i.e. when written scripts are made available to members of a research group in a shared network folder. For such scenarios it is now possible to change the default scripts folder in the "Scripts" tab of the "Global Preferences" dialog.
Splitting VTCs and MTCs	v2.4.1. The possibility to split VTC and MTC files has been added. This feature may be sometimes helpful, e.g. for creating sub-time courses for cross-validation purposes. Besides creating 2 or more partial time course data sets, the protocol of the source VTC/MTC file is also splitted accordingly and linked to the respective VTC/MTC split data sets (at present, this only is supported for protocols with "Volumes" resolution). The "Split VTC" dialog is availabe in the "Link 3D Volume Time Course (VTC)" dialog, and the "Split MTC" dialog is available in the "Mesh Time Courses" dialog.
POI Details and Peak Vertex Dialogs	v2.4.1. The "POI Details" dialog now shows p values of available maps next to the map (e.g. t) value; the x/y/z coordinates are no longer in internal BV coordinates but in Dicom/Talariach convention. The "Peak Vertex" table shows now also Talairach coordinates for the respective peak vertex positions in case that the underlying VMR is in Talairach space. Besides showing a peak vertex table, the "Peak Vertex" option always also created a new set of POIs automatically containing the peak vertices extracted from larger POIs. Although the new POIs were saved under a new name, the user had no control over this step. In this version, a new option (default: off) allows to decide whether new peak vertex POIs should be created.
AR(2) Model	Serial correlations need to be removed from measured fMRI time course data in order to get unbiased statistical results. While the method used in previous versions to remove serial correlations (pre-whitening with a voxel-wise first-order autoregressive (AR(1)) model) works well, it has been recently shown that a second-order (AR(2)) model outperforms all tested approaches currently used in fMRI. The AR(2) model is now available as the default approach to remove serial correlations from residual time courses. For more details, consult the User's Guide.
Baseline Z-Standardization for RFX Analysis	While z standardization of time course data is a useful step to normalize the influence of different subjects when performing RFX analyses, the variance during baseline episodes is an even better measure for normalization since it leads to better RFX analyses that are comparable to mixed effects (MFX) analyses incorporating the variability of beta estimates at the fist level. The baseline z-transformation feature was added for whole-brain analyses since it was only available for ROI analyses in previous versions. In case that not enough baseline points are available, the baseline z normalization step will automatically be switched to a standard z normalization (reported in the Log pane).
ANCOVA Improvements	In previous versions, the beta values from the baseline condition was included when starting from a GLM data file. While usually ignored, the baseline could in principle be used as a level of a within factor. Since this is not optimal for running ANOVA models, the baseline beta is now dropped when opening a GLM file in the "ANCOVA" dialog. When running a 1 within-subjects factor design for ROI data, the cell means are now plotted as part of the generated results. Furthermore, the simple "correlation of covariate with dependent variable" design is now better supported: In case of one dependent variable per subject (no full within factor) and no between-subjects factor specified, one can add covariates (w of simple Correlation model.
Creation of POIs from SMP Map Clusters	It is often useful to get a list of regions-of-interest (ROI) automatically from a calculated individual or group map. While this function is available for volume data, it was missing for surface data. This version introduces this possibility for the currently selected map. Clicking the "Convert" button in the "Create POIs from map clusters" field in the "Advanced" tab of the "Surface Maps" dialog creates a list of POIs from surface map clusters that pass the current map threshold as well as a specified cluster area threshold in order to avoid inclusion of many small active patches.
POI Map Peak Table	To summarize results, it is often useful to create a table containing the location of clusters providing the coordinates of the "peak" voxels within each cluster. While this feature is available in volume space, it was missing for surface data. This versin introduces this feature for patches-of-interest (POIs) in the "POI Map Peak Vertices" field in the "POI Functions" tab of the "POI Analysis Options" dialog.
VOI Transformations	It is now possible to directly apply spatial transformations to VOIs including rigid transformations (e.g. from native to ACPC space or back) and from ACPC to TAL space or back. The transformation tools are available in the new "Transformations" tab of the "VOI Analysis Options" dialog.
ACPC / TAL Framing Space	It is now possible to run rigid spatial transformations (e.g. ACPC transformation) and Talairach transformation in dimensions and voxel resolutions that differ from the default 256 framing space; this is especially useful for high-resolution data, e.g. with 0.5 mm voxels in a 512 framing space; if transformation matrices or Talairach landmarks are defined in a (resampled) 256 space, they will be automatically valid also in a higher resolution space (and vice versa). This is supported by storing information in spatial transformation (.TRF) and Talairach landmark (.TAL) files about the framing space and voxel resolution used during definition of a transformation (see also next point). This version also adds support for using a framing space with 768 voxels per dimension.
Sub-MM VTC Spaces	The possibility has been added to create VTCs in arbitrary (e.g. sub-millimeter) resolution for ACPC, TAL and sub-TAL (bounding box) space. The final resolution of a created VTC data set is determined by the resolution of the used native space VMR file and the relative resolution with respect to this file, i.e. if the relative resolution is "1", the VTC file will have the same resolution as the used VMR file. FMR-VMR alignment and ACPC / Talairach transformation may be performed in 1 mm space and applied to any other (e.g. higher) resolution (see point above). For details, consult the topic "Creation of High-Resolution VTCs" in the chapter "Tools for High-Resolution Data" of the User's Guide..
Intensity Inhomogeneity Correction	The intensity inhomogeneity correction (IIHC) tools have been enhanced. While the 16 bit results of IIHC were kept in working memory, they were not saved to disk for later use; in this version the option "Save resulting IIH corrected .V16 data to disk" has been added that is turned on as default, i.e. V16 results are automatically saved after IIHC if not turned off. The mapping from 16 to 8 bit data and the IIHC procedure work now robustly also in case that the input V16 data contains extremely high (outlier) values. The proton-density based pre-IIHC step has been improved allowing to scale the resulting data and it now stores resolution information in the resulting VMR/V16 data also in case that no mask VMR is provided.
EEG/MEG Analysis in Continous Mode	In the EEG-MEG module, a continous EEG/MEG data preparation (including artifact detection and time-frequency transform) is now possible allowing to perform cortical source distributed EEG/MEG analysis on arbitrary data segments (starting at any given time point specified in the protocol) or even on the entire CTC (if no protocol is specified). Before processing, the program performs a number of checks on the current settings to prevent unwanted huge file generation and endless calculations. In this "continous" mode, the resulting ACT files will contain not the event-related averages but the average power spectrum density (PSD) of the analyzed segment, and the cortical source analysis can be performed on the desired spectral (ACT) or spectro-temporal (TFD) measurements without specifying a target and a baseline interval, an important option for studying, e. g., resting-state and block-design EEG and MEG experimental data. For further details, consult the User's Guide.
EEG/MEG Channel Configuration Editor (Plugin Update)	In order to create, update and synchronize the channel configuration data (CCD) and the surface head (SFH) data, the old plugin "EEG-MEG Channel Configuration Update" (available from the Plugins menu, in the EEG-MEG plugins submenu) has now evolved to a fully-fledged 3D digital point and EEG configuration editor, that can be used to create new SFH files from scratch or modify existing ones (e. g. from standard configuration). In addition, it is possible to import digitized point configurations from a Polhemus device (if exported as ASCII "DAT" files).
Parameter-Assisted Selection of Temporal ICA Components (Plugin Update)	Selection of EEG and MEG temporal ICA components is not automatic. After the extraction step, all ICA components are now listed in a table and assigned with an individual check box to be used for retaining or not a component during the selection step. Besides the "Retain" column, useful spatial and temporal parameters are displayed in the same table for aiding the selection process. These include the spatial kurtosis, the time 1-lag autocorrelation, the spectral gradient and the maximal correlation with reference channels (if provided), all scaled to their z-scores over the entire set of components to quickly identify outliers. For further details, consult the EMEG chapter in the User's Guide.
Removal of BCG artifacts from EEG with Non-Linear Time Warping (Plugin Update)	When analyzing EEG data acquired simultanouesly with fMRI, the BCG artifacts are traditionally subtracted within a fixed time interval. However, besides the magnitude and the shape, the BCG is poorly stable in its duration as well, i. e. the ideal time scale is also variable across all detected BCGs. In order to correct for the different durations, a non-linear approach is now available, that applies a non-linear time warping (NLTW) procedure to equalize the duration of all BCGs prior to their subtraction. After NLTW and subtraction, the original time scale is restored and the BCG-clean data segments are replaced in the data .For further details, consult the EMEG chapter in the User's Guide.
Shortest Paths on Folded Meshes	In order to measure distances between vertices on a mesh, the paths created in previous versions were not necessarily shortest paths. With this release an optimized shortest path calculation (based on the Dijkstra algorithm) has been added that allows measurement of distances on folded meshes. After Ctrl/Cmd-clicking on two vertices, the "Shortest Path" dialog can be invoked from the local conext menu. By default, the calculated shortest path is represented as a (line) POI and its distance is written to the Log pane and can be also recalculated in the updated "Edit Patches-Of-Interest (POI)" dialog. For additional options, consult the "Shortest Path Creation" topic in the "Miscellaneous Tools" chapter of the User's Guide.
CBA Special Tools	Pairwise distance analysis for single-vertex (e.g. peak map vertex) POIs. Changed pairwise distance analysis of (peak map) single-vertex POIs to deviation from mean vertex as method to assess CBA funcROI improvement objectively, i.e. without thresholding and size issues.
Curvature-Flow Smoothing	Mean curvature-flow smoothing is available for smoothing initial reconstructed ("voxelated") folded mesh representations. This smoothing technique largely avoids (small) shrinkage of gyri and sulci that occurs when the standard smoothing approach is used. While the difference between the two available smoothing techniques is small, the curvature-flow smoothing is recommended when using surface meshes that sample high-resolution (e.g. in the range of 0.5 - 1.5 mm) functional data. The "Reconstructed Mesh Smoothing" dialog can be invoked from the "Meshes > Reconstructed Mesh Smoothing" menu item.
Reframing VMPs	For some processing steps, VMPs need to be in a common space with the same bounding box. The new "Reframe VMPs" dialog ("File > Reframe VMPs" menu) allows to put a set of selected VMP files in the same specified target bounding box. Note that the VMP files will not be spatially transformed, i.e. they need already be in the same target space (e.g. ACPC or TAL space) but with different bounding boxes.
Fiber Table	It is now possible to add fibers ("Add .FBR" button) to existing fibers in the "Fiber Table" dialog.
Skyra Mosaic Dicoms	The Dicom header reading code for a Siemens specific part has been updated to handle the slightly modified headers of the syngo software (VD11) coming with Skyra and othe rnew scanner models.
V16 Plugin Access	New commands have been added to the plugin API allowing direct (pointer) access to V16 data sets. The commands also include detaching, loading and saving V16 data sets as well as a convenience function to convert 16-bit data into 8-bit (VMR) data.
Bounding Box Tools	The possibility has been added to quickly define, visualize and save values for bounding box definitions; using the "Set Bounding Box" entry in the context menu, an initial bounding box can be defined from the position of the cross in one of the orthographic VMR sub-views and fine-adjusted using the bounding box spin boxes in the "Segmentation" tab of the "3D Volume Tools"; a defined bounding box can be saved to disk as a ".bbx" file and loaded at other places such as the "Create VTC Options" dialog and the "Reframe VMPs" dialog. This enables, for example, creation of consistent bounding boxes for each participant in a group study and is especially useful in the context of (high-resolution) non-whole brain measurements.
Rearranging Tabs	The tabbed documents (in the default "tabbed view mode") can now be rearranged simply by dragging the tab bars with the mouse to the left or right.

