| 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. |
