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BrainVoyager Installation & Introduction Release Notes BrainVoyager 21.2 Release Notes

BrainVoyager 21.2 Release Notes

BrainVoyager 21.2

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.


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.
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