Typical Usage

NVM is used to create "outlines" with assigned neuroanatomical labels.  This is done with "contours".  Contours can be drawn with the pencil tool , erased with the eraser , and also created with the isocontour tool .  After all editing, contours are "extracted" to become outlines, and then they can be labeled and adjusted with the nudge tool . 

As an example, choose the isocontour tool and left-click in the main scan image.  This will draw isointensity contours everywhere using the intensity under the mouse click.  Next, drag the rightmost mouse button to dynamically adjust the contour.  To refine the border, use the pencil and eraser (and zoom tool ) so that the result is a closed boundary surrounding the region of interest.  Next, convert this into an outline by moving the mouse so it is inside or directly under the contour and pressing "e" (extract).  Outlines are normally green, but they are white (selected) just after they are created.  NVM knows which contour to turn into an outline by starting at the tip of the mouse when "e" is pressed and searching above that point for the first contour.  To assign a label, select the label tool , then select a label from the drop-down list.  If the outline is still selected (if it is still white), that label will be assigned to that outline.  If the outline is not selected (it is green), just click inside the outline to assign the label.  To save all outlines on a slice, click the "save otl" button.  This will put all outlines in a file called <segpfx><slice#>.xml (e.g. seg65.xml) in the "otl" subdirectory of the current scan.  The segmenter prefix <segpfx>, e.g. "seg" are typically the operators initials and this can be changed by clicking on "Segmenter Prefix: " in the upper left corner of the window.

To modify an existing outline, convert it into a contour for editing, then extract it back into the outline.  The most recently created outline (the last on created for the current slice), can be turned back into a contour by pressing "w".  All outlines on a slice will convert to contours with "W".  A specific outline can be selected by clicking on it and then the Edit Menu item "Cut" will turn it into a contour.  Outlines loose their label when they are converted to a contour so they must be re-labeled when they are re-extracted.

Other tricks include: With most tools, dragging the middle mouse button adjusts brightness and contrast.  Multiple differently-colored contours can be used at the same time by clicking on the colors (just to the left of the "save otl" and "load otl" buttons).  The histogram tool  is a good way to create contours.  Press "x" to erase all contours of the current color and "X" to erase all contours of all colors.  Double-click with the arrow tool to adjust all other view's slices to show that point.  You can hide and show contours by pressing "r" and hide and show outlines by pressing "R".  Outlines can be color-filled to show their label by pressing "T".

Finally, to calculate the volumes, first save all outline by pressing ctrl-o, then select the Edit menu item, "Calculate and Save Volumes...".  That will write out a spreadsheet for the current scan.