Bug Fixes

ANCOVA	v2.4.2 There was an issue with the 2-within, 1-between factor model in previous releases: In case that the two within factors had different number of levels, the program could crash or produce incorrect results. This issue has been fixed. When using the covariate-contrast correlation model for ROIs, the program would crash. This has been fixed. In this correlation model the names of beta values were shown as "beta1", "beta2" etc. instead of names from the protocol-based predictors. This issue has been corrected.
Curvature for CBA	v2.4.2 Version v2.4.0 introduced a new, mathematically more precise, calculation of mesh (mean) curvature that was also used for calculating curvature information for folded SPH meshes as a prepaaratory step of cortex-based alignment (CBA). While CBA works fine with these new curvature maps, the final quality of alignment is less good as when using the previous curvature calculation since that produced less noisy results than the new, more locally operating, curvature calculation. To get optimal CBA results, the curvature calculation used in the context of CBA has been reverted back to the old calculation. Both curvature methods are now also available in the "Background And Curvature Colors" dialog where the old method is available by using the "Fast" option (turned on as default).
Residuals VTC Option	v2.4.2 When one would turn on the option to save VTC files containing the residuals of an estimated single-study or multi-study/multi-subject GLM, the setting was kept active also in all subsequent GLM calculations of a session. The settting is now turned off after each launched GLM and needs to be explicitly turned on if it should be used in subsequent analyses.
ROI to VOI Conversion	v2.4.2 When converting ROIs to VOIs in the "Region-Of-Interest" dialog of a FMR project, the position of the resulting VOIs could be displaced. This issue has been fixed.
High-Pass FFT Filter in Hz	v2.4.1 When using the (non-default) FFT-based method for high-pass filtering, one can specify the cut-off frequency in Hz (instead of number of cycles). Before running the filter, this value should internally be converted to cycles but this conversion was missing in previous versions in GUI mode (it worked fine when used via scripting). This issue has been fixed.
GLM with AR(1) Model	v2.4.1 When switching from the default AR(2) model for serial correlation correction to the AR(1) model when running a single-study GLM, the program would crash. This issue has been fixed.
Auto-ACPC Step	v2.4.1 When performing only the automatic ACPC transformation step (using the "Detect MSP, AC, PC" button in the "Talairach" tab of the "3D Volume Tools" dialog), the correctly calculated and stored transformation file was not applied to the current VMR file for proper visualization. This issue has been fixed.
Find AC/PC Dialogs	v2.4.1 When manually specifying Talairach reference points using the "Find AC" and "Find PC" dialogs, the program sometimes crashed, especially when switching to other programs and back. This issue has been fixed.
Moving POIs Up/Down	v2.4.1 When moving POIs up or down using the respective icons in the "Patch-Of-Interest Analysis" dialog, the POI definitions sometimes were messed up and the program could crash. This issue has been fixed.
Rigid CBA File Name	v2.4.1 When running the rigid alignment step prior to CBA, the produced ".rga" output file name contained a concatenation of all included subject initials; when using many subjects, this could lead to very long file names that may not be handled by the operating system; to avoid this issue, the file names now use a shorter string ("Group_N-[No. of subjects]_LH[or RH].rga") in case that 10 or more subjects are used during rigid CBA.
Plugins	v2.4.1 When starting the BLM plugin, a crash could occur. This issue has been fixed. Minor improvements are also implemented in the "SogICA" plugin (issue with unusual temporal similarity values) and the "ClusterThresh" plugin (consistent calculation of p values for correlation maps).
RFE with Unequal Number of Trials	v2.4.1 When running recursive feature elimination (RFE) from the "Multi-Voxel Pattern Analysis" dialog, the program could crash in case that the two classes contained an unequal number of trials. The present RFE version only supports two classes with an equal number of trials. In order to prevent the crash, the program now detects unsupported scenarios and presents an appropriate message.
Coordinates in Time Course Dialogs	v2.4.1 Coordinates of selected voxels or VOIs were displayed in "ROI Time Course Options" dialogs as Talairach coordinates even in case that the respective VMR/VTC data was in native reference space. A similar problem also happened in the "VOI Details" table. These issues have been fixed.
Calling GLM from Matlab/COM	v2.4.1 When calling the "ComputeMultiStudyGLM()" command via the COM scripting interface on Windows (e.g. from Matlab), the script halted with an error message "Unable to open GLM for writing!". This issue has been fixed.
Displaying Fibers	v2.4.1 When loading or adding fibers from the "Fibers Table" dialog, fibers were not immediately displayed. This issue has been fixed.
Referenced Volume for MC	The reference volume that will be used during FMR motion correction can be selected in the "3D Motion Correction Options" dialog. After motion detection and correction, the motion correction procedure also saves a (confound) design matrix (SDM) file that can be included in subsequent GLM analyses in order to potentially remove residual motion artefacts. In case that the specified reference volume was not the first volume (default), the motion parameters were not set to 0.0 at the corresponding time point in the .SDM file in previous versions. This issue has been fixed.
Export of PSC Time Course	The "ROI Signal Time Course" window allows to calculate the mean percent signal change of the plotted time course with respect to a reference function that can be specified in the "Display reference time course" field. The full percent-signal change (PSC) transformed time course can be exported with the "Export TXT" function but the exported values were slightly scaled due to rounding of reference percent signal change values. This issue has been fixed and the percent signal change values are now precisely calculated with respect to the mean value of all epochs with 0.0 values in the reference function.
Volume Renderer	The real-time volume renderer has been updated to increase overall stability. Specific bugs that have been removed are crahes that could occur when clicking the "Remove" button in the list of masks or in the list of color definitions. v2.4.1 A display bug on Windows has been fixed.

BrainVoyager QX 2.3 Release Notes

New Features

EEG-fMRI Artifact Correction	In EEG data acquired simultaneously with fMRI, the raw EEG data are contaminated by characteristic artifacts of both technical and physiological origins, such as the gradient (GRA) artifacts, related to the switching of magnetic field gradients, and the ballistocardiographic (BCG) artifacts, related to cardiac activities. These artifacts can now be detected and removed in high-sampling-rate (>=1kHZ) EEG data sets using the "EMEG FMRI Artifact Plugin". The new plugin produces a new protocol file that contains intervals centered in all detected artifacts. Besides detecting GRA and BCG artifacts, this plugin also removes GRA (but not BCG) artifacts using the classical average-artifact-subtraction (AAS) method. In order to also remove the BCG artifact, the "EMEG Artifact Removal Plugin" can be used subsequently; this plugin implements the optimal-basis-set (OBS) method to remove (in principle) any kind of artifact. For further details consult the "Simultaneous EEG-fMRI: FMRI Artifact Detection and Removal" topic in the EMEG chapter of the User's Guide.
POI Path Tools	A new set of tools is available to process and visualize "line POIs"; these POIs are defined as one dimensional lines such as demarcations between brain regions or lines labeling macroanatomical landmarks such as fundi of sulci. The POI path tools allow converting line POIs as fibers (as used in the DTI tools) for advanced visualization options; this conversion process includes a reordering of the vertices within a line POI forming a consecutive path from a starting vertex (usually the POIs reference vertex) to an end vertex. The tools also include the calculation of distances between paths (using a modified Hausdorf metric) that can be used to evaluate the results of cortex-based alignment on POIs used as landmarks across subjects. The POI path tools are available in the in new "Paths / CBA" tab of the"POI Analysis Options" dialog. For further details consult the "POI Path Tools" topic in the "Tools" chapter of the User's Guide.
AppleScript Support	This version adds support for AppleScript on the Mac 64-bit platform. This means that in addition to the standard in-process JavaScript based scripting interface, BrainVoyager QX can also be automated using AppleScript on the Mac. The main difference to the standard cross-platform scripting interface is that AppleScript works from outside of BrainVoyager QX and allows to write scripts that reach beyond a single application. This "out-of-process" scripting serves a similar role on the Mac as the COM interface on Windows with respect to scripting. The scripting interface that BrainVoyager QX exposes to AppleScript is very similar to the standard scripting interface but it has been designed with the particularities of AppleScript in mind. AppleScript is a scripting language targeted also to non-programmers using code with a very readable English-like appearance. For further details, consult the "BVQXAppleScriptingGuide.pdf" PDF file in the "GettingStartedGuides" folder or click on "AppleScript Guide" item in the "Help" menu.

