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BrainVoyager Installation & Introduction Release Notes BrainVoyager 21.4 Release Notes

BrainVoyager 21.4 Release Notes

BrainVoyager 21.4

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.


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.
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