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BrainVoyager Installation & Introduction Release Notes BrainVoyager 21.0 Release Notes

BrainVoyager 21.0 Release Notes

BrainVoyager 21.0

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.


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.
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