maskvol - Build mask, boxcar-smoothing within mask  

1997 Ulrik Kjems, DSP/IMM, Technical University of Denmark, uk@imm.dtu.dk

Use :
  maskvol [-p presmooth [-q npre]] {-[g|s|a] thres} [-o maskoutput] 
          [-b bx by bz] [-m readmaskfile] [-l siglevel] inputvolume outputvolume

Applies a mask to a volume. Smoothes of the image within mask is supported.
outputvolume is the smoothed inputvolume with respect to the mask.

A presmoothing step before determining the mask is is controlled with
-p (size of cubic box filter) and -q (number of times to apply the box
filter).  Note that the smoothed volume is discarded after the mask
has been computed.  The mask is 1 where voxels values x in the
(optionally presmoothed) input volume satisfy

       (x-min)/(max/min) > thres.

The min and max may either be slice based (-s) or global (-g). The
last type is absolute (-a) where mask = x > thres. The 3 thresholds
may be used simultaneoulsly. Ex.

   maskcreate -g 0.1 -s 0.3 -a 100 mask volume

All volumes have to be same size and they are converted to BYTE format 
internally. 

outputvolume      is the smoothed input volume in FLOAT format.
-p                size of cubic presmoother filter (voxels). Default
                  is 0
-q                Number of times to run the presmoother, 0 default
-g, -s, -a        Global, slice, absolute thresholds. Default 0.
-b bx by bz       Size of smoother within mask, default 0.
-o maskoutput     is the mask volume in BYTE format (1's and 0's).
-m readmaskfile   may be specified to use a custom mask file. The 'inputvolume'
                  will be smoothed according to this mask instead.
-l level          controls amount of information displayed when run,use
                  'info','std' or 'silent'

maskvol -h produces above information