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Hi, On 18 May 2007, at 02:23, Pat Vee wrote: > Hi all, > > I'm trying to use avwstats to count the number of voxels and find > the mean > within a masked image. What I've done is created a binary mask, then > multiplied that by an image to only leave values in the non-masked > regions. > > So, to count voxels I'm typing: > avwstats <input> -V > It outputs 2 values; I understand that the 1st value is the number > of voxels > that are non-zero. I've been getting whole numbers for this on the > order of > hundreds (e.g., 826), which is what I expect. However, I don't > understand > what the 2nd value is. I've been getting numbers on the order of > thousands, > with decimals for this (e.g., 13560.75). Can someone explain what > this > number is? If you just type "avwstats" you get the usage; the second number is the volume, i.e. the first number X voxel volume. > To find the mean, I'm typing: > avwstats <input> -M > It outputs a value that I believe is the mean for all the non-zero > voxels. > However, I realized that it's possible that some of the volumes > will have > zero values within the non-masked regions. So, is there some way > to mask > regions so that the masked area is converted to NaNs - or some > other method > that would allow me to include zeros when calculating the mean? We don't use NaNs, This is easy in avwstats++ with the -k (masking) option. Cheers. ------------------------------------------------------------------------ --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ------------------------------------------------------------------------ ---