Enhancements

Subject-Specific POI Analysis	v2.3.1. While homologue regions align better across subjects in cortex-aligned space than in Talairach space, functionally localized areas still exhibit some variability. In previous versions, a true subject-specific ROI GLM / ANCOVA analysis was only possible in volume space. This version adds subject-specific POI analyses in the "POI Analysis Options" dialog. The new "Access Options" tab allows to specify the "Use subject's POI for time course access" option if POIs have been properly defined for each subject. If, in addition, a multi-subject MDM file is provided, the POI GLM and POI ANCOVA functions will use the subject-specific POI definitions to extract time course data leading usually to improved statistical results when compared to a commonly defined POI.
MTC Preprocessing	v2.3.1. While most preprocessing is usually done before creation of MTC files (mainly in FMR space), preprocessing options might be useful also for mesh time course data, especially the possibility to spatially smooth the data along the cortical sheet. This version introduces the "MTC Preprocessing" dialog that allows to perform spatial smoothing as well as standard temporal preprocessing. The dialog is available under the "Analysis" menu.
Handling MTC Files	v2.3.1. It is now possible to quickly link MTC files from the local file menu of a mesh (SRF) document using the "Link MTC" item. Furthermore, MTC files are now listed in the "Files" pane in the new category "Recently opened MTC's"; this allows to quickly link an MTC file to the currently active mesh in a surface window; it is thus possible to conveniently establish SRF-MTC links in the same way as when creating VMR-VTC links. When launching the program, SRF-MTC links from the previous session are now also re-established (limited to the "current" mesh in cases when multiple meshes are available in a surface window).
MVPA Trial Estimation: Post-Trial Option	v2.3.1. When estimating single-trial responses in the context of multi-voxel pattern analyses, the specified data window for single-trial GLMs is specified with a "pre-onset" and a "post-onset" parameter in the "Trial Estimation" tab of the "Multi-Voxel Pattern Analysis" dialog. In many cases, it might be easier to specify the end of the data window relative to the end of a trial's interval duration. This is useful when using trials that last for several seconds (e.g. short blocks) and it is the appropriate way to handle situations where trials of the same conditon have different durations. When checking the new "Use trial duration" option, the "Post-onset" field will change into a "Post-trial" field allowing to specify the duration of time points relative to the end of each trial.
Scripting: Applying HRF	v2.3.1. When building design matrices via scripting, the "ApplyHemodynamicResponseFunctionToPredictor" script function used the Boynton function in previous versions. This script function now uses the standard 2-gamma function instead of the simpler Boynton function matching the default behavior of the GUI-based creation of HRF convolved predictors.
CTA Depth Maps	v2.3.1. When calculating cortical thickness maps, there is also a "depth map" calculated indicating the distance of a grey matter voxel from the white-grey matter border. This calculation has been improved. This leads to more precise creation of middle layer volumes (e.g. for cortex reconstruction) when using the "Create Volume" and "Create VOI" buttons in the "Mid-GM Volume" tab of the "Cortical Thickness Measurement" dialog.
SMP Dialog	v2.3.1. The "Surface Maps" dialog now allows to delete individual entries by using the DELETE or BACKSPACE key. Furthermore, the CTRL-A (CMD-A on Mac) key combination plus-selects all surface maps (switching from single- to multi-selection mode) and the CTRL-C (CMD-C on Mac) key combination deselects all surface maps.
Brain Extraction	This version contains an improved brain extraction tool that increases robustness as compared to the previous tool. As part of the automatic intensity inhomogeneity routine, the improved brain extraction tool handles now also "more difficult" data sets by incorporating basic intensity inhomogeneity correction (high-pass filtering) and improved calculation of bounds for region growing operations.
PD-Based Bias Field Correction	While the automatic intensity inhomogeneity correction (IIHC) tools work well for most data sets, scans at (ultra) high magnetic fields may exhibit huge intensity inhomogeneities that are difficult to correct with the existing tools. It has been shown (van der Mortele et al.,) that in such cases the recording of a proton-density (PD) weighted scan greatly helps in reducing large inhomogeneities when dividing the T1 weighted data set by the PD data set. When a PD data set is available, this step can now be performed using the "Volumes > Proton-Density Based IIHC Step" menu usually as a first step prior to automatic IIHC.
EMEG Channel Editor	The EEG/MEG tools now allow to visualize the time courses of all channels; the implemented fast "channel scroller" contains basic editing tools allowing to remove channels and intervals that, e.g. exhibit artifacts. If changes are made, the results are stored in updated CTC and PRT files. The channel scroller can be invoked using the "Plot & Edit" button in the "Channel Data Preprocessing" tab of the "EMEG Suite" dialog.
Plugins Updates: RFX-GCM, ICA, GIFTI	The "Random Effects Granger Causality Mapping" plugin now supports subject-specific VOI definitions for a homologue region-of-interest yielding usually better RFX results than when using the same VOI for all subjects. The plugin now also supports the (usual) case that subject data is located in different folders (in previous versions, all data needed to be copied to the same folder). Furthermore, the plugin now calculates "dGCM" instead of "dGCM_IT" maps (i.e. no thresholding with the INST maps in order to not filter (limit) the maps). The "Temporal ICA" GUI plugin now operates faster and adds max-lag auto-correlation ranking of the ICA components. The GIFTI converter plugin (version 1.4) is now also a GUI plugin and handles SMP, MTC and POI files besides SRF files.
POI Tools	The tools to inspect and edit patches-of-interest (POI) have been improved, including removal of a limit that allowed a maximum of 255 POIs; furthermore, the "Edit Patch-Of-Interest" dialog (invoked with "Edit" button in "Patch-Of-Interest Analysis" dialog) has been enhanced showing now the number of vertices for a selected POI, a list of all vertices included in the POI definition and an option to remove vertices. There is now also a new table available that shows the number of vertices for all loaded/defined POIs that can be invoked in the new "Paths / CBA" tab of the "POI Analysis Options" dialog. POI labels are now also drawn in higher resolution improving readability of displayed text.
Combining SSMs	It is now possible to integrate a sequence of SSM transformations into a single SSM file; this makes it easier to go back and forth between corresponding points in two brains in cases that one SSM step is not enough; this may, for example, happen in case that versions of cortex meshes are used that have different resolution than the one used during CBA requiring 2 or more SSM steps to reach corresponding points. The new tool is available in the "Map A to C" tab of the "Map Mesh to Mesh" dialog that can be invoked by clicking the "Map Meshes" button in the "Options" tab of the "Cortex-Based Alignment" dialog.
Scripting API Updates	When creating VMR projects, the internally created V16 data set is now stored to disk. When saving the VMR data with a new name ("save as" command used usually after VMR creation), both files will be renamed as long as they have the default "untitled.vmr/.v16" file name. The new command "CorrectSliceTimingWithSliceOrder" allows to run slice scan correction with a custom slice order (see "Preprocessing.js" script). The "getCurrentDirectory()" function is now a property, i.e. you can use "BrainVoyagerQX.CurrentDirectory" to read and set its value. There are also new properties pointing to common locations: The "PathToData" property points as default to the "BVQXData" folder in the user's "(My )Documents" folder and the "PathToSampleData" points as default to the "BVQXSampleData" folder.
V16 Data Sets	The V16 data sets (2-byte versions of 1-byte VMR data sets) are now better integrated in standard processing steps; they are now automatically loaded when specifying "ToSAG" or "IsoVoxel" transformations so that they stay in synch during basic anatomical preprocessing and they now also support the "framing cube" specification. A new option has been added in the "V16 Contrast / Brightness" dialog allowing to keep background voxels black when intensity values are inverted.
Default Location of Data Files	Since version 2.2, BrainVoyager sets the default folder to the path associated with the currently active data set in the multi-document workspace. If, however, no document is currently loaded, the default path pointed to the location of the program (or a rather random location). BrainVoyager now looks as default in the "(My )Documents/BVQXData" folder if the "Open Files" dialog is used and if no document is available in the workspace; it is thus recommended to put user data in this location. In case that this folder is not available, the program looks in the "(My )Documents/BVQXSampleData" folder and if this is also not available, it looks in the "(My )Documents" folder.
Surface Window Background Color	It is now possible to set an arbitrary color for the background of surface reandering windows, e.g. to white instead of black. This function is available in the "Scene" menu by clicking the "Background Color" item. The specified background color is also stored in the program settings and, thus, preset across program launches.
Vertex TAL Coordinates	When clicking on a vertex of a mesh in the surface rendering window, the program now tries to show not only the system coordinates but also the Talairach coordinates of the vertex in the status bar. Talairach coordinates are displayed only if the VMR that "owns" the surface rendering window is in Talairach space. For inflated and flattened meshes, a folded reference mesh needs to be linked to enable display of Talairach coordinates. v2.3.1. Talariach coordinates are now also shown in the "POI Details" dialog (available in the "POI Functions" tab of the "POI Analysis Options" dialog).
Import of TBV ROIs	Regions-of-interests (ROIs) can now be imported and visualized in FMR projects when post-analyzing data from TBV in BrainVoyager. Although TBV's multi-slice ROIs are not available in BVQX, the import function (via "Analysis -> Region-Of-Interest Analysis -> Load") displays them appropriately and uses data from exactly the same voxels from multiple slices to extract and display the mean ROI time course.

Bug Fixes

Averaging VTCs	v2.3.1. It was not possible in version 2.3.0 to average VTC files; when starting this function in the "Combine 3D Data Sets" dialog, the program stopped with an error message of non-matching reference spaces. This issue has been fixed. The dialog is available from the "Volumes" menu ("Combine 3D Data Sets" item) as well as via the "Combine Data Sets" button in the "Talairach" tab of the "3D Volume Tools dialog.
POI GLM With MDMs	v2.3.1. The POI GLM functionality did not work in previous versions when using a multi-study design matrix (MDM) file. This issue has been fixed (see also "subject-specific POI analysis" above).
Entering Protocol Dialog	v2.3.1. When opening the "Stimulation Protocol" dialog from the surface module, the program sometimes crashed on Windows. This problem has been fixed.
Non-Square AMRs	v2.3.1. In case that original slices are non-square, the program embeds them in square matrices during creation of functional FMR projects. This has been, however, not been done for related AMR projects in case they were created from a different recording (e.g. coplanar inplane scans) as opposed to using the first volume of the same functional scan. This issue has been fixed.
POI-GLM with SDM	It was not possible to use single-run design matrix (".sdm") files for specifying single-run POI-GLM analyses (only ".rtc" files could be specified) whin the "POI Analysis Options" dialog. This issue has been fixed.
VTC Averaging	It was often not possible to average VTC files since BVQX displayed a message indicating non-matching 3D reference spaces between the temporarily created VMR data and the VTC data. This problem has been fixed by properly initializing the reference space of the VMR data to the one of the first VTC data set.
Saving VDW with Attached Gradient Info	When a VDW file was saved that received gradient information by loading a .GRB file, the program crashed. As a workaround, the .GRB data could be attached to the DMR data set prior to VDW creation. This issue has been fixed.
FMR/DWI Data with 256 Matrix Size	Functional or difffusion-weighted Siemens DICOM data with an image matrix size of 256 was wrongly interpreted as of "mosaic" type leading to a crash when importing the data with the "Create Project Wizard". This issue has been fixed. Note that these large EPI matrices are often created simply due to upscaling (interpolation) on the scanner but this does not improve data quality; in order to save disk space and processing time, it is advised to turn interpolation off.
Plugin Command qxSaveDMRAndDWI	The "qxSaveDMRandDWI()" plugin command did not save the DWI data from memory in a file with the specified DWI prefix but did overwrite original DWI data. This issue has been fixed.
IIHC Mask Deselection	If in the "16 Bit 3D Tools" dialog (usually in the context of intensity inhomogeneity correction) an applied mask was deselected, this had no effect. This issue has been fixed: When deselecting the "Apply mask" option, the program now correctly will undo masking by reloading the original VMR file.
ACPC Transformation	When transforming a VMR into ACPC space, the "reference space" variable of the resulting VMR was not set to "ACPC" but to "unknown"; this subsequently produced a "non-matching reference space" warning when linking a ACPC-space VTC file; this error could be fixed by manually setting the "reference space" in the "VMR Properties" dialog. In this version, the "reference space" variable is set properly to ACPC space.
Applying Fiber TRF	When specifying and applying a spatial transformation in the "Spatial Transformation of Fibers" dialog, dismissing the dialog with a click on the "Ok" button performed another application of the specified transformation. This minor issue has been fixed.
POI Vertex MTC Table	When saving a table with time courses for all vertices of a POI ("POI Analysis Options" dialog > "MTC Data" tab > "Tables" button) in a text file, the program would crash. This issue has been fixed.
Script Command Logging	When running the "CreateProjectFMRSlicesTimeLooping()" scripting command, the Log pane wrongly reported that a "CreateProjectFMR()" routine is executed. This minor issue has been fixed.

BrainVoyager QX 2.2 Release Notes

New Features

Auto-Inhomogeneity Correction	This version adds the possibility to remove intensity inhomogeneities without the need to manually pre-segment white matter. The new automatic inhomogeneity correction (IIHC) tool can be launched from the "V16ToolsDlg" that can be invoked by clicking the "Volumes > Inhomogeneity Correction, V16 Tools" menu item. The automatic procedure runs several sub-processes including background cleaning, brain segmentation and masking, automatic detection of white matter voxels and fitting of the spatial intensity distribution through labelled white matter voxels. The tool corrects small intensity inhomogeneities from volume coils as well as more complex inhomogeneities resulting from surface coils at high fields. The fitted intensity distributions (bias field) is visualized as a secondary VMR and the improvement in grey / white matter separation can be inspected in displayed pre-/ post- intensity histograms. For details, see this blog entry and the section "Intensity Inhomogeneity Correction" in the User's Guide.
Quality Assurance Tools	An important goal of this and future releases is the addition of more quality assurance tools that help to assess the quality and validity of performed analysis steps. The most important verification tool introduced in this release is the "VTC Overlap" tool that allows to visualize those voxels that have been scanned in all subjects participating in a group analysis. For details see section "Verification of Functional Brain Coverage" in the User's Guide. Another quality assurance tool is the automatic creation of motion correction movies (MPEG4 videos in .MOV container on Mac OS X, and .AVI container on Windows); a produced movie shows the slices of the first and last functional volume of a FMR/DMR project as volumes with 3 orthographic cut planes; the movie shows these two volumesin rapid succession which allows to get a good impression of the amount of brain motion; since the same two volumes are also shown after motion correction, the movie also indicates whether motion correction was successuful; furthermore, the last frame of the movie shows a static view of motion (and its correction) with a difference image obtained by subtracting the last volume from the first volume. For more details, see section "Motion Correction" in the User's Guide. Another QA tool allows to check the effect of cortex-based alignment by visualizing the movement of vertices (see below).
Real-Time Volume Rendering	While BrainVoyager creates beautiful pictures using surface rendering, some visualizations may be better produced using volume rendering, e.g. in case that one wants to visualize anatomical and functional data with realistic transparency effects. Although BrainVoyager always had a volume rendering tool (in the "3D Volume Tools" dialog), it was working rather slowly and lacked advanced features. With this release a new volume-rendering tool is available that is able to create rendered views in a few 10th of milliseconds by exploiting the possibility of modern graphics hardware (GPU's); modern graphics cards are no longer simple fixed processors but they can be loaded with code that is executed within the graphics card. With the implemented fast GPU-based raycasting tools, rendered volumes can be rotated, translated and zoomed in a similar way as in the surface module using mouse and keyboard. The volume renderer allows to visualize multiple anatomical data sets using transparency and different color ranges. Arbitrary slices through volumes can be visualized using intensity values as color information. Furthermore, any statistical map that is defined for the current volume (VMR) is automatically visualized when calling the volume rendering tool. Supra-threshold fununctional voxels can be visualized on cut slices, by projection to the surface of the brain or by using transparency. Several advanced features including shadows ensure high-quality rendering output. For more details, see section "Real-Time Volume Rendering" in the User's Guide.

