BrainVoyager version: 22.4.4
Dataset used: Getting Started Guide data
This document shows in a step by step example how to create an anatomically defined region of interest (ROI). This is just one option among many others to define anatomical regions of interest, with one of them being the back-transformation of an atlas-based region into native non-normalized subject space.
However, in this document we will focus on describing the ROI definition based on an individual anatomy.
To start, we open a VMR document, in this case the non-normalized dataset of our sample dataset sub-01.
It is important to make sure that the visualisation of the anatomy is optimal. The settings can be changed in the "Contrast And Brightness" dialog in the “Options” menu.
To zoom into one of the standard views of the anatomical dataset, the shortcut CTRL+right mouse button can be used. Here, we zoom into the axial view of the dataset.
To switch to any of the other views (SAG, COR or full view), we can use the same shortcut.
To define a region of interest anatomically, you need to mark the specific region in the VMR. This can be done by coloring the voxels using either the "drawing" tool in the "3D Volume Tools" or using the segmentation functions of the Zoom view.
Region selection using the drawing tool
If you decide to use the "drawing" tool, you have to activate the respective option in the “Segmentation” tab of the “3D Volume Tools”.
The tool works either in 2D (in-plane) or in 3D mode. For a precise definition of areas, the 2D mode is optimal. As soon as the drawing tool has been enabled, a mouseclick + CTRL into the data will color voxels and a mouseclick + SHIFT will "delete" voxels, i.e. setting their intensity value to 0. The size of the marking tool, i.e. how many voxels will be selected with a single mouseclick, can be adapted using the "Size" spinbox.
If you have colored too many voxels accidentally, the “Reload All” button on the segmentation tab allows you to clear any voxel coloring and return to the initial VMR state. There is no “undo” function, so reloading will always delete the entire selection.
One can use the “A” button to switch off the crosshair. Now we can begin to mark a region of interest by CTRL+ clicking into the dataset.
In this case, only a single slice is marked because we chose the 2D drawing mode. This can be visualized when e.g. switching to the sagittal view (by pressing the shortcut “CTRL+T” twice).
To extend the region selection to neighbouring slices, we switch back to the axial view and move to the next slice (by using the arrow up / down button). Depending on the current slice view a different button combination is used to browse through the slices (right/left in the sagittal view and up/down + shift in the coronal view).
Region selection using the Zoom view
For very precise region definition it is advised to use the Zoom view which provides "Undo" and "Redo" functions as well as many other useful segmentation options, which are described in detail in the "Manual Segmentation Tools" section of the BrainVoyager User's Guide.
To invoke the Zoom view we select a region in a VMR document (primary volume) by holding down the ALT key while dragging with the mouse.
After the zoom area has been selected, the rectangular window for zooming can be moved using Alt + the left mouse button and moving the mouse.
Now we can start to select the voxels of interest by holding down the CTRL button and moving the mouse cursor over the respective voxels in the Zoom View. The "Undo" and "Redo" buttons help us to correct incorrectly marked voxels. As soon as all voxels of interest within a certain slice have been colored, one can use the "Forward" and "Backward" buttons to move to the next slice in either direction of the slice view that has been selected for the Zoom view, i.e. the axial view in the current example.
Also in the Zoom view the SHIFT key can be used to "delete" voxels, i.e. setting their intensity value to 0.
Saving the colored voxels as a region of interest
As soon as we have colored all voxels of our region of interest, we can save it. This can be done in the “Options” of the "Segmentation" tab of the "3D Volume Tools".
In the "Volume Tools Options" dialog, we have to press the “Define VOI” button.
The resultung VOI will be called "Untitled". By selecting the VOI in the "Volumes-Of-Interest list" and clicking on "Edit" one can change the name and the color of the selected VOI.
Now we can save the newly created VOI in a .voi (Volume of Interest) file. In a single VOI file, multiple VOIs / clusters can be saved.
Afterwards you can remove the color-labelling of the voxels in the VMR, by clicking on "Reload All" in the "Segmentation" tab of the "3DVolume Tools".
This is crucial when you would like to continue your VOI definition by marking other voxels in the VMR, e.g. in the other hemisphere and adding this region as a separate VOI to the same .voi file.