| 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. |