Enhancements

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.

Bug Fixes

POI CBA Alignment	v2.2.1. When applying CBA transformations to POIs that were defined on individual folded meshes (subject space), the SSM transformation (via a S2S file) wrongly added vertex "0" to the resulting aligned POIs. While this did not affect visualization, it produced slightly wrong results when subsequently calculating POI probability maps. This issue has been fixed.
Changing CBA Parameters	v2.2.1. When changing CBA parameters in the "Cortex-Based Group Alignment Parameters" dialog, subsequent CBA does not start showing a "do-not-find-file" message. This problem has been fixed.
S2S CBA Files	v2.2.1. When using S2S CBA files that were not located in a folder at a higher level than the referenced SSM files, the program did not find the transformation files. This issue has been fixed.
VMR Gaussian Smoothing	v2.2.1. When using the Gaussian smoothing option in the "Segmentation" tab of the 3D Volume Tools dialog (click on "Gaussian" button), smoothing does not work producing a "black" VMR result. This issue has been fixed.
Export To ANALYZE	v2.2.1. When exporting data to Analyze (either functional or anatomical projects), an empty project window was shown after successful export and the program could crash when not closing the empty window.. This issue has been fixed.
MTC Properties Dialog	v2.2.1. It was not possible to edit properties of a MTC file linked to a mesh since the "MTC Properties" item in the "File" menu was always disabled. This issue has been fixed.
Parametric Protocols and SRF-MTCs	v2.2.1. When applying parametric protocols to MTC data sets in the "Stimulation Protocol" dialog, the program could crash. Parametric protocols in SRF-MTC projects also lead to crashes when opening the "Event-Related Averaging Specification" dialog. This issue has been fixed.
CreateMTCFromVTC	v2.2.1. The "CreateMTCFromVTC" command could not be used from COM (e.g. Matlab) scripting but worked in BrainVoyagerQX scripts. This issue has been fixed.
Changing VMR Contrast/Brightness	v2.2.1. When changing the contrast or brightness for VMRs that do not have an associated V16 file, the resulting VMRs did not reflect the made adjustment, i.e. the VMR was "white". This issue has been fixed.
Project Creation	This version improves import of raw data with non-power-of-2 matrix sizes, e.g. FMRs with dimensions that are not 64 x 64 or 128 x 128 and VMRs with image dimensions that are not 256 x 256. While such data sets could be imported in earlier versions, several display option did not properly handle non-standard dimensions.
ROI Float Access	When clicking "Table" in the "Extract VTC data for every voxel in selected VOI" field in the "ROI Options" dialog, the extracted data was wrong when accessing VTC float data. This issue has been fixed. This problem did not occur for all other functions, e.g when accessing mean ROI time courses from VTC float data.
MVPA	Preparation of separate learn and test runs did not properly work in previous version, i.e. pattern (MVP) files were only created from the "Training runs" VTC list but not from the "Test runs" VTC list in the "Trial data" field of the "ROI-SVM" tab. This issue has been fixed.
Default Script	The default script setting in the "Global Preferences" dialog was still set to an old (.qsa) script file and browsing to a new script type was not possible. This has been updated to work with the new JavaScript files. The specified default script file will be automatically loaded when launching the script editor.
Plugins API	Access of multiple MTCs from plugins did not work in version 2.1. This problem has been fixed. When using the "qxSaveFMRAndSTC()" plugin command, the data storage format was not saved in FMR files in previous 2.x versions; also the access to the STC data referenced by the FMR was only accessible after closing and reopening the FMR document. These issues have been fixed.
AR(1) Maps	When choosing the option to create an AR(1) map before and after correction in the "Serial Correlation Options" dialog (invoked from "Single Study GLM Options" dialog) or in the "Multi-Study GLM Options" dialog, no AR(1) VMPs were created. This problem has been fixed.

BrainVoyager QX 2.1 Release Notes

New Features

GUI Plugins

BrainVoyager QX 2.1 introduces an important extension to the scripting and plugin system allowing to create graphical user interface (GUI) components. The new extensions have been defined on the basis of a new scripting layer (Qt Script) that replaces the scripting module (QSA) of previous versions. While also a version of BrainVoyager QX 2.1 will be made available with the old scripting module, we strongly suggest to adapt existing scripts to the new scripting environment since only the new environment allows to use the implemented GUI functionality for scripts and plugins. The adaptation of scripts to the new system is very easy since the old and new scripting language are both based on (slightly different versions of) JavaScript. The examples in the "BVQXExtensions/Scripts" folder and the documentation "Scripting in BrainVoyager QX 2.1+" help to quickly make this transition. Scripts play an important role for GUI plugins since they allow to link actions on GUI elements (e.g. clicking a button) with appropriate calls into the plugin C++ code. Check the blog entry GUI Scripts and GUI Plugins as well as the "Writing GUI Plugins" documentation in the User's Guide to learn how to create GUI plugins.

Enhancements

MVPA - Extracting Trial Responses	The Multi-Voxel Pattern Analysis (MVPA) dialog fits a separate GLM for each trial of a time series in order to obtain a trial response estimate as a t or beta value. In some cases, it might be more appropriate to extract values directly without the involvement of a GLM. In this release, the "Extract Trial Data" dialog has been added allowing to extract raw data values in a window with respect to the time point of trial onset. If the window consists of one time point, a single value is extracted; if the window comprises 2 or more values, the mean of the values is extracted. If in addition a baseline interval is also specified (recommended), the extracted trial response value can be related to the trial baseline as a percent signal value or by subtracting the baseline from the raw trial response value. The new dialog can be invoked by clicking the "Options" button in the "Trial Estimation" tab of the "Multi-Voxel Pattern Analysis" dialog.
EMEG Suite - fMRI / EEG Coupling	The EMEG module now allows to explore the signal coupling of simultaneously recorded EEG and fMRI time-series allowing to predict fMRI signals directly from spatio-temporally selective EEG responses. Specifically, it is possible to extract regional power time-courses for fMRI modeling and prediction with appropriate options for the Source Analysis. For details, consult topic "EEG Source Analysis with EEG-fMRI Coupling" in the User's Guide.
ACPC, TAL Transformation of NR-VMPs	While native-resolution VMPs have become the standard file format for almost any operation and the "anatomical-resolution" VMPs mostly serve visualization purposes now. in previous versions, it was, however, not possible to perform spatial transformations on native-resolution volume maps, but only on AR-VMPs. In order to obtain a NR-VMP in ACPC or TAL space, the time course (or diffusion-weighted) data had to be transformed first in that space followed by calculations leading to native resolution volume maps (recommended approach). Some users prefer, however, to calculate maps only in native space and would like to transform the resulting maps only into ACPC or Talairach space for visualization purposes and random effects analysis (e.g. of FA maps). The spatial transformation dialog ("Transform .VMP" button in "Spatial Transf" tab of "3D Volume Tools" dialog) as well as the Talairach and Un-Talairach dialogs ("ACPC -> TAL", "TAL -> ACPC" buttons in "Talairach" tab) have been extended allowing now to perform these transformations either on native-resolution (default) or anatomical-resolution VMPs.
Protocols with Parametric Weights	A new protocol version has been introduced (version 3) that allows to specify a weight for each defined interval. To add weights to a protocol, you need to turn on the "Enable parametric weights for intervals" flag in the "Stimulation Protocol" dialog. The specified weights are used in the "Single Study General Linear Model" dialog to scale intervals accordingly when defining predictors. When defining a predictor with non-constant trial weights, two predictors will be created: one predictor with weights "1.0" (identified as "Main" in the predictor name), and a second one having the amplitude modulated as indicated by the weights (identified as "parametric" in the predictor name). A new option field "Creation of parametric predictor" in the tab of the "Masking/Options" tab of the "Single Study GLM Options" dialog allows to decide whether the weights should be used as specified ("Use weights as defined" option), or whether the mean of the weights should be subtracted from each weight ("Subtract mean of weights" option, default) or whether the weights should be standardized ("Standardize weights" option). The latter two options are recommended since they ensure that the two defined predictors are orthogonal with respect to each other. The contribution of the parameric predictor can be tested in the "Overlay GLM Contrasts" dialog as usual by "plus selection"; it is recommended to perform a conjunction contrast of the two predictors (main and parametric). The implemented enhancement (changes in protocol and design matrix creation) makes it easier to specify parametric designs. In order to keep compatibility with previous protocol versions, a saved protocol is only stored as a new version 3 file if parametric weights are indeed used. In case parametric weights are not specified, protocols are still saved as version 2 PRT files allowing to use non-parametric protocols created in version 2.1 also in earlier versions of BrainVoyager.
Specification of Free Slice Scanning Order	While the standard slice order choices in the "FMR Preprocessing" dialog (ascending, descending, eventually combined with interleaved) are normally valid for most scans, there are cases that may have a special slice scanning order that is not captured by the default choices. For these cases, it is now possible to specify a free slice order. Furthermore, the specified slice order can be saved for later use. When running the slice scanning correction preprocessing step, the program now also prints detailed information about the performed temporal reordering of slices in the Log pane, also for the standard slice order choices.
Functional Connectivity Analysis	It has been possible in previous versions to calculate correlation maps using a reference function extracted from a voxel or region-of-interest. Such correlation maps are very useful to show how the respective voxel or ROI is functionally connected to other voxels. In previous versions, this required to first save an extracted time course to disk, swithcing to the correlation (or GLM) dialog, loading the reference function and then executing the calculation. In this version, this function is now directly available by the "Run Correlation" command from the context menu of any (FMR-STC, VMR-VTC, SRF-MTC based) "ROI Signal Time Course" dialog.
ANCOVA Dialog	The assignment of conditions was not updated in previous versions if within-factor levels has been deleted in the "Level list" of the "Design" tab of the "ANCOVA" dialog. This could lead to unexpected results when the user did not update the assignment in the "Assign Conditions" tab. In this release, the "auto-assign" functionality (available in the "Assign Conditions" tab) is now run automatically in the background when the user deletes factor levels in the "Design" tab. Other minor improvements have been made to increase overall stability of the ANCOVA module (e.g. the names of betas in the "ContrastPage" could be messed up in some cases).
Unified Color Dialog	In previous versions, the definition of mesh colors (background color, curvature color) was available in two different dialogs. In this version, the "Background and Curvature Color" dialog has been added that centralizes all options to change mesh colors. This includes setting the background color as well as the two modes (2 colors mode, 2 x 2 colors gradient mode) to specify curvature colors.
Scripting Commands	The scripting commands for creation of VTC and VDW data sets in native, ACPC and TAL space now support the new (5th) parameter "DataType" allowing to specify whether the resulting VTC/VDW files should contain float data (DataType = 2) or short integer data (DataType = 1). Note that existing scripts using one of the commands "CreateVTCInVMRSpace", "CreateVTCInACPCSpace", "CreateVTCInTALSpace" or the respective "CreateVDW" versions need to be updated. The "DataType" parameter must appear before the "Resolution" parameter. In order to support a more powerful creation of design matrices, the new properties "SDMContainsConstantPredictor" and "FirstConfoundPredictorOfSDM" have been added. The new properties "VMRVoxelResolutionX", "VMRVoxelResolutionY" and "VMRVoxelResolutionZ" can be used to read (and set) the resolution of VMR documents.
Cross in VMR Documents	The display and handling of the cross used to navigate in VMR documents has been improved in this release. The square in the center of the cross (VMR view) is now shown properly centered and its size may now be specified using the new "Rect. size" spin box in the "3D Coords" tab of the "3D Volume Tools" dialog. The square can also be hidden by setting the size value to "0".
Modeless VMR Properties	Similar as the "FMR Properties" and "DMR Properties" dialogs, the "VMR Properties" dialog has been made "modeless", i.e. it does no longer block inspection of documents when it is open.
Removing Non-Existing Files	A new "Clean" button has been added to the "Recent Files" pane allowing to remove those files from the recent files lists that are no longer availalbe on disk.

