After segmentation is completed, the Edit menu option, "Calculate and Save Volumes..." causes NVM to write out files: 1) a comma separated value (*Volumes.csv) spreadsheet file that contains voxel counts from all saved outline files, and 2) a text file (*Volumes.txt) that contains a list of structures and their actual volumes. When loaded into Excel, volumes are calculated in the spreadsheet by 1) multiplying the number of voxels enclosed in the outlines by their volume and 2) adding half of the volume of the voxels located on the outline itself. To make segmentation easier, NVM displays each slice image at twice the original in-plane size so the row and column voxel dimensions in the spreadsheet are half of their original values.
The names of these files can be set using the "-spreadSheetFilename" argument. The default is to put the files in the outline directory (usually "otl") and call them "<segmenter prefix>_Volumes.csv" and "<segmentor prefix>_Volumes.txt" where "segmentor prefix" is the prefix for outline file names (as described here). Using "-spreadSheetFilename <fileName> " will set the .csv file name to "fileName". You should be sure that what you give for "fileName" ends in ".csv". The name of the .txt file will substitute "txt" for "csv".
There are two ways to calculate volumes and this is controlled by the command line argument "-voxCountMethod #" where "#" is 0 or 1. The default (0) is to draw all outlines and then count the number of voxels of each label. This method is more what-you-see-is-what-you-get (WYSIWYG) than the other method because for multiple outlines at the same location, the last one drawn is the one that will show up in the volume output. The hidden outline will not contribute to any volume values.
The other way to count voxels is to give "-voxCountMethod 1" as a command-line argument to NVM. This method draws each outline individually and then counts voxels. Using this method, it is important to "link" any island region outlines inside another outline to the outside outline. This will cause the volume of the island outline to be excluded from the surrounding outline. The link is made by making the island outline connect with the outside outline as shown in the image below. Alternatively, the spreadsheet can be modified to subtract the islands volumes from the surrounding outlines (e.g. subtracting the white matter volume from the cerebral exterior volume to get gray matter volume).