NVM is a software tool designed to make precise quantitative measurements in volumetric MR brain images.
The program can: load 3D image data in a variety of formats, crop and reslice data into a normalized orientation, adjust image brightness and contrast, display data as slices in sagittal, axial, coronal, and arbitrary oblique views with arbitrary zoom factors. It displays multiple data sets overlaid on each other including: "contours", "outlines", "surfaces", "landmarks" and MRI image data. Outlines can be shown with or without filled-in colors.
The locations of other views ("projection lines") are displayed in each view. All slices can be displayed at once using a "Tile view". All types of data can be hidden or shown to allow complete inspection of underlying data. All data sets can be loaded and saved. The current slice can be saved as a .ppm image. 3D data sets can be "cropped" by designating landmarks. Then only the cropped region will be loaded and displayed. After setting three landmarks (inter hemisphere point, and the decussation of the anterior and posterior commisures), the scan can be resliced in 3D to give a coronal view aligned with the AC-PC axis (as in the Talairach coordinate system). This view can be saved as a new scan and then outlines can be created for this new scan. Preferences can be set for all features.
The main objective of NVM is to produce outlines around labeled brain regions using isointensity contours and manual drawing. These regions are represented as outline files (lists of points and a text name which describe a neuroanatomical structure). The user can select various tools to interact with the scan: selection, iso-contour, draw, nudge, erase, box, landmark, label, and histogram. Seven different colors can be used to create "contours" using the ISO-contour and drawing tools and these can be extracted (converted) into "outlines". Contours are used as temporary outlines that can be edited. A click using the iso-contour tool causes iso-intensity contours to be drawn everywhere in the image and the intensity that defines these contours is determined by the voxel under the mouse pointer during the click. Contours can be promoted and demoted to other colors to facilitate complicated editing operations where one set of contours can be erased while saving others. They can also be used as auxiliary lines drawn in one view that indicate a location as they pass through another view.
The Arrow (selection) Tool selects and un-selects contours and outlines. Double-clicking adjusts all views to show that point in all images. The landmark tool is used to designate locations in the scan that are used for cropping, positional normalization and registration of multiple data sets. The label tool allows a text label to be assigned to a particular outline. The histogram tool will bring up a window showing the histogram of a region defined by an outline and a click on the histogram will generate an iso-intensity contour. Outlines can be "cleaned" to remove extra locations introduced as contours. For instance, since contours can be 8-connected, when created using "dynamic contouring" or by drawing, the extra voxels can be eliminated by un-extracting (converting back to a contour) and then re-extracting them from the outside. This will make a clean 4-connected outline. Once outlines have been created and labeled, their volumes can be saved as a spreadsheet. First, all outlines are unloaded from memory and the saved outline files are re-loaded to make sure that the calculated volumes match the saved data. The AutoContour window has a list of named intensities that can be assigned to a contour color so that when changing slices, that contour color is drawn at that intensity. These intensities can be set a different slices and the value is interpolated between those slices.