Bug Fixes

SDM Check for RFX-GLMs	When running RFX-GLMs and a predictor (pooled across all runs of a subject) had only zero (or any constant) entries would lead to a RFX GLM result containing "not a number" (NAN) values for those predictors since no beta value can be estimated in that case. In order to avoid this issue and to inform the user about this problem, a consistency check of all subject-specific design matrices is now made when clicking the "GO" button in the "General Linear Model: Multi-Study, Multi-Subject" dialog. If (pooled) zero predictors are detected for a subject, an appropriate message is presented and the calculation is aborted.
Saving FMR/DMR Files	When a FMR or DMR project had been saved in previous versions, only the FMR/DMR text file itself had been saved but not the associated data files (STC/DWI, AMR, PRT). This issue has been fixed in this release. This also ensures that all associated files of a project are now stored in case that a FMR or DMR project is saved in a new folder.
Saving Residuals	When running a single-study GLM on a VTC data set, residuals were not saved when the "Save Residuals" option had been turned on in the "Serial Correlations Options" dialog. This problem has been fixed.
Multi-Run FMR GLM	When running a multi-study GLM analysis on the basis of FMRs created in float format (multiple runs of the same session with the same slice positioning), the resulting maps were not calculated correctly. This problem has been fixed.
VMP Threshold Setting	When the lower threshold of a VMP was set to value "0.0", the negative color (usually blue) disappered and only positive values were shown. This problem has been fixed in this release. Furthermore, values with a value of exactly 0.0 are no longer shown since they indicate missing values or indicate that a voxel is masked out.
Create VTC/VDW Memory Leak	When creating VTCs or VDWs, part of the allocated memory was not free'd when the procedure was finished. This could lead to lack of memory in case that several VTCs had been createed in succession, e.g. when executing scripts to create multiple VTC/VDW files. This issue has been fixed.
ANCOVA - 1B1W	When running a two-factorial ANCOVA with one between and one within factor, a scatterplot shows how the data of the different groups relates to the added covariate. In the previous version, the groups could not be distinguished since all data points received the same color. This issue has been fixed.
Transformation with Sinc Interpolation	When running transformations with sinc interpolation that did not include rotations (e.g. ACPC -> TAL transformation) "garbage" could be obtained on some platforms (64-bit Mac). This problem has been fixed.
Lag-SMP from VMP	When creating a surface map (SMP) from a volume map (VMP) containing lag values (e.g. from a cross-correlation analysis), the SMP did not contain lag values when this was done after loading the VMP to a VMR. It worked only when the VMP was calculated just before creating the SMP. This issue has been fixed.
Display of DMR-VMR TRF Params	When performing a DMR-VMR coregistration, inspection of position info using the "Pos Info" button in the "Initial Alignment" tab of the "DMR-VMR Coregistration" dialog displayed wrong data. This issue has been fixed.
Restrict VTC Option and Mask Creation	When mask files were created from cortex representations and the "Restrict within VTC boundaries" option was not checked in the "Create Cortex-Based VTC Mask" dialog, the program could crash. This issue has been fixed.
Cancel Mask Creation	If a VTC mask was planned to be created from a VMP but canceled when prompted to specify the MSK file name, the "busy" cursor was not reset. This problem has been fixed.
Axes and Lighting in Surface Window	When the display of axes was changed in the mesh display window (surface module), e.g. by pressing the "A" key repeatedly or by changing settings in the "3D Axes Options" dialog, the lighting could change on some platforms resulting in a "dark" mesh display. This issue has been fixed.
Switching Back from Other Programs	When working in sub-dialogs of the "3D Volume Tools" dialog, especially when using the "Find AC Point" or "Find AC-PC Plane" dialogs, switching to other applications and then back to BrainVoyager could result in a crash on some platforms or disappearance of the sub-dialogs. This issue has been fixed.
Edit Condition Name in Protocol	When one would click the "Edit Name" button when no condition had been selected in the "Stimulation Protocol" dialog, the program would crash. This issue has been fixed.
Update of Cluster Threshold Change	When one changed the cluster threshold value in the "Surface Maps" dialog, the display did not reflect the change always even when clicking the "Update SRF" button. This has been fixed now. In the updated program, ciclicking "Update SRF" is not strictly necessary - the display is now updated also when pressing "return" after editing the cluster threshold value.

BrainVoyager QX 2.0 Release Notes

New Features

Multi-Voxel Pattern Analysis (MVPA)	A comprehensive set of tools to analyze distributed patterns of activity is now available and accessible via the Multi-Voxel Pattern Analysis dialog. Using Support Vector Machines (SVMs), classifiers can be trained on data in small or large ROIs to discriminate activity patterns from different conditions. Furthermore, local information as well as sparse global patterns can be mapped in the whole brain using searchlight mapping and recursive feature elimination (RFE). As a preparatory step to use SVM classifiers, the MVPA dialog also offers tools to estimate single-trial responses at each voxel, which may also be of interest for univariate data exploration. For an introduction in SVMs and the available MVPA tools, check episodes 2-5 in the BrainVoyager QX 2.0 series in Rainer's BV Blog. For more details about the MVPA-related tools, consult the "Multi-Voxel Pattern Analysis (MVPA)" chapter in the BrainVoyager QX User's Guide.
EMEG Suite	The new EEG / MEG distributed source imaging tools allow to analyze prepared EEG and MEG data in BrainVoyager. Besides plotting time course and time-frequency channel data, the most important feature of the "EMEG Suite" is to map the channel data into cortical source space using all major inverse modeling approaches including weighted minimum-norm, LORETA, LAURA and LCMV beamforming. The obtained cortically constrained distributed source data can be visualized easily on cortex meshes; for any region-of-interest, source time courses can be reconstructed ("virtua electrode"). Furthermore, movies on cortex meshes of dynamic distributed solutions can be easily created using "Movie Studio" (see below). In combination with fMRI data, the EMEG Suite allows fully integrated EEG-fMRI and MEG-fMRI modeling and analysis, e.g. by providing fMRI-constrained distributed inverse modeling and by providing the possibility to add predictors to fMRI design matrices derived from source EEG/MEG data. For details about the EEG/MEG distributed source imaging tools consult the "EMEG Suite" chapter in the BrainVoyager QX User's Guide as well as the "EMEG Suite Getting Started Guide", which has been placed in the BrainVoyager QX folder during installation. Note that the EMEG Suite requires an extended license (EMEG Module); contact Brain Innovation for details about licensing and how to get a trial version to test the EMEG Suite.
Movie Studio	Movie Studio allows to create stunning movies for different purposes including visualization of dynamic activation patterns. Movies are created by adding the information contained in a current rendering scene as a "state frame". Between successive state frames, BrainVoyager then calculates additional inter-frames creating smooth transitions. States describe one or more meshes and store information about the viewpoint, mesh slicing levels as well as mesh vertex colors and vertex coordinates. If, for example, the mesh vertex coordinates change from one state (e.g. folded mesh) to the next (e.g. inflated mesh), Movie Studio will calculate a smooth inflation animation between the two states. Furthermore, bitmaps can be added to any state allowing to visualize stimuli on a virtual screen and to present explanatory information. For further details, check the chapter "Movie Studio" in the User's Guide.
64 Bit Versions	Previous versions of BrainVoyager only supported 64-bit on Linux. BrainVoyager QX 2.0 now supports 64-bit also for Windows and Mac OS X. While 64 bit versions do not increase computation speed (at least not substantially), they allow exploitation of working memory beyond 3 GB, which is the limit on most 32-bit operating systems. In practice, requesting a continuous piece of only 1 GB might be already rejected by a 32 bit operating system due to fragmentation of the available memory space. A 64 bit operating system solves these issues since it allows a program access to large (continuous) blocks of working memory beyond the practical “1-2 GB” limit. Even if a system has “only” 4 GB of working memory installed, 64 bit programs can successfully request considerably larger pieces of working memory than 32 bit versions, especially on Windows. And if more than 4 GB are installed, only a 64 bit system can use that memory. While BrainVoyager QX uses working memory carefully, several tools will greatly benefit from a large working memory space including advanced cortex segmentation, cortical thickness analysis, Multi-Voxel Pattern Analysis (MVPA) and EEG / MEG source imaging analysis.
Float Data	Functional (FMR, VTC) and diffusion-weighted (DMR, DWI) data has been stored as 2-byte integer values in previous versions. While this is sufficient to represent scanner data (usually 12 bit) without loss of precision, the execution of a series of (pre-)processing steps accumulates rounding errors since resulting values have to be rounded to the nearest integer. To avoid this problem, BrainVoyager 2.0 now uses floating point numbers (4-byte float) as default for functional and diffusion-weighted data. The only disadvantage of the float format is that the data occupies twice as much space on disk and computer memory. If you do not want to use the new storage format (for all your projects or for finishing a “integer” project), you may turn off the new storage format for FMR/DMR projects in the “Settings” dialog. The choice made here is stored to disk and used as the default storage format also for subsequent BV sessions until explicitly changed. If you create a project with the “Create Project” dialog, you can temporarily change the storage format for a new project in the “Advanced” section.

