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BrainVoyager Installation & Introduction Release Notes BrainVoyager 22.4 Release Notes

BrainVoyager 22.4 Release Notes

BrainVoyager 22.4

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.


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.
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