Enhancements

Graphical User Interface	The Graphical User Interface (GUI) has been substantially enhanced with efficiency in mind. The first new GUI feature one encounters when launching BrainVoyager QX 2.0 is a new option to reload the last session. When turned on, this option will load all documents that were open when the program was closed last time. Note that this function goes beyond a simple reload of a document (VMR, FMR, DMR, SRF); it includes reloading files linked to a document including VTCs, MTCs, GLMs, VMPs, and SMPs as long as they are still available on disk. Another GUI improvement is the separation of the "Files", "Log" and "Info" in separate panes that reside at different regions of the main window. This allows to have them visible simultaneously. In order to quickly show or hide these panes, three new toggle icons (“Files Pane”, “Log Pane” and “Info Pane”) are now available in the main toolbar (see snapshot above). The panes can also be shown or hidden via respective entries in the “View” menu. A new "Full Screen" icon allows to switch to full screen mode allowing to exploit all screen real estate for working with document(s). The Escape key (or Cmd-F / Ctrl-F) leaves fullscreen mode restoring the previous state. Furthermore, the workspace of now supports a “tabbed” multi-document interface (MDI). Combined with the classical sub-window view mode, BrainVoyager QX 2.0 aims to combine the best of both worlds in an elegant interface. For a more detailed and comprehensive description of the new GUI functionality, check Episode 1 of the BrainVoyager QX 2.0 blog series.
Improved FMR/DMR-VMR Alignment	While the fine-tuning alignment in previous versions worked often well, there were also cases when alignment failed, especially when (non-removed) inhomogeneities were present in the target intra-session VMR data set. This dependency on intensity inhomegeneities is the consequence of the used goodness of alignment measure, which considers the sum of squared intensity differences (the smaller the better). In BrainVoyager QX 2.0 a more robust alignment routine has been implemented, which does not use intensity per se but gradient information as its goodness of alignment measure. While intensity differences strongly depend on inhomogeneities in the data, gradient information is largely unaffected since it evaluates the change of signal intensity with respect to neighboring voxels. More specifically, the implemented "Normalized Gradient Field" (NGF) algorithm considers a source and target volume as aligned, when intensity changes in the same way in both volumes at corresponding positions. Another improvement of the new alignment routine is the (optional) inclusion of scale and shear parameters extending the previously performed 6 parameter rigid (3 translations + 3 rotations) alignment to 9 parameter (rigid + scale) and full affine (12 parameter) transformations. As default, the program starts with a rigid alignment followed by a 9 parameter alignment. The included fit of 3 scale parameters seem to be especially beneficial for some EPI images with different "stretch" in image space along the frequency and phase encoding gradient. The "FMR-VMR Alignment Options" dialog available in the "Fine-Tuning Alignment" tab of the "VMR-VMR Coregistration" dialog allows to include also the full 12 parameter alignment when desired. When turned on, a new pre-alignment step will search for good starting parameters; this initial explorative search step can be often even used in case that the FMR and VMR files were not scanned in the same session. While available as an option before, the edge overlay display is now used as the default visualization scheme for the two fused data sets.
Parallelized Spatial Transformations	BrainVoyager QX 2.0 continues a process aiming to parallelize all compute-intensive routines exploiting the power of multi-core, multi-CPU computer systems. In the 2.0 release, the creation of VTC and VDWs has been parallelized leading to a 2x (dual core laptop) to almost 10x (8 core hyperthreading desktop workstations) speed gain. When using trilinear interpolation, the gain may be less visible than when using sinc interpolation since disk IO performance may become a limiting factor. Due to the obtained speed gain, the usage of sinc interpolation for DWI/VTC creation becomes a more viable option, e.g. when analyzing DTI or high-resolution fMRI data. The spatial transformation of VMR data sets using trilinear or sinc interpolation has also been parallelized with similar speed gains. This will reduce, for example, the creation of VMRs with 0.5^3 resolution from 1mm^3 data sets as is performed usually for advanced segmentation. Due to this speed gain, it is also recommended to run the "Re-Apply" tool with sinc interpolation when a VMR data set has been trasformed into ACPC or Talairach space with several successive interpolation steps.
CBA Improvements	Cortex-based alignment (CBA) is a useful tool to align macroanatomical structures (gyri and sulci). Since CBA is based on curvature information, homologue sulci and gyri need not explicitly be labelled in different brains. It is, however, important to start CBA at a stage where sulci and gyri are already close to each other on the sphere. In previous versions, hemispheres of different brains could be so much deviating (despite initial ACPC or Talairach normalization) that in some cases wrong alignments would result where a sulcus (gyrus) in one brain would be matched with a non-homologue sulcus (gyrus) in another brain. In order to reduce the likelihood of partial mis-alignments, BrainVoyager QX 2.0 offers now the possibility to run a rigid spherical pre-alignment step prior to CBA. In this "rigid" alignment step, a source sphere is rotated in a specified range and the alignment error for each parameter set (rotation values for three axes) is recorded. The parameter set producing the best fit (smallest alignment errror) with the selected target sphere will be selected and used to perform a rigid pre-alignment when starting the CBA procedure. While this step is not an absolute guarantee for avoiding mis-alignments, the likelihood to get optimal results is substantially improved after performing this step. Besides rigid pre-alignment, the coarse-to-fine strategy has been improved including better default parameters for cortex-based alignment at different curvature smooth levels providing better and more robust alignment results.
CTA Improvements	The aalysis of cortical thickness requires precise segmentation of both the inner (white matter / grey matter) and outer (grey matter / CSF) boundary of grey matter. The advanced segmentation tools use, among other things, local intensity histogram analysis to determine the inner grey matter boundary producing good results. For the detection of the outer boundary, however, only global intensity histogram analysis was used in previous versions. The 2.0 release adds local histogram analysis leading to substantially improved estimates also of the outer boundary. The "Advanced Segmentation dialog" also offers the new possibility to create volumes-of-interest (VOIs) from the estimated boundaries. The created VOI contours can be (transparently) overlaid on the original 3D intensity data allowing a more easy check of the quality of resulting grey matter segmentations. Furthermore, the "Cortical Thickness Measurement" dialog has a new "Mid-GM Volume" tab allowing to create a segmented volume running through the middle of grey matter. The created volume can serve as the basis for better cortex reconstructions since a surface through the middle of grey matter does not bias surface curvature towards gyri or sulci. These and other improvements are described in the updated "Cortical Thickness Analysis" chapter of the User's Guide.
VOIs and VOMs	The tools to work with volumes-of-interest (VOIs) have been improved, e.g. by adding support for different resolutions, VMR offsets and left/right conventions making them more flexible but also more secure, e.g. by prohibiting linking VOIs to non-matching VMRs. The new "VOI -> Draw in VMR" function in the "VOI Functions" tab tab of the "VOI Analysis Options" dialog allows to transform VOIs back into marked VMR clusters allowing to apply VMR tools for further VOI processing. VOIs may also be "dilated" using the "Expand selected VOIs" option in the same dialog, which is especially useful in the context of ROI-based fiber tracking. While getting more powerful, VOIs are always defined in VMR voxels, which makes them not ideal for some applications, for example in the context of ROI-based MVPA (see above). The new "VOM" data has been introduced to solve this issue as well as providing additioanal possibilities. A VOM file stores (at present only one) "volumes-of-interest" in "native resolution", i.e. the coordinate space matches the one of native resolution VMPs instead of that of VMRs. While VOIs can, of course, be transformed internally into native resolution space, an explicit storage of voxels in that space has many advantages. In addition to native resolution space, a VOM file may store associated map data for each voxel. As opposed to VOIs "knowing" only that a voxel with a certain coordinate belongs to a VOI, the voxels in a VOM file may each have an associated floating point value. In the context of support vector machines, for example, VOMs are used to attach weight values to voxels in native resolution space. VOMs can be created using the "Create VOM" dialog accessible through the "Options -> Create VOI-Map" menu item; VOMs can be visualized using the "Visualize VOMs" dialog accessible through the "Options -> Visualize VOI-Map" menu item. This dialog offers the possibility to visualize VOM map values as surface plots across selected sagittal, coronal or axial slices. Furthermore, a VOM can be transformed in a volume map with the same native resolution allowing to visualize the contained map values using standard 3D browsing.
Minimized VMRs	A helpful feature introduced in the context of advanced segmentation is the possibility to remove the empty space around a VMR and only save the data block containing non-zero data. Similarly as for VTCs and VMPs, a set of offset values are stored in VMR files to keep the knowledge about the "real" position of the sub-volume in a specific embedding space (e.g. 256^3 or 512^3). When using the "Minimize" button in the "VMR Properties Options" dialog (e.g. after brain peeling), not only memory and disk space is saved but also the visualization of the MRI data is improved (e.g. larger view of the brain) due to the removal of the empty space around the brain/head. A problem of this approach in previous versions was that VOI and VTC data were unaware of this approach with the result that VOIs and time course data were not placed correctly in a minimized VMR, e.g. in ACPC or Talairach space. In BrainVoyager QX 2.0, all major file formats linked to a VMR (VOIs, VMPs and VTCs) are now aware of minized VMRs respecting the VMR offset values. Moreover, when new VOIs or maps are created, the new routines make sure that it does not matter whether the data is created on minimized or non-minimized VMRs since coordinates are now interpreted with respect to the framing cube and not the actual dimensions of a VMR.
Plugins	Since each platform now supports both a 32 bit and a 64 bit version, plugins are no longer installed in the "BVQXExtensions/Plugins" folder but in either "BVQXExtensions/Plugins_32" or "BVQXExtensions/Plugins_64" depending on the installed BV version. This avoids (accidental) overrides and to have at the same computer both versions (this is possible, e.g. on Mac OS X). The plugin API has been updated to support the new float format for FMR/DMR and VTC/VDW data sets (see above). While the update has been done with minimal changes, some commands had to be modified and some new functions had to be added. The FMR header, for example, has a new entry called "STCDataType"; depending on its value (1 integer data, 2 -> float data), a corresponding command to access the correct pointer to the data must be used (e.g. qxGetSTCIntDataOfCurrentFMR or qxGetSTCFloatDataOfCurrentFMR). For details on this and other changes, consult the remarks in the "Plugin_FMR_Header.h" and "Plugin_VTC_Header.h" header files and the general "BVQXPluginInterface.h" header file as well as the updated description in the User's Guide.
Surface Maps Dialog	As opposed to the "Volume Maps" dialog, the "Surface Maps" dialog was still "blocking" (modal) in previous versions. With the 2.0 release, this dialog is now also non-blocking allowing to keep the dialog open when performing related tasks, e.g. to navigate in the surface window. The dialog now also comes with tabs in order to reduce the size of the dialog. These changes may help increase work productivity.
New Plotting Options	Several new plotting dialogs have been created, including plotters for matrix data, multi-plot layouts and surface plots. The matrix plotter is used in the context of MVPA (to plot training data) and EMEG (to plot single-trial time course as well as time-frequency data). The multiple sub-plots dialog is used to present averaged channel time course data in the EMEG module. Also the standard plotting dialog, used in many places (e.g. beta plots, GLM fits, histograms), has been improved, especially the associated "Options" dialog, which can be called (as before) by clicking within the dialog. The available options are now better arranged using a tabbed layout. Furthermore, the defined colors for plotting lines are now directly visualized in the list of plot items.

Bug Fixes

FMR Preprocessing	v2.0.8: When several FMR preprocessing steps were selected in the "FMR Preprocessing" dialog in the previous version (2.0.7), the final peprocessing result would not always contain the results of all performed preprocessing steps. There was no problem when executing single preprocessing steps or when using scripted preprocessing. This issue has been fixed. To be on the safe side, we recommend repeating FMR preprocessing with this version for FMR files analyzed in earlier versions of 2.0.
Plugins	v2.0.8: On some platforms not all plugins provided were visible in the menu. This has been fixed. You can also use the "Help >Plugins Web Page" menu item to inspect and eventually download plugins from the BrainVoyager web site.
Average VMR	v2.0.8: The function to average VMRs (typically used to get an average VMR file in Talairach space for a group of subjects) did not work in previous 2.0 versions. This problem has been fixed.
Patch Selection Size	v2.0.8: When clicking on a mesh to show an associated time course, the patch size (determining the number of vertices included) can be adjusted in the "Time Course Selection Options" dialog available from the "Meshes > ROI Time Course Selection Options" menu item. This function did, however, not work in previous 2.0 versions. This issue has been fixed.
Rename DICOM	v2.0.7: In the first release of 2.0 (version 2.0.6), the "Rename DICOM" tool did not work for all data sets. This problem has been fixed.
MTC Creation	When creating a MTC file from a VTC file, the calculation of intensity values for a given voxel was suboptimal due to wrong interpolation of values of voxels in the neighborhood. This problem has been fixed. It is recommended to re-create MTC files with BVQX 2.0 (a fix for the 1.10.4 version is also available) if possible, in order to obtain MTCs with the highest precision. Note that the direct creation of surface maps from volume maps (not via MTCs) was not affected.

BrainVoyager QX 1.10 Release Notes

Maintenance Update - 1.10.4 (build 1250) - Enhancements and Bug Fixes

Important Info at Start-Up	When starting the program, the "Known Issues and Program Updates" web page will be shown within the "Known Issues and Program Updates" dialog. Since this web page is loaded directly from the web, it provides a fast communication channel to users of BrainVoyager QX informing about important known issues as well as available program and help updates. The rules when to show the page can be specified in the "Automatically display page" field, e.g. the web page may be shown at each program start, once per day, once per week, never, or only when the web page has been updated. The latter option is turned on as default. The "Known Issues and Program Updates" dialog can also be called from the "Help" menu.
New ANCOVA Models	A new model has been added to the ANCOVA module supporting designs with 2 within-subjects factors and 1 between-subjects (group) factor. The model is specified by chosing the respective number of within and between factors in the "Design" tab of the "ANCOVA" dialog. Furthermore, the ANCOVA model with one grouping factor now supports using more than one covariate.
Segmentation in ACPC Space	The advanced and standard segmentation tools were fully supported only in Talairach space since a template file (BrainTalMask.vmr) is used for some segmentation steps (to find ventricles and subcortical structures and to remove the cerebellum). While it was possible to "Un-TAL" segmented brains, these tools now explicitly support ACPC space, which may be an important option for some applications, e.g. cortical thickness analysis. The required BrainTalMask.vmr file is transformed from Talairach into ACPC space using a provided subject-specific ".TAL" file. While a VMR in ACPC space must be loaded before starting the segmentation, a ".TAL" file must be created prior to starting the standard or advanced segmentation routines.
Tow-Gamma HRF for Linear Correlation	When linear correlation maps were calculated using the "Linear Correlation" dialog, only the Boynton hemodynamic response function was supported in previous versions. It is now possible to use the Two-Gamma function as the hemodynamic impulse function in the same way as in the context of the GLM. The two-gamma function is chosen as default, but another HRF can be selected in the "Linear Correlation Options" dialog.
Plugin API	In previous versions, called plugins had only access to the "current" document. There are now new API functions allowing to access all documents available in BrainVoyager's workspace. This allows to run plugins across multiple documents or to implement functionality requiring the integation of different document types. The "qxGetNumberOfDocsInWorkspace()" function provides the number of documents in the workspace, which can be used to traverse through the available documents. The "qxGetDocumentType(int doc_i)" and "qxGetDocumentTypeName(int doc_i)" functions provide information about the type of a document. The currently "active" document may be retrieved using the "qxGetIDOfCurrentDocument()" function and a new active document can be specified using the "qxSetAsCurrentDocument(int doc_i)" function.
Script-Based VDW Creation	While it was possible to create DMR DTI projects in previous versions, it was not possible to transform the diffusion weighted data into 3D space via script functions. The "CreateVDWInVMRSpace", "CreateVDWInACPCSpace" and "CreateVDWInTALSpace" script functions have been added to perform this transformation. The parameters of these functions are the same as those in the corresponding "CreateVTC" functions.
DTI Calculations	When calculating diagonlized tensor (DDT) files in DMR or VDW space, an intensity threshold was implicitly used to exclude voxels in the background. This intensity-based thresholding could potentially exclude also voxels in the brain for some DTI data sets. To avoid potential problems, this intensity-based masking method has been turned off as default now. It is, however, possible to turn it on and specify explicitly a threshold value using the new "Intensity-based masking using the b0 volume" option in the "Calculations" tab of the "DWI Data" dialog or in the "Data" tab of the "VDW Analysis" dialog. If the option is turned on, the "Intensity threshold" spin box can be used to specify a threshold value (default: 100). When creating VDW files, the default settings have been changed in order to better fit the requirments of DTI data processing. More specifically, the intensity threshold for calculating a bounding box has been turned off (to avoid potential exclusion of brain voxels) and "sinc interpolation" has been set as the default interpolation method. You may change these settings in the "Create VDW Options" dialog. Mean diffusivity and fractional anisotropy maps (DMR/DWI-based MAPs and VMR/VDW-based VMPs) are now represented with specific map types (ID 21 or "MD" and ID 22 or "FA"). Values of FA maps are now in the range 0.0 - 1.0 instead of 0.0 - 10.0.
DTI Fiber Seeding	When fibers are calculated after Ctrl-clicking in the surface module or using the "VOI Fiber Tracking" dialog, the created fibers were seeded with a default spatial range and density. The "Fiber Tracking and Rendering" dialog now contains two new entries, "Seed range" and "Density" allowing to specify explicitly how fibers should be seeded. When using large VOIs, it is recommended to lower the density setting to "1" or "2" (default value is "3" resulting in 27 (3 x 3 x 3) fiber seeds per VOI voxel) in order to avoid long waiting times. As opposed to previous versions, changed settings in the "Fiber Tracking and Rendering" dialog are now always used when starting fiber tracking from the "VOI Fiber Tracking" dialog.
Coregistration Slice Lines	The possibility to show slice lines had been introduced in a previous version to visualize how FMR slices are located within a VMR volume during FMR-VMR (and DMR-VMR) coregistration. This feature could, however, not be turned off. This is now possible by unchecking the "Show slice lines" option in the "Source Options" tab of the "FMR-VMR Coregistration" dialog.
CBA	When running cortex-based alignment (CBA), the alignment sphere could disappear and CBA crash on some oprating system environments. This problem has been fixed. When using multiple cores/processors, CBA reported erroneously "AlignmentError: 0.0". The state of the alignment error is now reported correctly for each cortex hemisphere as CBA progresses.
Loading RTC's in GLM Dialog	When loading a RTC file in the "Single Study General Linear Model" dialog, the program could crash. This problem has been fixed.

Maintenance Update - 1.10.3 (build 1202) - Bug Fixes

RFX-GLM	While calculated correctly, a wrong value of the beta for the constant predictor has been stored at each voxel when running a RFX-GLM in 1.10.2. This problem has been fixed. The problem did not affect interpretation of RFX-GLM contrasts since all values used for contrasts (betas, explained variance etc.) were calculated and used correctly. While also subsequent within-subjects ANCOVA models were not affected, models using between-subject factors will report wrong results for that factor. If such models were used, it is, thus, necessary to re-calculate the respective between-subjects analyses. Note that this problem did not affect any ROI-based ANCOVA results and it did not affect any design using VMP or CMP data as input.
Saving Data Tables	When saving table data from event-related averaging plots and ROI-GLMs to disk, the program would crash. This problem has been fixed.
Adding and Moving VOIs	When adding VOIs to the VOI list in the "Volume-Of-Interest Analysis" dialog, the program sometimes confused the identities of the VOIs. This problem has been fixed.
VMR Project Creation	After browsing the first file of a VMR project in the "Create Project" dialog, the "Number of slices" field could wrongly report a value of "1000". This problem could be solved simply by overwriting this value with the correct number. This minor problem has been fixed.
VMP LUT Update	When changing the overlay look-up table using the "Overlay Look-Up-Table" dialog, VMPs not using an own color table were not updated immediately. This minor problem has been fixed.

Maintenance Update - 1.10.3 (build 1202) - Enhancements

Confound Predictors	Confound predictors of a GLM analyses are now displayed as default in the "Overlay GLM Contrasts" dialog. Display of confounds can be turned off in the "Overlay GLM Options" dialog. In order to separate confound predictors from main predictors, names of confounds are now drawn in a yellow color while names of predictors of interest are drawn in a blue color.
High-Pass Filter Default	While differences are rather minimal, several tests have shown that the best high-pass filter FMR preprocessing results are obtained using the GLM-based Fourier option. The "High-pass (GLM-Fourier)" option is therefore now set as the default high-pass filter in the "FMR Data Preprocessing" dialog. To switch to another high-pass filter approach, use the "High-Pass Filter Options" dialog.

New Features

Probabilistic Maps	It is now possible to create probabilistic functional maps from multi-subject VOIs, POIs as well as VMP and SMP contrast maps. For details, check the "Probabilistic Maps" chapter of the User's Guide and the BV Blog entry Probabilistic Functional Maps. A new map type has been defined for probabilistic maps showing the number of subjects overlapping at a voxel or vertex as a percent value.
Temporal High-Pass Filtering	In addition to temporal high-pass filtering in the frequency domain, the "FMR Preprocessing" dialog now offers also to filter in the time domain using a GLM-based approach; the design matrix can be specifyied as a Fourier or Discrete Cosine Transform basis set. The residuals (original data minus fitted data) of the GLM is used as the filtered FMR data. For details, consult the "Preprocessing" chapter of the User's Guide. Temporal high-pass filtering can now also be integrated within statistical data analysis; more specifically, the "Single-Study General Linear Model" dialog now allows to add a Fourier or Discrete Cosine Transfor (DCT) basis set as confound predictors to the design matrix in the "Predictor Functions" tab. The advantages and disadvantages of this approach as compared to a separate preprocessing step are discussed in the User's Guide.
High-Pass Filtering of Design Matrix	Temporal high-pass filtering can now also applied to the main predictors of a specified design matrix. Applying the same filter to the design matrix (predictors of interest) as to the data allows to reveal whether a high-pass filter affects signal changes of interest in the data. This feature helps to ensure that the high-pass filter removes only signal changes, which are in a lower frequency band than the signal changes of interes, which is sometimes a source of error in fMRI data analysis.
Cluster Peak Table	The "VOI Analysis Options" dialog allows to produce tables showing the center-of-gravity of each VOI as well as additional information. This version extends these capabilities providing the possibility to create a table containing the Talairach coordinates for the peak voxel within a VOI. This option requires overlaying a volume map in order to inspect the map values within each VOI. In a typical application a volume map (e.g. a GLM contrast) is calculated (or loaded) first, then the significant map clusters are converted into VOIs using the "Options > Create Volumes-Of-Interest From Map Clusters" menu followed by a click of the "Table" button in the "Map Peak Voxels" field in the "VOI Analysis Options" dialog. The displayed table can be saved to disk but can also be used interactively: If a cluster (row) is selected, a click on the "Show Voxel" button highlights the voxel with the maximum statistics value by setting the cross to the respective coordinates.
CBA of POIs and SMPs	If POIs had been defined on individual (SPH) cortex meshes participating in cortex-based alignment, the defined POIs could not be transformed into aligned space. This is now possible with new functions available in the "Apply cb-alignment to POIs created in subject space" field of the "POI Functions" tab of the "Patch-Of-Interest Analysis Option" dialog. The POI alignment is, for example, necessary when calculating probabilistic POI maps. In order to be able to apply matching CBA (SSM) file for the POIs of different subjects, the new "Subject To CBA Data Assignment" dialog allows to link subject identifiers to SSM files. Established assignments can be saved to disk in the new "S2S" file format for later use. The same tools can also be applied to align surface maps (SMPs) defined in individual space using the "Apply cb-alignment to maps created in subject space" field in the "Surface Map Options" dialog. While SMP alignment is not necessary for GLM-derived surface maps (since CBA GLM's internally apply SSM files to subject's data), it is important for surface maps created with other analysis tools, such as the cortical thickness measurement tool. In order to separate aligned from unaligned versions of POIs and SMPs, the "_ALIGNED" substring is appended to transformed output files.

Enhancements

Single-Run Design Matrix Files	The "Single-Study General Linear Model" dialog now saves and loads defined design matrices in a new file format, called "SDM" (ssingle-run design matrix). The previously used RTC format can still be read into the dialog. Among other information, the new format stores the number of confound predictors in the design matrix by indicating the first confound predictor; this information allows to build consistent multi-study design matrices (MDMs) even if individual runs have different numbers of confound predictors. For more details, consult the updated User's Guide.
Improved Multi-Subject Design Matrix Creation	In previous versions, multi-subject design matrices could only be built if the number of predictors was identical. With the new support of splitting single-run design matrices in a main predictors and confound predictors part (see above), multi-subject design matrices can now be flexibly build from single-run design matrices by splitting main and confound predictors also in the overall design matrix (MDM file). This provides the flexibility that different subjects/runs may contain different amounts of confounds. The improved creation of design matrices takes this into account and will only require a matching number (and names) for main predictors. This improvement has been implemented for both the standard separate-subject/study GLM as well as for the RFX GLM.
Multiple Confound Predictors	A defined design matrix is now explicitly separated in a sub-matrix with predictors of main interest and a sub-matrix with confound predictors. This allows to keep main predictors separated from multiple confound predictors, which may include temporal high-pass filter sets, motion parameters, and artefact rejection predictors. A separating predictor index for the two sub-matrices is automatically defined but can also be manually specified in the "Masking / Options" field of the "Single Study GLM Options" dialog. For more details, consult the User's Guide.
Resolution-Aware Meshes	In previous versions, meshes were reconstructed in a space with units of voxel indices. This lead to non-matching meshes when reconstruction was done after advanced segmentation vs standard segmentation tools. The same cause also produced wrong slicing results of meshes from advanced segmentation. These issues have been fixed by reconstructing meshes in millimeter units as opposed to voxel index resolution. Since now the voxel resolution values in VMR files are taken into account, a VMR with 0.5 mm voxels of a subject will be reconstructed in the same space as a VMR with 1.0 mm voxels. This improvement allows to integrate meshes reconstructed from advanced segmentation tools into the standard inflation/flattening pipeline, especially in combination with the mesh simplification tool.
VMP Smoothing	Native resolution volume maps (nVMPs) can now be smoothed by using the options in the "Smooth map with Gaussian kernel" field in the "Map Options" tab of the "Volume Maps" dialog. This field includes parameters to specify the full-width-at-half-maximum (FWHM) of the Gaussian smoothing kernel and various options including specification of a repeat value and how lag maps should be treated.
ROI Dialogs	The "Volume-Of-Interest Analysis" and "Patch-Of-Interest Analysis" dialogs have been improved allowing now to add additional VOIs / POIs using the "Add" button. Furthermore, the order of VOIs / POIs in the respective list can now be changed using the "Move up" and "Move down" buttons. Editing POI features has also been extended allowing to specify the reference vertex connecting the mesh with the displayed POI name. Besides allowing to edit a POI's "Info" text, the "Edit Patch-Of-Interest" dialog (invoked by clicking the "Edit" button) now helps in editing the shape of a selected POI; to start modifying a POI, the "Draw Mesh Colors" button can be used to project the POI on the mesh by setting the vertices mesh color (i.e. not as an overlay); the marked POI vertices can then be edited using the mesh drawing tools, which automatically will use the correct color index; finally the modified set of vertices can be defined as the new POI definition by clicking the "Set Vertices" button in the re-entered "Edit Patch-Of-Interest" dialog.
POI Area	The "POI Details" function has been extended now providing a measure of the area of a POI. To calculate the POI area, it's vertices are projected (internally) on the current mesh; then all triangles "covered" completely by the POI vertices are identified and their area calculated; finally the sum of the areas of all identified triangles is determined as the area of the POI. Note that this implies that POIs with line shapes report an area of zero since such POIs usually do not cover all three vertices of "touched" triangles.
RFX Summary Statistic Approach	The ANCOVA module now supports the summary statistics approach of random effects analysis. After specifying a GLM (or reading table data), this approach is enabled by setting the number of all factors and covariates to zero. At this stage, the "Contrast" page appears allowing to specify a contrast, which is applied to the data of each subject (this is the same procedure as used for correlation of subject's effects values with covariate values). The mean of these contrast values is then compared to zero using a t test, which implements the same statistic as is performed in the "old" RFX approach available in the "Overlay GLM Options" dialog. For more details, check the User's Guide, which contains also a comparison of the summary statistics approach with the one within-factor ANOVA model.
Brain Peeling	In previous versions, the borders of the segmented brain could show small "holes" (missing voxel values) after running the "brain peeling" tool; this problem has been fixed by using a post-segmentation "get fringe" procedure. As default, a single (one voxel expansion) "get fringe" step is performed now when clicking "Segregate Brain From Head Tissue" in the "Volumes" menu. For more fine-grained control, the "No. of post get-fringe steps" option has been added in the "Brain peeling" field of the "Segmentation Options" dialog. Furthermore, the "Advanced Segmentation Tools" dialog now also provides this option with a default value of "2" steps (as had been implicitly performed in previous versions).
Multi-VOI Event-Related Averaging	It is often useful to compare averaged event-related time courses across different regions-of-interest (ROIs). This could be done in previous versions by adding the averaged event-related output from individual ROIs into a common plot window by using the "Load Data" and "Add Data" buttons in the "Plot Options" dialog. As a convenience function, this is now possible for VOIs in one step by using the "Multi-VOI event-related averaging plot" field in the "VOI Functions" tab of the "VOI Analysis Options" dialog. First select the desired VOIs in the "Volume-Of-interest Analysis" dialog, then use the "Browse" button in the "Multi-VOI event-related averaging plot" field to select an event-related averaing (AVG) file, and finally press the "Generate Plot" button to create the multi-VOI event-related averaging plot. Note that the color for the resulting plot line(s) belonging to the same VOI are set as the color specified for that VOI.
Motion Correction Scripting	The motion correction commands "CorrectMotionEx" and "CorrectMotionTargetVolumeInOtherRunEx" always used trilinear interpolation in previous versions. The third parameter "InterpolationMethod" allows now to specify the same interpolation methods as used in the GUI; value "1" (or "0") is interpreted as trilinear interpolation, value "2" is interpreted as "trilinear-sinc" (trilinear interpolation for detection of motion parameters, sinc interpolation for final transformation) and value "3" is interpreted as "sinc-sinc" (sinc interpolation is used for detection and transformation).
Individual VMP and SMP LUTs	The "Volume Maps" and "Surface Maps" dialogs now allow to specify overlay look-up tables (OLT) for individual sub-maps. While sub-maps could have individual color ranges in previous versions (interpolated between a specified "min" and "max" color), look-up tables allow to define optimized color palettes for special purposes. As an example, new OLT's are provided in the "MapLUTs" folder, which are optimized for highlighting transitions in probabilistic maps.
GUI Improvements	Many minor GUI improvements have been performed, including: selecting contrast values ("+", "-") behaved unintuitvely when clicking in quick succession; clicking the "RFX ANCOVA" button in the "Overlay RFX GLM Contrasts" dialog did not open the ANCOVA dialog when launched from a surface-based GLM; default names of overlaid ANCOVA tests have been made more meaningful; the "Interpolation" flag in the "Overlay Maps" dialog was not always synchronized with newly created maps; when creating multiple contrasts (for each subject) using the "Create maps for all defined contrasts" feature in the "Overlay GLM" dialog, the new option "Show maps during creation" allows to turn off display of the successively created maps, which speeds up the batch creation of maps substantially; the "Volume Maps" (native resolution) and "Surface Maps" dialogs now show the doc file (VMR or SRF) and the name of the VMP or SMP in the dialog's title bar.
Cross-VTC Intersubject Correlation	While available in earlier versions, the intersubject correlation feature has been improved and extended in this release. This feature allows to correlate the time course from two subjects for homologue Talairach voxels. For further details consult the "Cross-VTC Intersubject Correlation" topic in the "Additional Tools" chapter of the User's Guide.
Deletion of sub-SMPs	In previous versions, the current set of maps in the "Surface Maps" dialog could be deleted using the "Delete All" button. As in the "Volume Maps" dialog, it is now possible to delete individual sub-maps by selectin a map followed by a press of the "DELETE" key.
Colors in Voxel-Beta Plot	Colors for conditions were sometimes not correctly drawn in the "Voxel Beta Plot". In combination with other enhancements (predictor colors are now saved in the new SDM file), the correct colors should now be displayed in all cases.
File Format Changes	The file format to store GLM data has been changed slightly containing information about confound predictors. The User's Guide contains a specification of GLM files in the "File Formats" chapter.
Design Matrix Dialog	Visualization of design matrices has been improved. The "Design Matrix" dialog now handles also large design matrices when zooming in and out; it also has now a "stretch" factor allowing to change the width of columns in relation to the height of rows in graphical display mode.
Correlation	For convenience, the reference time course defined in the "Linear Correlation" dialog is automatically saved to disk and it will be available for immediate display in a subsequently opened "ROI Signal Time Course" dialog.
TMS Neuronavigation	The neuronavigation module did not work properly in the 1.9 versions. This problem has been fixed. Furthermore, some improvements have been added including saving of coil and beam positions allowing to calculate statistics about targeting a desired area.

Bug Fixes

Covariate Correlation in ANCOVA module	When using Volumes-Of-Interest (VOIs), the calculation of correlation values between subject's effect (contrast) and covariate values did not work properly in previous versions. This problem has been fixed. Futhermore, the output of the VOI covariate correlation has been extended to now show all included covariate and dependent variable values used for calculation. The mentioned problem did not occur when maps were calculated as long as covariate values were provided as integer values; furthermore, covariate values are now interpreted as real values as originally intended.
Saving RTCs from Linked MTCs	When a time course from a linked MTC file was displayed in the "POI Signal Time Course" dialog, saving the time course using the "Save RTC" button produced a crash in previous 1.9 versions. This bug has been fixed.
Saving Residuals	The possibility to save GLM residuals did not work correctly in previous versions. While the residuals were computed correctly, negative values resulted in most cases due to z-normalization, which can not be represented in the present unsigned two-byte integers of VTCs and STCs. This has been fixed in this version by turning off z-normalization in the "Single Study GLM Options" dialog as soon as "Save residuals" is selected in the "Serial Correlations Options" dialog, which can be invoked by pressing the "Residuals" button in the "Single Study GLM Options" dialog; furthermore, the "Keep mean" option is forced to be on. In this way, the calculated residuals are stored correctly and can subsequently be used as expected.
Contrast Map Creation For Each Subject	When creating multiple contrasts for each subject using the "Create maps for all defined contrasts" feature in the "Overlay GLM" dialog, the created map names were not always suitable for direct VMP import in the ANCOVA module since the name of a subject could appear more than once in the map name, e.g. "Subject 1: Faces > Subject 1: Houses"; this has been fixed, e.g. the name used as an example now becomes "Subject 1: Faces > Houses".
Predictor Colors in GLM Dialog	Since 1.9.10 it is possible to display predictors in color in the "Single-Study General Linear Model" dialog using information from an attached protocol. In case that the first condition was not droppped when defining the design matrix, colors could be assigned wrongly. This problem has been fixed.
Mesh Morphing	A (small) memoery leak has been fixed. This could potentially lead to a memory error during cortex-based alignment with many (e.g. 50) hemispheres.
Detach VTC/MTC	Detaching a VTC by pressing the "Detach VTC" button in the "Link 3D Volume Time Course (VTC)" dialog did not detach the linked VTC data from the current VMR. Likeweise, when detaching a MTC by pressing the "Detach MTC" button in the "Mesh Time Courses" dialog did not detach the linked MTC data from the current mesh. This problem has been fixed for both cases.
ROI Details	The "VOI Details" feature (available in the "VOI Functions" tab of the "VOI Analysis Options" dialog) reports information about individual voxels belonging to a VOI including information about map values, if available. This feature did not provide information about beta maps introduced in the last release. Information about beta values has been added now. Furthermore, values from the newly introduced probabilistic maps are also reported.

Most Popular Articles

LiveAgent

BrainVoyager Release Notes

BrainVoyager 23.2

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

21.4.5 Patch Release

21.4.4 Patch Release

21.4.2 Patch Release

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

New Features

Enhancements

Bug Fixes

Maintenance Update - 1.10.4 (build 1250) - Enhancements and Bug Fixes

Maintenance Update - 1.10.3 (build 1202) - Bug Fixes

Maintenance Update - 1.10.3 (build 1202) - Enhancements

New Features

Enhancements

Bug Fixes

Most Popular Articles